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• 1. [Article] Where Have All the Native Fish Gone? The Fate of Fish that Lewis and Clark Encountered on the Lower Columbia River

  As part of a special issue of the 'Oregon Historical Quarterly,' discusses the native species of fish in the lower Columbia River described by Meriwether Lewis and William Clark in 1805-06. They identified ...

  Citation × Citation Citation Abstract Copy Title: Where Have All the Native Fish Gone? The Fate of Fish that Lewis and Clark Encountered on the Lower Columbia River Author: Butler, Virginia L. Year: 2004 As part of a special issue of the 'Oregon Historical Quarterly,' discusses the native species of fish in the lower Columbia River described by Meriwether Lewis and William Clark in 1805-06. They identified red charr, salmon trout, sturgeon, anchovy, skeet, and other fish that Indians caught and used as trade items with the Corps of Discovery. However, editors of the Lewis and Clark journals have often erred in identifying the fish Lewis and Clark described; the challenge in identifying anadromous fish lies in changing coloration, markings, and examination of habitat. There has been a drastic decline of native fish since 1805 and a growing dominance of exotic species. Title: Where Have All the Native Fish Gone? The Fate of Fish that Lewis and Clark Encountered on the Lower Columbia River Author: Butler, Virginia L. Year: 2004 As part of a special issue of the 'Oregon Historical Quarterly,' discusses the native species of fish in the lower Columbia River described by Meriwether Lewis and William Clark in 1805-06. They identified red charr, salmon trout, sturgeon, anchovy, skeet, and other fish that Indians caught and used as trade items with the Corps of Discovery. However, editors of the Lewis and Clark journals have often erred in identifying the fish Lewis and Clark described; the challenge in identifying anadromous fish lies in changing coloration, markings, and examination of habitat. There has been a drastic decline of native fish since 1805 and a growing dominance of exotic species. Close

• 2. [Article] Infection of smallmouth bass and goldfish by two species of Saprolegnia

  This study consisted of several experiments designed to compare the ability of two species of fungi, Saprolegnia ferax and S. parasitica to grow on two species of fish, smallmouth bass (Micropterus dolomieui) ...

  Citation × Citation Citation Abstract Copy Title: Infection of smallmouth bass and goldfish by two species of Saprolegnia Author: McGinley, Cheryl A. Year: 1974 This study consisted of several experiments designed to compare the ability of two species of fungi, Saprolegnia ferax and S. parasitica to grow on two species of fish, smallmouth bass (Micropterus dolomieui) and goldfish (Carassius auratus), and to determine the criteria necessary for the development of these infections. The results indicate that water in the fish tanks must be slightly acid (pH 6), warm (22°C), nonmoving, and that the fish must be wounded in order for fungal infection to occur. Cool water (18°C) and moving water, caused by aeration and filtration, are detrimental to fungal colony formation so that no infection occurs. Both S. ferax and S. parasitica infected both species of fish, on an average of three days after innoculation. The S. ferax infected a higher percentage of both fishes than did the S. parasitica. The difference in susceptibility of the two fish species to the fungi was negligible. Title: Infection of smallmouth bass and goldfish by two species of Saprolegnia Author: McGinley, Cheryl A. Year: 1974 This study consisted of several experiments designed to compare the ability of two species of fungi, Saprolegnia ferax and S. parasitica to grow on two species of fish, smallmouth bass (Micropterus dolomieui) and goldfish (Carassius auratus), and to determine the criteria necessary for the development of these infections. The results indicate that water in the fish tanks must be slightly acid (pH 6), warm (22°C), nonmoving, and that the fish must be wounded in order for fungal infection to occur. Cool water (18°C) and moving water, caused by aeration and filtration, are detrimental to fungal colony formation so that no infection occurs. Both S. ferax and S. parasitica infected both species of fish, on an average of three days after innoculation. The S. ferax infected a higher percentage of both fishes than did the S. parasitica. The difference in susceptibility of the two fish species to the fungi was negligible. Close

• 3. [Article] House Bill 1302 : An Armistice in the Fish War on the Columbia

  In late Spring of 1969, shortly before the Oregon Legislative Session adjourned, House Bill No. 1302 as amended passed the last legislative hurdle and was signed by the Governor. The new statute recognized ...

  Citation × Citation Citation Abstract Copy Title: House Bill 1302 : An Armistice in the Fish War on the Columbia Author: Albertson, Emery Lewellyn Year: 1975 In late Spring of 1969, shortly before the Oregon Legislative Session adjourned, House Bill No. 1302 as amended passed the last legislative hurdle and was signed by the Governor. The new statute recognized steelhead trout as a game fish and provided for an incidental catch of these fish by the commercial fishery. HB 1302 was a turning point in a century of conflict over anadromous fish of the Columbia River. The bill served as an armistice in a long sports-commercial steelhead conflict by providing some protection for these fish from commercial fishing. However the bill held off a major shift in the sports-commercial balance of power for only five years. The "final" victory went to the sports fishermen in 1974--the voters approved Ballot Measure No. 15 which banned steelhead from sale. Although the sportsmen finally won the steelhead battle, they may have lost the war. Unless the erosion of fish runs caused primarily by dams is checked the fishery may disappear. Chapter I gives an overview of HB 130 and discusses the significance of the Columbia River anadromous fishery to Oregon. Chapter II is a history of the Columbia River fishery and traces the conflict between the various fishing interest groups. Chapter III details the causes of the conflict and describes the relationship between dams and declining runs of fish. Chapter IV discusses the Legislative passage of HB 1302. Chapter V discusses lobbying and pressure group activities concerning HB 1302. Chapter VI chronicles events subsequent to passage of HB 1302. Chapter VII contains summary and concluding remarks. Title: House Bill 1302 : An Armistice in the Fish War on the Columbia Author: Albertson, Emery Lewellyn Year: 1975 In late Spring of 1969, shortly before the Oregon Legislative Session adjourned, House Bill No. 1302 as amended passed the last legislative hurdle and was signed by the Governor. The new statute recognized steelhead trout as a game fish and provided for an incidental catch of these fish by the commercial fishery. HB 1302 was a turning point in a century of conflict over anadromous fish of the Columbia River. The bill served as an armistice in a long sports-commercial steelhead conflict by providing some protection for these fish from commercial fishing. However the bill held off a major shift in the sports-commercial balance of power for only five years. The "final" victory went to the sports fishermen in 1974--the voters approved Ballot Measure No. 15 which banned steelhead from sale. Although the sportsmen finally won the steelhead battle, they may have lost the war. Unless the erosion of fish runs caused primarily by dams is checked the fishery may disappear. Chapter I gives an overview of HB 130 and discusses the significance of the Columbia River anadromous fishery to Oregon. Chapter II is a history of the Columbia River fishery and traces the conflict between the various fishing interest groups. Chapter III details the causes of the conflict and describes the relationship between dams and declining runs of fish. Chapter IV discusses the Legislative passage of HB 1302. Chapter V discusses lobbying and pressure group activities concerning HB 1302. Chapter VI chronicles events subsequent to passage of HB 1302. Chapter VII contains summary and concluding remarks. Close

• 4. [Article] CE-QUAL-W2 Water Quality and Fish-bioenergetics Model of Chester Morse Lake and the Cedar River

  Many communities are currently seeking to balance urban water needs with preservation of sensitive fish habitat. As part of that effort, CE-QUAL-W2, a hydrodynamic and temperature model, was developed ...

  Citation × Citation Citation Abstract Copy Title: CE-QUAL-W2 Water Quality and Fish-bioenergetics Model of Chester Morse Lake and the Cedar River Author: Wells, Vanessa I. Year: 2011 Many communities are currently seeking to balance urban water needs with preservation of sensitive fish habitat. As part of that effort, CE-QUAL-W2, a hydrodynamic and temperature model, was developed for Chester Morse Lake and the lower Cedar River, WA. Chester Morse Lake is approximately 10 km long with a maximum depth at full pool of 40 m. The Cedar River model started immediately downstream of the Chester Morse dam and ended 21 km downstream at Landsburg, where drinking water is diverted for the City of Seattle. This water quality model was coupled with a fish habitat and bioenergetics model for bull trout and was calibrated to temperature data between 2005 and 2008. Bull trout fish bioenergetics parameters were provided by the USGS. The CE-QUAL-W2 model was found to be highly accurate in modeling temperature variation in the lake - at most locations having an average absolute mean error of between 0.5 and 0.8 oC. The Cedar River model had an average absolute mean error of 0.7oC. This tool is designed to allow managers and operators to estimate the impact to fish habitat and growth potential from various management decisions including extent of drawdown, timing/volume of flows, and various pumping operations. Future studies could include incorporating further water quality parameters such as nutrients, algae, and zooplankton as they relate to fish productivity. Title: CE-QUAL-W2 Water Quality and Fish-bioenergetics Model of Chester Morse Lake and the Cedar River Author: Wells, Vanessa I. Year: 2011 Many communities are currently seeking to balance urban water needs with preservation of sensitive fish habitat. As part of that effort, CE-QUAL-W2, a hydrodynamic and temperature model, was developed for Chester Morse Lake and the lower Cedar River, WA. Chester Morse Lake is approximately 10 km long with a maximum depth at full pool of 40 m. The Cedar River model started immediately downstream of the Chester Morse dam and ended 21 km downstream at Landsburg, where drinking water is diverted for the City of Seattle. This water quality model was coupled with a fish habitat and bioenergetics model for bull trout and was calibrated to temperature data between 2005 and 2008. Bull trout fish bioenergetics parameters were provided by the USGS. The CE-QUAL-W2 model was found to be highly accurate in modeling temperature variation in the lake - at most locations having an average absolute mean error of between 0.5 and 0.8 oC. The Cedar River model had an average absolute mean error of 0.7oC. This tool is designed to allow managers and operators to estimate the impact to fish habitat and growth potential from various management decisions including extent of drawdown, timing/volume of flows, and various pumping operations. Future studies could include incorporating further water quality parameters such as nutrients, algae, and zooplankton as they relate to fish productivity. Close

• 5. [Article] Using Archaeological Fish Remains to Determine the Native Status of Anadromous Salmonids in the Upper Klamath Basin (Oregon, USA) Through mtDNA and Geochemical Analysis

  Within the Upper Klamath Basin, Oregon, the native status of anadromous salmonids (Oncorhynchus spp.) has been a long standing question. Ongoing efforts to establish if these fish were native to the region ...

  Citation × Citation Citation Abstract Copy Title: Using Archaeological Fish Remains to Determine the Native Status of Anadromous Salmonids in the Upper Klamath Basin (Oregon, USA) Through mtDNA and Geochemical Analysis Author: Stevenson, Alexander E. Year: 2011 Within the Upper Klamath Basin, Oregon, the native status of anadromous salmonids (Oncorhynchus spp.) has been a long standing question. Ongoing efforts to establish if these fish were native to the region prior to the construction of the Copco I Dam on the Klamath River (c.1917) have relied on sparse, contradictory and sometimes unreliable historic documentation and informant testimony. Current restoration projects with very high financial and social costs necessitate accurate and reliable data on salmonid species which once called the region home. Often, archaeolofaunal remains present a novel way to determine species present in an area prior to major habitat losses. This project analyzed fish remains from five previously excavated archaeological sites within the Upper Klamath Basin to determine which salmonid species were present prior to dam construction. A total of 5,859 fish remains were identified to at least taxonomic order using morphological distinctions. Site collections were dominated by those of catostomids (suckers) and cyprinids (minnows). Archaeological deposits at these sites dated as far back as approximately 7,500 BP but were primarily from the last 2,000 years. Only eighty-one salmonid remains were observed within the sites included in this project. The low frequency of salmonid remains in these sites may be the result of cultural and/or natural processes such as density mediated attrition and archaeological sampling. Of these 81 specimens, 38 were subjected to mtDNA analysis for species identification. Seven specimens did not yield DNA sufficient for species identification, six specimens were identified as O. tshawytscha (Chinook) and the remaining 25 specimens were identified as O. mykiss (steelhead or redband trout). Geochemical analysis was used to determine the life history of the fish represented by the remains within these collections. Strontium Calcium (Sr:Ca) ratios were measured on twenty-eight specimens. Three specimens were determined to be from freshwater resident fish and 25 were determined to be from anadromous fish. The specimens which were genetically identified as O. tshawytscha were all determined to be anadromous. Of the 18 specimens which were identified as O. mykiss and were subjected to geochemical analysis two were from freshwater resident fish and sixteen were from anadromous fish. Four samples were not characterized genetically but were subjected to geochemical analysis; three of these were determined to be from anadromous fish and one from a freshwater resident fish. Thus, the remains of anadromous O. mykiss and O. tshawytscha were identified in archaeological deposits predating construction of the Copco I dam in the Upper Klamath Basin While the genetic and geochemical analyses confirm the presence of skeletal remains from anadromous salmonids in the Upper Klamath Basin archaeological sites prior to dam construction these remains may, represent fish caught elsewhere and traded in. Two hypotheses address the introduction of these fish remains into pre-dam archaeological deposits, either they were traded/transported in from elsewhere (Trade/Transport Hypothesis) or they were caught locally (Local Catch Hypothesis). Expectations linked to each of these hypotheses were generated using ethnographic information from across the Pacific Northwest, including modern testimony from the Klamath Basin. Fish heads were often removed soon after capture in order to reduce spoilage of the rest of the fish. Thus, assemblages with many head parts are probably the result of local catch while those without head parts are probably the result of trade and/or transport. Two approaches were used to estimate the extent to which fish heads were deposited in sites. Basic proportions of cranial to post cranial remains from two sites provided a varied picture and did not readily support either the Local Catch or Trade/Transport hypotheses. Evaluation using scaled proportions based on frequency of skeletal elements within the body (Minimum Animal Units) show that four of the five assemblages were dominated by cranial remains and therefore suggest these fish were locally caught. Small samples sizes make it difficult to rigorously evaluate the hypotheses, though the dominance of cranial remains suggests salmonids were taken locally. Together these data indicate that anadromous O. tshawytscha and O. mykiss were taken from waters within the Upper Klamath Basin prior to the construction of Copco I. This study has provided accurate and reliable data, using a novel approach, on which restoration efforts in the region can rely for proper species reintroduction and habitat restoration efforts. Title: Using Archaeological Fish Remains to Determine the Native Status of Anadromous Salmonids in the Upper Klamath Basin (Oregon, USA) Through mtDNA and Geochemical Analysis Author: Stevenson, Alexander E. Year: 2011 Within the Upper Klamath Basin, Oregon, the native status of anadromous salmonids (Oncorhynchus spp.) has been a long standing question. Ongoing efforts to establish if these fish were native to the region prior to the construction of the Copco I Dam on the Klamath River (c.1917) have relied on sparse, contradictory and sometimes unreliable historic documentation and informant testimony. Current restoration projects with very high financial and social costs necessitate accurate and reliable data on salmonid species which once called the region home. Often, archaeolofaunal remains present a novel way to determine species present in an area prior to major habitat losses. This project analyzed fish remains from five previously excavated archaeological sites within the Upper Klamath Basin to determine which salmonid species were present prior to dam construction. A total of 5,859 fish remains were identified to at least taxonomic order using morphological distinctions. Site collections were dominated by those of catostomids (suckers) and cyprinids (minnows). Archaeological deposits at these sites dated as far back as approximately 7,500 BP but were primarily from the last 2,000 years. Only eighty-one salmonid remains were observed within the sites included in this project. The low frequency of salmonid remains in these sites may be the result of cultural and/or natural processes such as density mediated attrition and archaeological sampling. Of these 81 specimens, 38 were subjected to mtDNA analysis for species identification. Seven specimens did not yield DNA sufficient for species identification, six specimens were identified as O. tshawytscha (Chinook) and the remaining 25 specimens were identified as O. mykiss (steelhead or redband trout). Geochemical analysis was used to determine the life history of the fish represented by the remains within these collections. Strontium Calcium (Sr:Ca) ratios were measured on twenty-eight specimens. Three specimens were determined to be from freshwater resident fish and 25 were determined to be from anadromous fish. The specimens which were genetically identified as O. tshawytscha were all determined to be anadromous. Of the 18 specimens which were identified as O. mykiss and were subjected to geochemical analysis two were from freshwater resident fish and sixteen were from anadromous fish. Four samples were not characterized genetically but were subjected to geochemical analysis; three of these were determined to be from anadromous fish and one from a freshwater resident fish. Thus, the remains of anadromous O. mykiss and O. tshawytscha were identified in archaeological deposits predating construction of the Copco I dam in the Upper Klamath Basin While the genetic and geochemical analyses confirm the presence of skeletal remains from anadromous salmonids in the Upper Klamath Basin archaeological sites prior to dam construction these remains may, represent fish caught elsewhere and traded in. Two hypotheses address the introduction of these fish remains into pre-dam archaeological deposits, either they were traded/transported in from elsewhere (Trade/Transport Hypothesis) or they were caught locally (Local Catch Hypothesis). Expectations linked to each of these hypotheses were generated using ethnographic information from across the Pacific Northwest, including modern testimony from the Klamath Basin. Fish heads were often removed soon after capture in order to reduce spoilage of the rest of the fish. Thus, assemblages with many head parts are probably the result of local catch while those without head parts are probably the result of trade and/or transport. Two approaches were used to estimate the extent to which fish heads were deposited in sites. Basic proportions of cranial to post cranial remains from two sites provided a varied picture and did not readily support either the Local Catch or Trade/Transport hypotheses. Evaluation using scaled proportions based on frequency of skeletal elements within the body (Minimum Animal Units) show that four of the five assemblages were dominated by cranial remains and therefore suggest these fish were locally caught. Small samples sizes make it difficult to rigorously evaluate the hypotheses, though the dominance of cranial remains suggests salmonids were taken locally. Together these data indicate that anadromous O. tshawytscha and O. mykiss were taken from waters within the Upper Klamath Basin prior to the construction of Copco I. This study has provided accurate and reliable data, using a novel approach, on which restoration efforts in the region can rely for proper species reintroduction and habitat restoration efforts. Close

• 6. [Article] A Case for Collaborative Resource Management: Comparative Analysis of Public Resources to Establish Fish Consumption Advisories in the Pacific Northwest

  Fish consumption advisories (FCAs) are intended to protect the public from toxicants, such as methylmercury, that bioaccumulate in fish tissues. Women of childbearing age, children and subsistence fishers ...

  Citation × Citation Citation Abstract Copy Title: A Case for Collaborative Resource Management: Comparative Analysis of Public Resources to Establish Fish Consumption Advisories in the Pacific Northwest Author: Clayton, Alyssa Year: 2017 Fish consumption advisories (FCAs) are intended to protect the public from toxicants, such as methylmercury, that bioaccumulate in fish tissues. Women of childbearing age, children and subsistence fishers are particularly vulnerable to methylmercury exposure, as it is a known neurotoxin that harms the central nervous system. Resources, collaboration and protocols to establish FCAs vary from state to state. This study examines resources available to states in the Pacific Northwest to develop and institute statewide largemouth bass (Micropterus salmoides) and smallmouth bass (Micropterus dolomieu) advisories. Similarities and differences are identified between public agencies that facilitate FCAs in Oregon, Washington and Idaho. My findings revealed funding and collaboration between federal and state agencies is inconsistent, as long-term, direct funding mechanisms do not exist for personnel, sampling and laboratory analyses, impacting the ability to establish and update advisories. I recommend increased funding and data sharing amongst agencies, standardized reporting of fish tissue data, and formalized collaborative governance amongst federal and state agencies to ensure consistent and long-term support of FCAs. Title: A Case for Collaborative Resource Management: Comparative Analysis of Public Resources to Establish Fish Consumption Advisories in the Pacific Northwest Author: Clayton, Alyssa Year: 2017 Fish consumption advisories (FCAs) are intended to protect the public from toxicants, such as methylmercury, that bioaccumulate in fish tissues. Women of childbearing age, children and subsistence fishers are particularly vulnerable to methylmercury exposure, as it is a known neurotoxin that harms the central nervous system. Resources, collaboration and protocols to establish FCAs vary from state to state. This study examines resources available to states in the Pacific Northwest to develop and institute statewide largemouth bass (Micropterus salmoides) and smallmouth bass (Micropterus dolomieu) advisories. Similarities and differences are identified between public agencies that facilitate FCAs in Oregon, Washington and Idaho. My findings revealed funding and collaboration between federal and state agencies is inconsistent, as long-term, direct funding mechanisms do not exist for personnel, sampling and laboratory analyses, impacting the ability to establish and update advisories. I recommend increased funding and data sharing amongst agencies, standardized reporting of fish tissue data, and formalized collaborative governance amongst federal and state agencies to ensure consistent and long-term support of FCAs. Close

• 7. [Article] Forecasted Range Shifts of Arid-Land Fishes in Response to Climate Change

  Climate change is poised to alter the distributional limits, center, and size of many species. Traits may influence different aspects of range shifts, with trophic generality facilitating shifts at the ...

  Citation × Citation Citation Abstract Copy Title: Forecasted Range Shifts of Arid-Land Fishes in Response to Climate Change Author: Whitney, James E., Whittier, Joanna B., Paukert, Craig Patrick, Olden, Julian D., Strecker, Angela L. Year: 2017 Climate change is poised to alter the distributional limits, center, and size of many species. Traits may influence different aspects of range shifts, with trophic generality facilitating shifts at the leading edge, and greater thermal tolerance limiting contractions at the trailing edge. The generality of relationships between traits and range shifts remains ambiguous however, especially for imperiled fishes residing in xeric riverscapes. Our objectives were to quantify contemporary fish distributions in the Lower Colorado River Basin, forecast climate change by 2085 using two general circulation models, and quantify shifts in the limits, center, and size of fish elevational ranges according to fish traits. We examined relationships among traits and range shift metrics either singly using univariate linear modeling or combined with multivariate redundancy analysis. We found that trophic and dispersal traits were associated with shifts at the leading and trailing edges, respectively, although projected range shifts were largely unexplained by traits. As expected, piscivores and omnivores with broader diets shifted upslope most at the leading edge while more specialized invertivores exhibited minimal changes. Fishes that were more mobile shifted upslope most at the trailing edge, defying predictions. No traits explained changes in range center or size. Finally, current preference explained multivariate range shifts, as fishes with faster current preferences exhibited smaller multivariate changes. Although range shifts were largely unexplained by traits, more specialized invertivorous fishes with lower dispersal propensity or greater current preference may require the greatest conservation efforts because of their limited capacity to shift ranges under climate change. Title: Forecasted Range Shifts of Arid-Land Fishes in Response to Climate Change Author: Whitney, James E., Whittier, Joanna B., Paukert, Craig Patrick, Olden, Julian D., Strecker, Angela L. Year: 2017 Climate change is poised to alter the distributional limits, center, and size of many species. Traits may influence different aspects of range shifts, with trophic generality facilitating shifts at the leading edge, and greater thermal tolerance limiting contractions at the trailing edge. The generality of relationships between traits and range shifts remains ambiguous however, especially for imperiled fishes residing in xeric riverscapes. Our objectives were to quantify contemporary fish distributions in the Lower Colorado River Basin, forecast climate change by 2085 using two general circulation models, and quantify shifts in the limits, center, and size of fish elevational ranges according to fish traits. We examined relationships among traits and range shift metrics either singly using univariate linear modeling or combined with multivariate redundancy analysis. We found that trophic and dispersal traits were associated with shifts at the leading and trailing edges, respectively, although projected range shifts were largely unexplained by traits. As expected, piscivores and omnivores with broader diets shifted upslope most at the leading edge while more specialized invertivores exhibited minimal changes. Fishes that were more mobile shifted upslope most at the trailing edge, defying predictions. No traits explained changes in range center or size. Finally, current preference explained multivariate range shifts, as fishes with faster current preferences exhibited smaller multivariate changes. Although range shifts were largely unexplained by traits, more specialized invertivorous fishes with lower dispersal propensity or greater current preference may require the greatest conservation efforts because of their limited capacity to shift ranges under climate change. Close

• 8. [Article] Study of Prestige and Resource Control Using Fish Remains from Cathlapotle, a Plankhouse Village on the Lower Columbia River

  Social inequality is a trademark of Northwest Coast native societies, and the relationship between social prestige and resource control, particularly resource ownership, is an important research issue ...

  Citation × Citation Citation Abstract Copy Title: Study of Prestige and Resource Control Using Fish Remains from Cathlapotle, a Plankhouse Village on the Lower Columbia River Author: Rosenberg, J. Shoshana Year: 2015 Social inequality is a trademark of Northwest Coast native societies, and the relationship between social prestige and resource control, particularly resource ownership, is an important research issue on the Northwest Coast. Faunal remains are one potential but as yet underutilized path for examining this relationship. My thesis work takes on this approach through the analysis of fish remains from the Cathlapotle archaeological site (45CL1). Cathlapotle is a large Chinookan village site located on the Lower Columbia River that was extensively excavated in the 1990s. Previous work has established prestige distinctions between houses and house compartments, making it possible to examine the relationship between prestige and the spatial distribution of fish remains. In this study, I examine whether having high prestige afforded its bearers greater access to preferred fish, utilizing comparisons of fish remains at two different levels of social organization, between and within households, to determine which social mechanisms could account for potential differences in access to fish resources. Differential access to these resources within the village could have occurred through household-level ownership of harvesting sites or control over the post-harvesting distribution of food by certain individuals. Previous work in this region on the relationship between faunal remains and prestige has relied heavily on ethnohistoric sources to determine the relative value of taxa. These sources do not provide adequate data to make detailed comparisons between all of the taxa encountered at archaeological sites, so in this study I utilize optimal foraging theory as an alternative means of determining which fish taxa were preferred. Optimal foraging theory provides a universal, quantitative analytical rule for ranking fish that I was able to apply to all of the taxa encountered at Cathlapotle. Given these rankings, which are based primarily on size, I examine the degree to which relative prestige designations of two households (Houses 1 and 4) and compartments within one of those households (House 1) are reflected in the spatial distribution of fish remains. I also offer a new method for quantifying sturgeon that utilizes specimen weight to account for differential fragmentation rates while still allowing for sturgeon abundance to be compared to the abundances of other taxa that have been quantified by number of identified specimens (NISP). Based on remains recovered from 1/4" mesh screens, comparisons between compartments within House 1 indicate that the chief and possibly other elite members of House 1 likely had some control over the distribution of fish resources within their household, taking more of the preferred sturgeon and salmon, particularly more chinook salmon, for themselves. Comparisons between households provide little evidence to support household-based ownership of fishing sites. A greater abundance of chinook salmon in the higher prestige House 1 may indicate ownership of fishing platforms at major chinook fisheries such as Willamette Falls or Cascades Rapids, but other explanations for this difference between households are possible. Analyses of a limited number of bulk samples, which were included in the study in order to examine utilization of very small fishes, provided insufficient data to allow for meaningful intrasite comparisons. These data indicate that the inhabitants of Cathlapotle were exploiting a broad fish subsistence base that included large numbers of eulachon and stickleback in addition to the larger fishes. This study provides a promising approach for examining prestige on the Northwest Coast and expanding our understanding of the dynamics between social inequality and resource access and control. Title: Study of Prestige and Resource Control Using Fish Remains from Cathlapotle, a Plankhouse Village on the Lower Columbia River Author: Rosenberg, J. Shoshana Year: 2015 Social inequality is a trademark of Northwest Coast native societies, and the relationship between social prestige and resource control, particularly resource ownership, is an important research issue on the Northwest Coast. Faunal remains are one potential but as yet underutilized path for examining this relationship. My thesis work takes on this approach through the analysis of fish remains from the Cathlapotle archaeological site (45CL1). Cathlapotle is a large Chinookan village site located on the Lower Columbia River that was extensively excavated in the 1990s. Previous work has established prestige distinctions between houses and house compartments, making it possible to examine the relationship between prestige and the spatial distribution of fish remains. In this study, I examine whether having high prestige afforded its bearers greater access to preferred fish, utilizing comparisons of fish remains at two different levels of social organization, between and within households, to determine which social mechanisms could account for potential differences in access to fish resources. Differential access to these resources within the village could have occurred through household-level ownership of harvesting sites or control over the post-harvesting distribution of food by certain individuals. Previous work in this region on the relationship between faunal remains and prestige has relied heavily on ethnohistoric sources to determine the relative value of taxa. These sources do not provide adequate data to make detailed comparisons between all of the taxa encountered at archaeological sites, so in this study I utilize optimal foraging theory as an alternative means of determining which fish taxa were preferred. Optimal foraging theory provides a universal, quantitative analytical rule for ranking fish that I was able to apply to all of the taxa encountered at Cathlapotle. Given these rankings, which are based primarily on size, I examine the degree to which relative prestige designations of two households (Houses 1 and 4) and compartments within one of those households (House 1) are reflected in the spatial distribution of fish remains. I also offer a new method for quantifying sturgeon that utilizes specimen weight to account for differential fragmentation rates while still allowing for sturgeon abundance to be compared to the abundances of other taxa that have been quantified by number of identified specimens (NISP). Based on remains recovered from 1/4" mesh screens, comparisons between compartments within House 1 indicate that the chief and possibly other elite members of House 1 likely had some control over the distribution of fish resources within their household, taking more of the preferred sturgeon and salmon, particularly more chinook salmon, for themselves. Comparisons between households provide little evidence to support household-based ownership of fishing sites. A greater abundance of chinook salmon in the higher prestige House 1 may indicate ownership of fishing platforms at major chinook fisheries such as Willamette Falls or Cascades Rapids, but other explanations for this difference between households are possible. Analyses of a limited number of bulk samples, which were included in the study in order to examine utilization of very small fishes, provided insufficient data to allow for meaningful intrasite comparisons. These data indicate that the inhabitants of Cathlapotle were exploiting a broad fish subsistence base that included large numbers of eulachon and stickleback in addition to the larger fishes. This study provides a promising approach for examining prestige on the Northwest Coast and expanding our understanding of the dynamics between social inequality and resource access and control. Close

• 9. [Article] A Landscape Approach to Determining and Predicting Juvenile Coho Salmon (<i>Oncorhynchus kisutch</i>) Movement Timing and Growth Patterns Prior to Ocean Entry

  Coho salmon (Oncorhynchus kisutch) rely on unique habitats during the winter season, which may dictate how much individuals may grow and when migration from freshwater rearing habitat to the ocean occurs. ...

  Citation × Citation Citation Abstract Copy Title: A Landscape Approach to Determining and Predicting Juvenile Coho Salmon (<i>Oncorhynchus kisutch</i>) Movement Timing and Growth Patterns Prior to Ocean Entry Author: Johnson, Amelia Lee Year: 2016 Coho salmon (Oncorhynchus kisutch) rely on unique habitats during the winter season, which may dictate how much individuals may grow and when migration from freshwater rearing habitat to the ocean occurs. Here I analyze movement timing and growth patterns for coho salmon through a field-based study and a literature review. For the field portion, I examined hatchery-stocked juvenile coho salmon across four stream basins in the Russian River watershed, California to determine the relative importance of climate, landscape, and fish size metrics in predicting movement and growth patterns over a winter rearing and spring smolt outmigration time period (December 2014-June 2015). I observed three unique movement strategies: winter parr movement, spring smolt movement, and inter-tributary movement. Movement was predicted in relation to daily temperature and precipitation, followed by in-stream and upslope basin conditions in random forest modeling. Specifically, fish that moved later were associated with basins that contained higher productivity and low-gradient floodplain habitats, while fish that moved earlier came from streams that lacked invertebrate prey and had limited low-gradient rearing habitat. Fish size and timing of movement were the primary predictors of growth, with relatively larger fish in the spring growing faster than fish that were relatively smaller prior to winter. These relationships suggest that hatchery-release fish are still highly influenced by environmental conditions once released, especially in terms of initial seasonal movement, and that watershed conditions should be considered when utilizing hatchery-rearing programs to supplement wild fish populations. In North America, coho salmon populations are distributed from Alaska through California, and may exhibit unique movement and growth patterns in relationship to population-scale vulnerability (Endangered Species Act listing), basin area, and availability and types of rearing habitat. For the second part of my thesis, I conducted a literature review to assess what factors are commonly considered in predicting movement and growth patterns for these fish, as well as the types (season and life stage) and number of movement strategies reported. Eighteen studies were summarized, of which sixteen identified unique movement strategies, ranging from one to four. Despite a wide range of basin areas and latitudes, winter parr and spring smolt movements were commonly observed, with authors primarily relating these behaviors to in-stream habitat and fish size metrics. Additionally, growth was linked positively and primarily with off-channel winter rearing, which may outweigh the importance of fish size in predicting growth when high quality rearing habitats are available during the winter season. Recognizing movement timing diversity and its drivers can help recover threatened coho salmon populations. More widely distributed populations may have unique phenotypic expressions based on localized genetic and environmental interactions, increasing diversity and overall stability across the population, a concept known as the portfolio effect. Understanding fish-habitat relationships can aid recovery efforts by providing a framework of climatic and watershed conditions that support unique behaviors, even in already severely limited populations. Title: A Landscape Approach to Determining and Predicting Juvenile Coho Salmon (<i>Oncorhynchus kisutch</i>) Movement Timing and Growth Patterns Prior to Ocean Entry Author: Johnson, Amelia Lee Year: 2016 Coho salmon (Oncorhynchus kisutch) rely on unique habitats during the winter season, which may dictate how much individuals may grow and when migration from freshwater rearing habitat to the ocean occurs. Here I analyze movement timing and growth patterns for coho salmon through a field-based study and a literature review. For the field portion, I examined hatchery-stocked juvenile coho salmon across four stream basins in the Russian River watershed, California to determine the relative importance of climate, landscape, and fish size metrics in predicting movement and growth patterns over a winter rearing and spring smolt outmigration time period (December 2014-June 2015). I observed three unique movement strategies: winter parr movement, spring smolt movement, and inter-tributary movement. Movement was predicted in relation to daily temperature and precipitation, followed by in-stream and upslope basin conditions in random forest modeling. Specifically, fish that moved later were associated with basins that contained higher productivity and low-gradient floodplain habitats, while fish that moved earlier came from streams that lacked invertebrate prey and had limited low-gradient rearing habitat. Fish size and timing of movement were the primary predictors of growth, with relatively larger fish in the spring growing faster than fish that were relatively smaller prior to winter. These relationships suggest that hatchery-release fish are still highly influenced by environmental conditions once released, especially in terms of initial seasonal movement, and that watershed conditions should be considered when utilizing hatchery-rearing programs to supplement wild fish populations. In North America, coho salmon populations are distributed from Alaska through California, and may exhibit unique movement and growth patterns in relationship to population-scale vulnerability (Endangered Species Act listing), basin area, and availability and types of rearing habitat. For the second part of my thesis, I conducted a literature review to assess what factors are commonly considered in predicting movement and growth patterns for these fish, as well as the types (season and life stage) and number of movement strategies reported. Eighteen studies were summarized, of which sixteen identified unique movement strategies, ranging from one to four. Despite a wide range of basin areas and latitudes, winter parr and spring smolt movements were commonly observed, with authors primarily relating these behaviors to in-stream habitat and fish size metrics. Additionally, growth was linked positively and primarily with off-channel winter rearing, which may outweigh the importance of fish size in predicting growth when high quality rearing habitats are available during the winter season. Recognizing movement timing diversity and its drivers can help recover threatened coho salmon populations. More widely distributed populations may have unique phenotypic expressions based on localized genetic and environmental interactions, increasing diversity and overall stability across the population, a concept known as the portfolio effect. Understanding fish-habitat relationships can aid recovery efforts by providing a framework of climatic and watershed conditions that support unique behaviors, even in already severely limited populations. Close

• 10. [Article] Effects of intraperitoneal and intracerebral injections of Triiodothyronine on temperature selection in fish

  Goldfish (Carassius auratus) of 15-28g were maintained at 23 C and subsequently were intraperitoneally injected with saline (controls) and varying doses of Triiodothyronine (T3). Following the injection, ...

  Citation × Citation Citation Abstract Copy Title: Effects of intraperitoneal and intracerebral injections of Triiodothyronine on temperature selection in fish Author: Grahn, Dennis A. Year: 1984 Goldfish (Carassius auratus) of 15-28g were maintained at 23 C and subsequently were intraperitoneally injected with saline (controls) and varying doses of Triiodothyronine (T3). Following the injection, the fish were placed in a thermal gradient and temperature selection and activity monitored for 30 min. There was no- significant difference between the responses of the experimental fish to the 2 different doses of T3. However, there was a significant difference in response between the experimental and control groups (P < 0.001). The decreased temperature selection occurred early in the test runs, while the increased activity began later. Larger goldfish (175-205g) received 0.5 μl intracerebral injections of 1.5-3.0 ng T3 in the anterior brainstem via an indwelling cannula injection system. These fish responded to the injections by selecting cooler water. The magnitude of the response was related to the distance of the injection site from the preoptic/anterior hypothalamic region. I conclude that increased plasma levels of T3 lead to the selection of cooler water. This effect appeared to be mediated via the anterior brainstem. Injected T3 also produced hyperactivity. This latter effect developed more slowly and appeared to be more diffusely mediated. Title: Effects of intraperitoneal and intracerebral injections of Triiodothyronine on temperature selection in fish Author: Grahn, Dennis A. Year: 1984 Goldfish (Carassius auratus) of 15-28g were maintained at 23 C and subsequently were intraperitoneally injected with saline (controls) and varying doses of Triiodothyronine (T3). Following the injection, the fish were placed in a thermal gradient and temperature selection and activity monitored for 30 min. There was no- significant difference between the responses of the experimental fish to the 2 different doses of T3. However, there was a significant difference in response between the experimental and control groups (P < 0.001). The decreased temperature selection occurred early in the test runs, while the increased activity began later. Larger goldfish (175-205g) received 0.5 μl intracerebral injections of 1.5-3.0 ng T3 in the anterior brainstem via an indwelling cannula injection system. These fish responded to the injections by selecting cooler water. The magnitude of the response was related to the distance of the injection site from the preoptic/anterior hypothalamic region. I conclude that increased plasma levels of T3 lead to the selection of cooler water. This effect appeared to be mediated via the anterior brainstem. Injected T3 also produced hyperactivity. This latter effect developed more slowly and appeared to be more diffusely mediated. Close

• 11. [Article] Tracking Fish and Human Response to Earthquakes on the Northwest Coast of Washington State, USA: A Preliminary Study at Tse-whit-zen

  Evidence of large earthquakes occurring along the Pacific Northwest Coast is reflected in coastal stratigraphy from Oregon to British Columbia, where there also exists an extensive archaeological record ...

  Citation × Citation Citation Abstract Copy Title: Tracking Fish and Human Response to Earthquakes on the Northwest Coast of Washington State, USA: A Preliminary Study at Tse-whit-zen Author: Mohlenhoff, Kathryn A., Butler, Virginia L. Year: 2017 Evidence of large earthquakes occurring along the Pacific Northwest Coast is reflected in coastal stratigraphy from Oregon to British Columbia, where there also exists an extensive archaeological record of Native American occupation. Tse-whit-zen, a large Native American village dating between ∼2800 yrs BP and the historic era, located on the Olympic Peninsula of Washington State, was excavated with exceptionally fine stratigraphic control allowing for precise comparison of these natural and cultural records. Here we report on the ∼10,000 fish remains from one 2 × 2 m excavation block; this assemblage spans the timing of one seismic event, allowing study of changes in relative taxonomic abundance through time that may coincide with earthquakes or other environmental changes. Results indicate a wide variety of fish taxa were used throughout the dated occupation. Comparisons of fish use before and after one earthquake event shows a decline in salmon (Oncorhynchus sp.) and an increase in herring (Clupea pallasii), shifts consistent with earthquake-related habitat loss. This serves as a pilot study for a large-scale collaborative project that is drawing on the range in animal types (invertebrates, mammals, birds, and fishes) to assess human response to gradual and abrupt environmental change at Tse-whit-zen. Title: Tracking Fish and Human Response to Earthquakes on the Northwest Coast of Washington State, USA: A Preliminary Study at Tse-whit-zen Author: Mohlenhoff, Kathryn A., Butler, Virginia L. Year: 2017 Evidence of large earthquakes occurring along the Pacific Northwest Coast is reflected in coastal stratigraphy from Oregon to British Columbia, where there also exists an extensive archaeological record of Native American occupation. Tse-whit-zen, a large Native American village dating between ∼2800 yrs BP and the historic era, located on the Olympic Peninsula of Washington State, was excavated with exceptionally fine stratigraphic control allowing for precise comparison of these natural and cultural records. Here we report on the ∼10,000 fish remains from one 2 × 2 m excavation block; this assemblage spans the timing of one seismic event, allowing study of changes in relative taxonomic abundance through time that may coincide with earthquakes or other environmental changes. Results indicate a wide variety of fish taxa were used throughout the dated occupation. Comparisons of fish use before and after one earthquake event shows a decline in salmon (Oncorhynchus sp.) and an increase in herring (Clupea pallasii), shifts consistent with earthquake-related habitat loss. This serves as a pilot study for a large-scale collaborative project that is drawing on the range in animal types (invertebrates, mammals, birds, and fishes) to assess human response to gradual and abrupt environmental change at Tse-whit-zen. Close

• 12. [Article] Alternate Developmental Pathways

  Chapter from the book, Annual Fishes: Life History Strategy, Diversity, and Evolution -- the first comprehensive reference on current knowledge of diverse species that exhibit unique survival strategies ...

  Citation × Citation Citation Abstract Copy Title: Alternate Developmental Pathways Author: Podrabsky, Jason E., Romney, Amie L., Culpepper, Kristin M. Year: 2015 Chapter from the book, Annual Fishes: Life History Strategy, Diversity, and Evolution -- the first comprehensive reference on current knowledge of diverse species that exhibit unique survival strategies and provide important models for basic and applied research. This work fills a void, covering the life cycle, reproductive biology, evolutionary ecology, reproductive behavior, sexual selection, genetics, speciation, and integrative and conservation strategies of annual fishes. Bringing together researchers in different areas of annual fishes to summarize previous work, overview the current research, and highlight promising areas of research, the book is organized into three sections focusing on: Diversity, life history, and reproductive biology Ecology and conservation Evolution The book provides a thorough understanding of the complexity of annual fishes and emphasizes their usefulness as a unique model organism for studies in vertebrate biology, particularly in areas such as speciation and senescence. It also notes the gaps in knowledge that challenge future research and encourages the continued expansion and development of research studies on annual fishes to address these gaps so that general vertebrate biology can be better understood. It serves as a valuable resource for scientists in a range of disciplines such as ichthyology, zoology, developmental and evolutionary biology, molecular biology and genetics, and ecology. Title: Alternate Developmental Pathways Author: Podrabsky, Jason E., Romney, Amie L., Culpepper, Kristin M. Year: 2015 Chapter from the book, Annual Fishes: Life History Strategy, Diversity, and Evolution -- the first comprehensive reference on current knowledge of diverse species that exhibit unique survival strategies and provide important models for basic and applied research. This work fills a void, covering the life cycle, reproductive biology, evolutionary ecology, reproductive behavior, sexual selection, genetics, speciation, and integrative and conservation strategies of annual fishes. Bringing together researchers in different areas of annual fishes to summarize previous work, overview the current research, and highlight promising areas of research, the book is organized into three sections focusing on: Diversity, life history, and reproductive biology Ecology and conservation Evolution The book provides a thorough understanding of the complexity of annual fishes and emphasizes their usefulness as a unique model organism for studies in vertebrate biology, particularly in areas such as speciation and senescence. It also notes the gaps in knowledge that challenge future research and encourages the continued expansion and development of research studies on annual fishes to address these gaps so that general vertebrate biology can be better understood. It serves as a valuable resource for scientists in a range of disciplines such as ichthyology, zoology, developmental and evolutionary biology, molecular biology and genetics, and ecology. Close

• 13. [Article] Tolerance of Environmental Stress

  Chapter from the book, Annual Fishes: Life History Strategy, Diversity, and Evolution -- the first comprehensive reference on current knowledge of diverse species that exhibit unique survival strategies ...

  Citation × Citation Citation Abstract Copy Title: Tolerance of Environmental Stress Author: Podrabsky, Jason E., Riggs, Claire L., Wagner, Josiah Tad Year: 2015 Chapter from the book, Annual Fishes: Life History Strategy, Diversity, and Evolution -- the first comprehensive reference on current knowledge of diverse species that exhibit unique survival strategies and provide important models for basic and applied research. This work fills a void, covering the life cycle, reproductive biology, evolutionary ecology, reproductive behavior, sexual selection, genetics, speciation, and integrative and conservation strategies of annual fishes. Bringing together researchers in different areas of annual fishes to summarize previous work, overview the current research, and highlight promising areas of research, the book is organized into three sections focusing on: Diversity, life history, and reproductive biology Ecology and conservation Evolution The book provides a thorough understanding of the complexity of annual fishes and emphasizes their usefulness as a unique model organism for studies in vertebrate biology, particularly in areas such as speciation and senescence. It also notes the gaps in knowledge that challenge future research and encourages the continued expansion and development of research studies on annual fishes to address these gaps so that general vertebrate biology can be better understood. It serves as a valuable resource for scientists in a range of disciplines such as ichthyology, zoology, developmental and evolutionary biology, molecular biology and genetics, and ecology. Title: Tolerance of Environmental Stress Author: Podrabsky, Jason E., Riggs, Claire L., Wagner, Josiah Tad Year: 2015 Chapter from the book, Annual Fishes: Life History Strategy, Diversity, and Evolution -- the first comprehensive reference on current knowledge of diverse species that exhibit unique survival strategies and provide important models for basic and applied research. This work fills a void, covering the life cycle, reproductive biology, evolutionary ecology, reproductive behavior, sexual selection, genetics, speciation, and integrative and conservation strategies of annual fishes. Bringing together researchers in different areas of annual fishes to summarize previous work, overview the current research, and highlight promising areas of research, the book is organized into three sections focusing on: Diversity, life history, and reproductive biology Ecology and conservation Evolution The book provides a thorough understanding of the complexity of annual fishes and emphasizes their usefulness as a unique model organism for studies in vertebrate biology, particularly in areas such as speciation and senescence. It also notes the gaps in knowledge that challenge future research and encourages the continued expansion and development of research studies on annual fishes to address these gaps so that general vertebrate biology can be better understood. It serves as a valuable resource for scientists in a range of disciplines such as ichthyology, zoology, developmental and evolutionary biology, molecular biology and genetics, and ecology. Close

• 14. [Article] Factors for Improved Fish Passage Waterway Construction

  Streambeds are important fish passageways in Oregon; they provide for the necessary habitats and spawning cycles of a healthy fish population. Oregon state law requires that hydraulic structures located ...

  Citation × Citation Citation Abstract Copy Title: Factors for Improved Fish Passage Waterway Construction Author: Sillars, David N., Moradkhani, Hamid, Tymvios, Nicholas, Smith, Trevor D. Year: 2011 Streambeds are important fish passageways in Oregon; they provide for the necessary habitats and spawning cycles of a healthy fish population. Oregon state law requires that hydraulic structures located in water properly provide fish passage. Increasingly stringent state and federal regulations apply to these fish passageways, and designers must become more cognizant of conditions over a range of flows to accommodate fish movement and avoid expensive structural failure of these passageways. Fish passage structures are built when roads cross streambeds and may include culverts, or bridges. When these structures are built, the streambeds are re-created using a technique called “roughened channels”. Roughened channels are man-made stream channels utilized for re-creating the hydraulics necessary for adequate stream passage, and this may include new constructions or retrofits of older, inadequate structures. Mixtures of materials are used to construct the bed of roughened channels, ranging from fines such as sand, silt and gravel to coarse elements like cobbles and boulders. Fines are a critical element in limiting permeability of the constructed bed thus keeping stream flow at the surface of the roughened channel during low flow periods. This report discusses work of a research project designed to discover factors that are key to successful long-term implementation of fish passageways, especially focused on the construction process. Areas of inquiry postulated in this study are that failures experienced in actual installations may be due to inadequate range and/or mix of soil and rock material gradation; unexpected water velocity, especially during high flows; inadequate mixing of rock and soil materials during construction; and inadequate compaction of rock and soil materials during construction. This report suggests that several factors may be especially important considerations in fish passage success. These factors are the relationship of downstream slope to structure slope, well-graded fine soil materials in the channel fill (improved by choice of fill source), and frequent site visits. Improving fish passages for cost-efficient fish movement is a priority for government agencies such as Oregon Department of Transportation (ODOT) and Oregon Transportation Research and Education Consortium (OTREC). Title: Factors for Improved Fish Passage Waterway Construction Author: Sillars, David N., Moradkhani, Hamid, Tymvios, Nicholas, Smith, Trevor D. Year: 2011 Streambeds are important fish passageways in Oregon; they provide for the necessary habitats and spawning cycles of a healthy fish population. Oregon state law requires that hydraulic structures located in water properly provide fish passage. Increasingly stringent state and federal regulations apply to these fish passageways, and designers must become more cognizant of conditions over a range of flows to accommodate fish movement and avoid expensive structural failure of these passageways. Fish passage structures are built when roads cross streambeds and may include culverts, or bridges. When these structures are built, the streambeds are re-created using a technique called “roughened channels”. Roughened channels are man-made stream channels utilized for re-creating the hydraulics necessary for adequate stream passage, and this may include new constructions or retrofits of older, inadequate structures. Mixtures of materials are used to construct the bed of roughened channels, ranging from fines such as sand, silt and gravel to coarse elements like cobbles and boulders. Fines are a critical element in limiting permeability of the constructed bed thus keeping stream flow at the surface of the roughened channel during low flow periods. This report discusses work of a research project designed to discover factors that are key to successful long-term implementation of fish passageways, especially focused on the construction process. Areas of inquiry postulated in this study are that failures experienced in actual installations may be due to inadequate range and/or mix of soil and rock material gradation; unexpected water velocity, especially during high flows; inadequate mixing of rock and soil materials during construction; and inadequate compaction of rock and soil materials during construction. This report suggests that several factors may be especially important considerations in fish passage success. These factors are the relationship of downstream slope to structure slope, well-graded fine soil materials in the channel fill (improved by choice of fill source), and frequent site visits. Improving fish passages for cost-efficient fish movement is a priority for government agencies such as Oregon Department of Transportation (ODOT) and Oregon Transportation Research and Education Consortium (OTREC). Close

• 15. [Article] Effect of ethanol on thermoregulation in the goldfish, Carassius auratus

  In an attempt to elucidate the mechanism by which ethanol affects vertebrate thermoregulation, the effect of ethanol on temperature selection was studied in the goldfish, Carassius auratus. Ethanol was ...

  Citation × Citation Citation Abstract Copy Title: Effect of ethanol on thermoregulation in the goldfish, Carassius auratus Author: O'Connor, Candace Sharon Year: 1986 In an attempt to elucidate the mechanism by which ethanol affects vertebrate thermoregulation, the effect of ethanol on temperature selection was studied in the goldfish, Carassius auratus. Ethanol was administered to 10 to 15 g fish by mixing it in the water of a temperature gradient. The dose response curve was very steep between 0.5% (v/v) ethanol (no response) and 0.7% (significant lowering of selected temperature in treated fish). Fish were exposed to concentrations of ethanol as high as 1.7%, at which concentration most experimental fish lost their ability to swim upright in the water. At concentrations higher than 0.7%, the magnitude of the effect did not increase with increasing concentration of ethanol; treated animals continued to select temperatures about 2 C below temperatures selected by controls. Experiments alternating exposure to 1.0% ethanol and water showed that the rate of onset and disappearance of the ethanol effect was rapid (within 10 min). Other experiments exposing fish to 1.0% ethanol for up to 3 hr showed that the effect remained stable for this period of time. The thermoregulatory responses of fish are behavioral, and therefore relatively easy to observe and quantify. Ethanol produces a prompt, stable and reproducible depression of selected temperature in the goldfish. Because the temperature at which fish regulate is controlled by a central nervous system set point and not altered by effects on peripheral effector systems, it appears that ethanol may cause hypothermia in goldfish by directly acting to lower the set point. Title: Effect of ethanol on thermoregulation in the goldfish, Carassius auratus Author: O'Connor, Candace Sharon Year: 1986 In an attempt to elucidate the mechanism by which ethanol affects vertebrate thermoregulation, the effect of ethanol on temperature selection was studied in the goldfish, Carassius auratus. Ethanol was administered to 10 to 15 g fish by mixing it in the water of a temperature gradient. The dose response curve was very steep between 0.5% (v/v) ethanol (no response) and 0.7% (significant lowering of selected temperature in treated fish). Fish were exposed to concentrations of ethanol as high as 1.7%, at which concentration most experimental fish lost their ability to swim upright in the water. At concentrations higher than 0.7%, the magnitude of the effect did not increase with increasing concentration of ethanol; treated animals continued to select temperatures about 2 C below temperatures selected by controls. Experiments alternating exposure to 1.0% ethanol and water showed that the rate of onset and disappearance of the ethanol effect was rapid (within 10 min). Other experiments exposing fish to 1.0% ethanol for up to 3 hr showed that the effect remained stable for this period of time. The thermoregulatory responses of fish are behavioral, and therefore relatively easy to observe and quantify. Ethanol produces a prompt, stable and reproducible depression of selected temperature in the goldfish. Because the temperature at which fish regulate is controlled by a central nervous system set point and not altered by effects on peripheral effector systems, it appears that ethanol may cause hypothermia in goldfish by directly acting to lower the set point. Close

• 16. [Article] Sampling Fish: A Case Study from the Čḯxwicən Site, Northwest Washington

  Researchers on the Northwest Coast (NWC) are often interested in complex questions regarding social organization, resource intensification, resource control, and impacts of environmental change on resources ...

  Citation × Citation Citation Abstract Copy Title: Sampling Fish: A Case Study from the Čḯxwicən Site, Northwest Washington Author: Syvertson, Laura Maye Year: 2017 Researchers on the Northwest Coast (NWC) are often interested in complex questions regarding social organization, resource intensification, resource control, and impacts of environmental change on resources and in turn human groups. However, the excavation strategies used on the NWC often do not provide the spatial and chronological control within a site that is necessary to document their variability and answer these research questions. The Čḯxwicən site has the potential to address some of the limitations of previous Northwest Coast village site excavations because of its unique and robust sampling strategy, the wide expanse of time that it was occupied, and the multiple house structures present. An on-going project is examining changing human ecodynamics over the breadth of site occupation, focusing on zooarchaeology and geoarchaeological records. This site, located on the Strait of Juan de Fuca in Port Angeles, WA was excavated in 2004 as part of a Washington State Department of Transportation (WSDOT) undertaking to build parts for the Hood Canal Bridge Large scale excavation (261.4 m3 528 m2) generated enormous quantities of faunal remains. Radiocarbon dates and historic records show occupation extends from 2750 cal. BP to the early 20th century. Statistical sampling methods provide an empirical way to maximize the amount of information obtained with the least amount of effort. My thesis addressed the utility of Sampling to Redundancy (STR) as a statistical sampling method for sampling faunal remains from large village sites. My project has documented the variability of fish family representation across time and space in one part of the Čḯxwicən village, while minimizing the time and effort required to do so. This thesis applies STR to "S" (> 1/4 in.) 10 Liter bucket samples from eight excavation units and a total of 26 separate unique temporal and spatial contexts. I focused on 1/ 4 in. samples for my study for a particular reason. Previous fish faunal studies have focused on effects of mesh size on fish representation; and emphasized the need to use fine mesh (e.g., 1/ 8 in. or finer) to document small-bodied fishes. This focus on fine mesh typically means that only limited volumes of matrix are studied, which in turn may mean that remains of rarer, large- bodied fishes are under- represented. The on-going research project has focused on buckets screened to 1/ 8 in. mesh (called "C" buckets). I used STR to sample additional volumes of matrix screened to 1/ 4 in. to examine whether expanding the volume studied would affect fish representation, which was a second goal of my project. Overall, I studied remains from 269 "S" buckets out of a total of 419 buckets, or 47% of the buckets. STR was most helpful for six of the high bone abundance and density contexts, where I analyzed less than 50% of the total buckets, was moderately helpful for 14 contexts, and not at all helpful for the six contexts with low fishbone abundance, where I analyzed 100% of the buckets. This analysis took me a total of 154 hours, and based on the percentage of material analyzed, 174 hours were saved. As to the second project goal, to assess whether adding fish remains documented from additional matrix volume affected fish representation, I found the differences were minimal. Both for my study units as a whole, and for each time period, adding the fish records from the "S" buckets did not alter the main trends in fish representation as documented by the larger study, using a smaller volume. To further examine whether the added volume from >1/ 4 in "S" buckets affected results, I explored specific research questions that are relevant to the larger project regarding environment-animal interactions and fishbone deposition and bone condition inside and outside of a house structure. Adding the "S" bucket samples did not affect fish representation or fishbone distribution and condition, which affirms that the sampling strategy used in the larger research project was sufficient in most cases to characterize the fish record at the site. My approach to STR has focused on fish remains that were previously excavated from a Pacific coastal village site with dense archaeological deposits. STR could be employed in other types of archaeological settings in a range of environments (coast or interior) representing a range of cultural contexts (from hunting camps to urban centers) to establish sample redundancy after an excavation is complete. STR could be used during on-going excavation. Further research is required to explore the implications of STR in these settings, however it is likely that the success of STR in other contexts will be dependent on the density and overall abundance of remains, the diversity or material types being studied, as well of course in the range and specificity of questions in each case. Title: Sampling Fish: A Case Study from the Čḯxwicən Site, Northwest Washington Author: Syvertson, Laura Maye Year: 2017 Researchers on the Northwest Coast (NWC) are often interested in complex questions regarding social organization, resource intensification, resource control, and impacts of environmental change on resources and in turn human groups. However, the excavation strategies used on the NWC often do not provide the spatial and chronological control within a site that is necessary to document their variability and answer these research questions. The Čḯxwicən site has the potential to address some of the limitations of previous Northwest Coast village site excavations because of its unique and robust sampling strategy, the wide expanse of time that it was occupied, and the multiple house structures present. An on-going project is examining changing human ecodynamics over the breadth of site occupation, focusing on zooarchaeology and geoarchaeological records. This site, located on the Strait of Juan de Fuca in Port Angeles, WA was excavated in 2004 as part of a Washington State Department of Transportation (WSDOT) undertaking to build parts for the Hood Canal Bridge Large scale excavation (261.4 m3 528 m2) generated enormous quantities of faunal remains. Radiocarbon dates and historic records show occupation extends from 2750 cal. BP to the early 20th century. Statistical sampling methods provide an empirical way to maximize the amount of information obtained with the least amount of effort. My thesis addressed the utility of Sampling to Redundancy (STR) as a statistical sampling method for sampling faunal remains from large village sites. My project has documented the variability of fish family representation across time and space in one part of the Čḯxwicən village, while minimizing the time and effort required to do so. This thesis applies STR to "S" (> 1/4 in.) 10 Liter bucket samples from eight excavation units and a total of 26 separate unique temporal and spatial contexts. I focused on 1/ 4 in. samples for my study for a particular reason. Previous fish faunal studies have focused on effects of mesh size on fish representation; and emphasized the need to use fine mesh (e.g., 1/ 8 in. or finer) to document small-bodied fishes. This focus on fine mesh typically means that only limited volumes of matrix are studied, which in turn may mean that remains of rarer, large- bodied fishes are under- represented. The on-going research project has focused on buckets screened to 1/ 8 in. mesh (called "C" buckets). I used STR to sample additional volumes of matrix screened to 1/ 4 in. to examine whether expanding the volume studied would affect fish representation, which was a second goal of my project. Overall, I studied remains from 269 "S" buckets out of a total of 419 buckets, or 47% of the buckets. STR was most helpful for six of the high bone abundance and density contexts, where I analyzed less than 50% of the total buckets, was moderately helpful for 14 contexts, and not at all helpful for the six contexts with low fishbone abundance, where I analyzed 100% of the buckets. This analysis took me a total of 154 hours, and based on the percentage of material analyzed, 174 hours were saved. As to the second project goal, to assess whether adding fish remains documented from additional matrix volume affected fish representation, I found the differences were minimal. Both for my study units as a whole, and for each time period, adding the fish records from the "S" buckets did not alter the main trends in fish representation as documented by the larger study, using a smaller volume. To further examine whether the added volume from >1/ 4 in "S" buckets affected results, I explored specific research questions that are relevant to the larger project regarding environment-animal interactions and fishbone deposition and bone condition inside and outside of a house structure. Adding the "S" bucket samples did not affect fish representation or fishbone distribution and condition, which affirms that the sampling strategy used in the larger research project was sufficient in most cases to characterize the fish record at the site. My approach to STR has focused on fish remains that were previously excavated from a Pacific coastal village site with dense archaeological deposits. STR could be employed in other types of archaeological settings in a range of environments (coast or interior) representing a range of cultural contexts (from hunting camps to urban centers) to establish sample redundancy after an excavation is complete. STR could be used during on-going excavation. Further research is required to explore the implications of STR in these settings, however it is likely that the success of STR in other contexts will be dependent on the density and overall abundance of remains, the diversity or material types being studied, as well of course in the range and specificity of questions in each case. Close

• 17. [Article] Coupling the Hydrodynamic and Water Quality Model CE-QUAL-W2 With a Multi-Trophic Fish Bio-Energetics Model for Lake Roosevelt, Washington

  Grand Coulee Dam created Franklin D. Roosevelt Lake as part of the Columbia Basin Project. Located in northeastern Washington State, the Project provides economically important hydropower (19 billion kilowatt ...

  Citation × Citation Citation Abstract Copy Title: Coupling the Hydrodynamic and Water Quality Model CE-QUAL-W2 With a Multi-Trophic Fish Bio-Energetics Model for Lake Roosevelt, Washington Author: McKillip, Michael Lee Year: 2008 Grand Coulee Dam created Franklin D. Roosevelt Lake as part of the Columbia Basin Project. Located in northeastern Washington State, the Project provides economically important hydropower (19 billion kilowatt hours per year), irrigation (225,000 ha), flood control, and sport fishing ($5 to 20 million annually). A good system understanding aids in balancing these beneficial uses for the 230 km long reservoir. The reservoir's atypical 45-day mean residence time is much shorter than a typical lake, and much longer than for a riverine dam. The spring freshet requires drawdowns of 15 to 20 m for flood control—the driving characteristic of reservoir operations. A physically based two-dimensional hydrodynamic and water quality model, CE-QUAL-W2 Version 3.5 (Cole and Wells, 2006), is coupled with a fish bioenergetics model based on the Stockwell and Johnson model (1997, 1999) to examine the effects of hydrodynamics on the reservoir algae-zooplankton-kokanee food web. This model was applied and calibrated to Lake Roosevelt with model improvements of multiple zooplankton compartments and zooplankton omnivory. Calibration parameters included temperature, dissolved oxygen, nutrients, algae, and zooplankton. The fish bioenergetics model is applied over the entire reservoir model space to generate a spatial and temporal fish growth potential distribution. The fish model refinements include sub-daily time-steps and an optimized vertical foraging strategy. The linked model suggests that kokanee fish growth potential is seasonally limited by both warm water and prey densities. While the lake ecology is significantly affected by the reservoir operations in general, the pelagic fish growth potential did not appear sensitive to minor changes in reservoir operations. However, the model suggests that the advantageous foraging locations shift seasonally and that optimal foraging strategies are dependent on fish size. Title: Coupling the Hydrodynamic and Water Quality Model CE-QUAL-W2 With a Multi-Trophic Fish Bio-Energetics Model for Lake Roosevelt, Washington Author: McKillip, Michael Lee Year: 2008 Grand Coulee Dam created Franklin D. Roosevelt Lake as part of the Columbia Basin Project. Located in northeastern Washington State, the Project provides economically important hydropower (19 billion kilowatt hours per year), irrigation (225,000 ha), flood control, and sport fishing ($5 to 20 million annually). A good system understanding aids in balancing these beneficial uses for the 230 km long reservoir. The reservoir's atypical 45-day mean residence time is much shorter than a typical lake, and much longer than for a riverine dam. The spring freshet requires drawdowns of 15 to 20 m for flood control—the driving characteristic of reservoir operations. A physically based two-dimensional hydrodynamic and water quality model, CE-QUAL-W2 Version 3.5 (Cole and Wells, 2006), is coupled with a fish bioenergetics model based on the Stockwell and Johnson model (1997, 1999) to examine the effects of hydrodynamics on the reservoir algae-zooplankton-kokanee food web. This model was applied and calibrated to Lake Roosevelt with model improvements of multiple zooplankton compartments and zooplankton omnivory. Calibration parameters included temperature, dissolved oxygen, nutrients, algae, and zooplankton. The fish bioenergetics model is applied over the entire reservoir model space to generate a spatial and temporal fish growth potential distribution. The fish model refinements include sub-daily time-steps and an optimized vertical foraging strategy. The linked model suggests that kokanee fish growth potential is seasonally limited by both warm water and prey densities. While the lake ecology is significantly affected by the reservoir operations in general, the pelagic fish growth potential did not appear sensitive to minor changes in reservoir operations. However, the model suggests that the advantageous foraging locations shift seasonally and that optimal foraging strategies are dependent on fish size. Close

• 18. [Article] Effects of Types 1 and 2 Herpes Simplex Viruses on Several Fish Tissue Culture Systems

  The purpose of this investigation was to observe changes induced by types 1 and 2 herpes simplex viruses (HSY 1 and HSY 2) when these viruses were cultivated in fish 2 cells. The possibility of attempting ...

  Citation × Citation Citation Abstract Copy Title: Effects of Types 1 and 2 Herpes Simplex Viruses on Several Fish Tissue Culture Systems Author: Harry, Raymond Charles Year: 1977 The purpose of this investigation was to observe changes induced by types 1 and 2 herpes simplex viruses (HSY 1 and HSY 2) when these viruses were cultivated in fish 2 cells. The possibility of attempting to use human strains of herpesviruses in order to transform normal fish tissue culture preparations was considered. Three different fish cell cultures were tested: CHSE-214 cell lines were derived from embryonic chinook salmon (Oncorhynohus tshawytscha), and STE-137 cell lines were obtained from embryonic steelhead trout (Salmo gairdneri). Cells isolated from immature ovaries of rainbow trout (Salmo gairdneri) were propagated by the investigator in these studies. Both HSV 1 and HSV 2 demonstrated cytopathic effects on the 3 different cell types described above when these cells were observed during the exponential growth phase. If virus was added before cells were dividing actively, or when the cells were maintained in a stationary phase of growth, no effect was observed. Several methods were employed in an attempt to trans- form fish cells grown in tissue culture. Different quantities of live virus, preparations of ultraviolet light in- activated virus and purified viral DNA were used in these studies but malignant conversion by known viral components was not achieved. In these experiments, the 2B strain of cells obtained originally from immature ovaries of rainbow trout appeared to undergo spontaneous transformation thereby becoming established as a permanent cell line. To date tissue cultures designated 2B have undergone 25 transfers in this laboratory. Title: Effects of Types 1 and 2 Herpes Simplex Viruses on Several Fish Tissue Culture Systems Author: Harry, Raymond Charles Year: 1977 The purpose of this investigation was to observe changes induced by types 1 and 2 herpes simplex viruses (HSY 1 and HSY 2) when these viruses were cultivated in fish 2 cells. The possibility of attempting to use human strains of herpesviruses in order to transform normal fish tissue culture preparations was considered. Three different fish cell cultures were tested: CHSE-214 cell lines were derived from embryonic chinook salmon (Oncorhynohus tshawytscha), and STE-137 cell lines were obtained from embryonic steelhead trout (Salmo gairdneri). Cells isolated from immature ovaries of rainbow trout (Salmo gairdneri) were propagated by the investigator in these studies. Both HSV 1 and HSV 2 demonstrated cytopathic effects on the 3 different cell types described above when these cells were observed during the exponential growth phase. If virus was added before cells were dividing actively, or when the cells were maintained in a stationary phase of growth, no effect was observed. Several methods were employed in an attempt to trans- form fish cells grown in tissue culture. Different quantities of live virus, preparations of ultraviolet light in- activated virus and purified viral DNA were used in these studies but malignant conversion by known viral components was not achieved. In these experiments, the 2B strain of cells obtained originally from immature ovaries of rainbow trout appeared to undergo spontaneous transformation thereby becoming established as a permanent cell line. To date tissue cultures designated 2B have undergone 25 transfers in this laboratory. Close

• 19. [Article] CCAAT/Enhancer-Binding Protein Delta (C/EBP-delta) Expression in Antarctic Fishes: Implications for Cell Cycle and Apoptosis

  Chapter 1: Antarctic fishes are extremely cold adapted. Despite their inability to upregulate heat shock proteins, recent studies have demonstrated a capacity for heat response in these animals. A cDNA ...

  Citation × Citation Citation Abstract Copy Title: CCAAT/Enhancer-Binding Protein Delta (C/EBP-delta) Expression in Antarctic Fishes: Implications for Cell Cycle and Apoptosis Author: Sleadd, Isaac Martin Year: 2013 Chapter 1: Antarctic fishes are extremely cold adapted. Despite their inability to upregulate heat shock proteins, recent studies have demonstrated a capacity for heat response in these animals. A cDNA microarray study looked at the Notothenioid fish Trematomus bernacchii and revealed heat sensitivities for hundreds of genes, two of which code for members of the CCAAT/Enhancer-binding protein (C/EBP) family of transcription factors. These molecular switches are best known for their roles in apoptosis, inflammation and cell cycle arrest. This dissertation further elucidates the role of C/EBP-delta in the Antarctic fishes T. bernacchii and Pagothenia borchgrevinki. Chapter 2: C/EBP-delta is constitutively expressed in unstressed, field-acclimated (ca. -1.86°C) animals in a highly tissue-specific manner. White muscle tissue contains the highest C/EBP-delta concentration, which is further increased in response to sublethal heat stress at 2.0 or 4.0°C. This response is mostly acute and transitory, but a lesser upregulation was observed in fishes held for one month at 4.0°C. Chapter 3: The heat-induced nuclear translocation of C/EBP-delta--as determined by immunohistochemistry--appears to be time, tissue and species specific with spleen, heart and retinae being particularly responsive in certain situations. Chapter 4: Protein concentrations of proliferating cell nuclear antigen are tissue specific and variably heat responsive. Surprisingly, levels appear to be positively correlated with C/EBP-delta. Chapter 5: Flow cytometry revealed increasingly high temperatures reduce the proportion of G1 cells while increasing the abundance of apoptotic cells. Chapter 6: These findings are discussed in the context of global climate change and the cellular stress response. Title: CCAAT/Enhancer-Binding Protein Delta (C/EBP-delta) Expression in Antarctic Fishes: Implications for Cell Cycle and Apoptosis Author: Sleadd, Isaac Martin Year: 2013 Chapter 1: Antarctic fishes are extremely cold adapted. Despite their inability to upregulate heat shock proteins, recent studies have demonstrated a capacity for heat response in these animals. A cDNA microarray study looked at the Notothenioid fish Trematomus bernacchii and revealed heat sensitivities for hundreds of genes, two of which code for members of the CCAAT/Enhancer-binding protein (C/EBP) family of transcription factors. These molecular switches are best known for their roles in apoptosis, inflammation and cell cycle arrest. This dissertation further elucidates the role of C/EBP-delta in the Antarctic fishes T. bernacchii and Pagothenia borchgrevinki. Chapter 2: C/EBP-delta is constitutively expressed in unstressed, field-acclimated (ca. -1.86°C) animals in a highly tissue-specific manner. White muscle tissue contains the highest C/EBP-delta concentration, which is further increased in response to sublethal heat stress at 2.0 or 4.0°C. This response is mostly acute and transitory, but a lesser upregulation was observed in fishes held for one month at 4.0°C. Chapter 3: The heat-induced nuclear translocation of C/EBP-delta--as determined by immunohistochemistry--appears to be time, tissue and species specific with spleen, heart and retinae being particularly responsive in certain situations. Chapter 4: Protein concentrations of proliferating cell nuclear antigen are tissue specific and variably heat responsive. Surprisingly, levels appear to be positively correlated with C/EBP-delta. Chapter 5: Flow cytometry revealed increasingly high temperatures reduce the proportion of G1 cells while increasing the abundance of apoptotic cells. Chapter 6: These findings are discussed in the context of global climate change and the cellular stress response. Close

• 20. [Article] Comparison of Fish Assemblages in Restored and Natural Mangrove Habitats Along an Urban Shoreline

  The installation of living shorelines is one strategy used to ameliorate habitat degradation along developed coastlines. In this process, existing hard structures, such as sea walls and riprap revetments, ...

  Citation × Citation Citation Abstract Copy Title: Comparison of Fish Assemblages in Restored and Natural Mangrove Habitats Along an Urban Shoreline Author: Peters, Joseph R., Yeager, Laura A., Layman, Craig A. Year: 2015 The installation of living shorelines is one strategy used to ameliorate habitat degradation along developed coastlines. In this process, existing hard structures, such as sea walls and riprap revetments, are supplemented with habitat forming species, e.g., oysters and mangrove trees, to improve habitat quality and function. Shoreline restorations in Biscayne Bay, Florida, USA, often utilize red mangroves, Rhizophora mangle (Linneaus, 1753), in addition to riprap revetments, to help stabilize the shoreline. This riprap-mangrove habitat provides structure for marine organisms to utilize and is believed to improve shoreline habitats in areas previously cleared of mangroves. We examined whether habitat provisioning was similar between restored mangrove habitat with the inclusion of riprap boulders and natural mangrove shorelines. We compared fish assemblages between natural mangrove and riprapmangrove habitats within two areas of northern Biscayne Bay. Fish community structure and certain benthic cover types varied between mangroves and riprap-mangrove habitats. Total fish abundance was greater in mangrove habitat, while taxonomic richness was highest in riprap-mangrove sites in the northern part of the bay. Our findings suggest that fish assemblages and community structure are different between these habitat types, although the geographic context may mediate the effect of habitat type. Therefore, it is likely that these restored mangroves provide different ecological services than unaltered mangrove shorelines. Title: Comparison of Fish Assemblages in Restored and Natural Mangrove Habitats Along an Urban Shoreline Author: Peters, Joseph R., Yeager, Laura A., Layman, Craig A. Year: 2015 The installation of living shorelines is one strategy used to ameliorate habitat degradation along developed coastlines. In this process, existing hard structures, such as sea walls and riprap revetments, are supplemented with habitat forming species, e.g., oysters and mangrove trees, to improve habitat quality and function. Shoreline restorations in Biscayne Bay, Florida, USA, often utilize red mangroves, Rhizophora mangle (Linneaus, 1753), in addition to riprap revetments, to help stabilize the shoreline. This riprap-mangrove habitat provides structure for marine organisms to utilize and is believed to improve shoreline habitats in areas previously cleared of mangroves. We examined whether habitat provisioning was similar between restored mangrove habitat with the inclusion of riprap boulders and natural mangrove shorelines. We compared fish assemblages between natural mangrove and riprapmangrove habitats within two areas of northern Biscayne Bay. Fish community structure and certain benthic cover types varied between mangroves and riprap-mangrove habitats. Total fish abundance was greater in mangrove habitat, while taxonomic richness was highest in riprap-mangrove sites in the northern part of the bay. Our findings suggest that fish assemblages and community structure are different between these habitat types, although the geographic context may mediate the effect of habitat type. Therefore, it is likely that these restored mangroves provide different ecological services than unaltered mangrove shorelines. Close

• 21. [Article] Policy Analysis for Optimizing Native Fisheries on the McKenzie River

  The impact of hatchery fish on native populations has been extensively studies, especially as environmental management has generally moved toward a conservation focus. In Oregon, the McKenzie River native ...

  Citation × Citation Citation Abstract Copy Title: Policy Analysis for Optimizing Native Fisheries on the McKenzie River Author: Ray, Mary Year: 2001 The impact of hatchery fish on native populations has been extensively studies, especially as environmental management has generally moved toward a conservation focus. In Oregon, the McKenzie River native rainbow trout population has been the focus of recent interest groups attempting to induce a change in management practices to support native fisheries. The McKenzie River Chapter of Trout Unlimited is interested in learning more about the impacts that hatchery stocked rainbow trout have on native river populations. It is the group's intent to seek a rule change to management by the Oregon Department of Fish and Wildlife. A review of the historical and scientific information regarding fish stocking was needed to provide information for Trout Unlimited to make informed recommendations to the managing agency. Examples of successful management changes for conservation of native fish were used as case studies to examine the implications of stocking cessation on the viability of trout populations in Oregon. This paper provides details on the background information needed to understand the case studies, their relation to the situation on the McKenzie, and how those outcomes may support recommendations for fisheries management on the McKenzie. It is the intent that these recommendations and supporting details may provide Trout Unlimited with the information needed to make a meaningful recommendation to the Oregon Department of Fish and Wildlife regarding the native rainbow trout fishery in the McKenzie. Title: Policy Analysis for Optimizing Native Fisheries on the McKenzie River Author: Ray, Mary Year: 2001 The impact of hatchery fish on native populations has been extensively studies, especially as environmental management has generally moved toward a conservation focus. In Oregon, the McKenzie River native rainbow trout population has been the focus of recent interest groups attempting to induce a change in management practices to support native fisheries. The McKenzie River Chapter of Trout Unlimited is interested in learning more about the impacts that hatchery stocked rainbow trout have on native river populations. It is the group's intent to seek a rule change to management by the Oregon Department of Fish and Wildlife. A review of the historical and scientific information regarding fish stocking was needed to provide information for Trout Unlimited to make informed recommendations to the managing agency. Examples of successful management changes for conservation of native fish were used as case studies to examine the implications of stocking cessation on the viability of trout populations in Oregon. This paper provides details on the background information needed to understand the case studies, their relation to the situation on the McKenzie, and how those outcomes may support recommendations for fisheries management on the McKenzie. It is the intent that these recommendations and supporting details may provide Trout Unlimited with the information needed to make a meaningful recommendation to the Oregon Department of Fish and Wildlife regarding the native rainbow trout fishery in the McKenzie. Close

• 22. [Article] Interactions in the Frequencies of Electric Organ Discharge by Eigenmannia Virescens (Sternopygidae, Pisces) During Social Behavior

  The extent to which individuals of Eigenmannia virescens modulate their electric organ discharge frequencies to accommodate the frequencies of others of the same species during social interactions was ...

  Citation × Citation Citation Abstract Copy Title: Interactions in the Frequencies of Electric Organ Discharge by Eigenmannia Virescens (Sternopygidae, Pisces) During Social Behavior Author: Gaddis, Philip Year: 1975 The extent to which individuals of Eigenmannia virescens modulate their electric organ discharge frequencies to accommodate the frequencies of others of the same species during social interactions was investigated. Recordings of the fish's discharge frequencies, taken with Tektronix 3L5 and 5L4N spectrum analyzers, showed that, although movements of up to 60 Hz in a day may be made, the frequency movements would be made more or less synchronously by all fish in the group. An apparent preference for, and a tendency of the fish to follow one another in frequency, at frequency ratios of 2:3 (a musical fifth), 3:4 (fourth), and even 4:5 (major third) was observed. The appearance of a circadian rhythm was also noticed. Title: Interactions in the Frequencies of Electric Organ Discharge by Eigenmannia Virescens (Sternopygidae, Pisces) During Social Behavior Author: Gaddis, Philip Year: 1975 The extent to which individuals of Eigenmannia virescens modulate their electric organ discharge frequencies to accommodate the frequencies of others of the same species during social interactions was investigated. Recordings of the fish's discharge frequencies, taken with Tektronix 3L5 and 5L4N spectrum analyzers, showed that, although movements of up to 60 Hz in a day may be made, the frequency movements would be made more or less synchronously by all fish in the group. An apparent preference for, and a tendency of the fish to follow one another in frequency, at frequency ratios of 2:3 (a musical fifth), 3:4 (fourth), and even 4:5 (major third) was observed. The appearance of a circadian rhythm was also noticed. Close

• 23. [Article] Temporary Environments

  This is a book chapter within Extremophile Fishes. This book summarizes the key adaptations enabling extremophile fishes to survive under harsh environmental conditions. It reviews the most recent research ...

  Citation × Citation Citation Abstract Copy Title: Temporary Environments Author: Polacik, Matej, Podrabsky, Jason E. Year: 2015 This is a book chapter within Extremophile Fishes. This book summarizes the key adaptations enabling extremophile fishes to survive under harsh environmental conditions. It reviews the most recent research on acidic, Antarctic, cave, desert, hypersaline, hypoxic, temporary, and fast-flowing habitats, as well as naturally and anthropogenically toxic waters, while pointing out generalities that are evident across different study systems. Knowledge of the different adaptations that allow fish to cope with stressful environmental conditions furthers our understanding of basic physiological, ecological, and evolutionary principles. In several cases, evidence is provided for how the adaptation to extreme environments promotes the emergence of new species. Furthermore, a link is made to conservation biology, and how human activities have exacerbated existing extreme environments and created new ones. The book concludes with a discussion of major open questions in our understanding of the ecology and evolution of life in extreme environments. Title: Temporary Environments Author: Polacik, Matej, Podrabsky, Jason E. Year: 2015 This is a book chapter within Extremophile Fishes. This book summarizes the key adaptations enabling extremophile fishes to survive under harsh environmental conditions. It reviews the most recent research on acidic, Antarctic, cave, desert, hypersaline, hypoxic, temporary, and fast-flowing habitats, as well as naturally and anthropogenically toxic waters, while pointing out generalities that are evident across different study systems. Knowledge of the different adaptations that allow fish to cope with stressful environmental conditions furthers our understanding of basic physiological, ecological, and evolutionary principles. In several cases, evidence is provided for how the adaptation to extreme environments promotes the emergence of new species. Furthermore, a link is made to conservation biology, and how human activities have exacerbated existing extreme environments and created new ones. The book concludes with a discussion of major open questions in our understanding of the ecology and evolution of life in extreme environments. Close

• 24. [Article] The fisheries of the Lower Columbia River, 1792 to 1850, based on EuroAmerican explorer and fur company accounts

  The role of fish in the Native American economy of the lower Columbia River has never been considered in detail. My study focused on the Columbia River from its mouth to the Cascades and the Willamette ...

  Citation × Citation Citation Abstract Copy Title: The fisheries of the Lower Columbia River, 1792 to 1850, based on EuroAmerican explorer and fur company accounts Author: Martin, Michael A. Year: 2006 The role of fish in the Native American economy of the lower Columbia River has never been considered in detail. My study focused on the Columbia River from its mouth to the Cascades and the Willamette River from its confluence with the Columbia to Willamette Falls. For this study I asked: How was salmon used? What other fish were important? Where and how were these fish taken and used? To address these questions, I evaluated historical documents, including explorer's accounts and the administrative records of fur companies dating from the late 1700's through the 1850's. I used fishery data, physical descriptions, migratory and spawning habits, and foraging patterns to identify fish in historic accounts. I annotated historic information and provided a synthesis of the historic fisheries. White sturgeon (Acipenser transmontanus), eulachon (Thaleichthys pacificus) and chinook salmon (Oncorhynchus tshawytscha) dominated the trade. Chum (O.keta) and lamprey (Lampetra sp.) were available, although not traded in large numbers. White sturgeon, eulachon, fall chinook, chum and lamprey were smoke cured. Steel head (0. mykiss) , coho (O.kisutch), perch (Embiotocidae), and resident trout were traded in small numbers indicating that other fish were part of the economy. Sockeye. salmon (O.nerka) was not traded. f "~{.' Indians captured white sturgeon with: multiple hooks on set-lines and funnel nets to take white sturgeon during the winter; scoop nets and the eulachon rake took eulachon; spring and summer chinook were taken with hoop nets and platforms in the Cascades rapids and at Willamette Falls; gaffs were used to take chinook and sturgeon during the summer in Baker Bay; and hoop nets took fall chinook in streams. Seine nets were noted but not were not discussed except for the chinook fishery of Baker Bay. Historic information on fishes used and methods of capture contrasts with the archaeological record of the Portland Basin. Resident freshwater fish, minnows (Cyprinidae) and suckers (Catostomus sp.), are abundant in the archaeological faunal record, but are rarely mentioned in historic accounts. Artifacts such as net weights are common in archaeological contexts in contrast with the limited discussions in the historic record. Possible explanations for these discrepancies are reviewed. Title: The fisheries of the Lower Columbia River, 1792 to 1850, based on EuroAmerican explorer and fur company accounts Author: Martin, Michael A. Year: 2006 The role of fish in the Native American economy of the lower Columbia River has never been considered in detail. My study focused on the Columbia River from its mouth to the Cascades and the Willamette River from its confluence with the Columbia to Willamette Falls. For this study I asked: How was salmon used? What other fish were important? Where and how were these fish taken and used? To address these questions, I evaluated historical documents, including explorer's accounts and the administrative records of fur companies dating from the late 1700's through the 1850's. I used fishery data, physical descriptions, migratory and spawning habits, and foraging patterns to identify fish in historic accounts. I annotated historic information and provided a synthesis of the historic fisheries. White sturgeon (Acipenser transmontanus), eulachon (Thaleichthys pacificus) and chinook salmon (Oncorhynchus tshawytscha) dominated the trade. Chum (O.keta) and lamprey (Lampetra sp.) were available, although not traded in large numbers. White sturgeon, eulachon, fall chinook, chum and lamprey were smoke cured. Steel head (0. mykiss) , coho (O.kisutch), perch (Embiotocidae), and resident trout were traded in small numbers indicating that other fish were part of the economy. Sockeye. salmon (O.nerka) was not traded. f "~{.' Indians captured white sturgeon with: multiple hooks on set-lines and funnel nets to take white sturgeon during the winter; scoop nets and the eulachon rake took eulachon; spring and summer chinook were taken with hoop nets and platforms in the Cascades rapids and at Willamette Falls; gaffs were used to take chinook and sturgeon during the summer in Baker Bay; and hoop nets took fall chinook in streams. Seine nets were noted but not were not discussed except for the chinook fishery of Baker Bay. Historic information on fishes used and methods of capture contrasts with the archaeological record of the Portland Basin. Resident freshwater fish, minnows (Cyprinidae) and suckers (Catostomus sp.), are abundant in the archaeological faunal record, but are rarely mentioned in historic accounts. Artifacts such as net weights are common in archaeological contexts in contrast with the limited discussions in the historic record. Possible explanations for these discrepancies are reviewed. Close

• 25. [Article] Phenotypic Variation in the Model Organism, Danio Rerio

  Model organisms are used to study evolutionary conserved traits. Zebrafish (Danio rerio) are used a model organism because of their highly fecundity, external fertilization, and robust nature, making them ...

  Citation × Citation Citation Abstract Copy Title: Phenotypic Variation in the Model Organism, Danio Rerio Author: Champaigne, Rachel D, Brown, Kim H. Year: 2014 Model organisms are used to study evolutionary conserved traits. Zebrafish (Danio rerio) are used a model organism because of their highly fecundity, external fertilization, and robust nature, making them highly adaptable to environmental and genetic variation. In an effort to limit data variation that lies outside of topic interest, phenotypic measures of variation must be performed, understood, and taken into consideration for future studies. A common measurement of phenotypic variation in fish is in the maximum (Ucrit) swimming speeds. Inter and intra-strain variation in zebrafish Ucrit swimming speeds will be observed in a swim tunnel. Baseline values will be recorded from ten fish from each of two families in each of three strains: WIK, Tubigan and AB. Environmental variation in zebrafish raised (beginning at one month of age) in tanks with various volumes and densities of fish will also be recorded from each strain. Mitochondrial density in white muscle will be compared in each strain in each condition. Diet, take salinity, pH, temperature, and light exposure will all remain constant for all fish. Title: Phenotypic Variation in the Model Organism, Danio Rerio Author: Champaigne, Rachel D, Brown, Kim H. Year: 2014 Model organisms are used to study evolutionary conserved traits. Zebrafish (Danio rerio) are used a model organism because of their highly fecundity, external fertilization, and robust nature, making them highly adaptable to environmental and genetic variation. In an effort to limit data variation that lies outside of topic interest, phenotypic measures of variation must be performed, understood, and taken into consideration for future studies. A common measurement of phenotypic variation in fish is in the maximum (Ucrit) swimming speeds. Inter and intra-strain variation in zebrafish Ucrit swimming speeds will be observed in a swim tunnel. Baseline values will be recorded from ten fish from each of two families in each of three strains: WIK, Tubigan and AB. Environmental variation in zebrafish raised (beginning at one month of age) in tanks with various volumes and densities of fish will also be recorded from each strain. Mitochondrial density in white muscle will be compared in each strain in each condition. Diet, take salinity, pH, temperature, and light exposure will all remain constant for all fish. Close

• 26. [Article] The effect of cold acclimation on the temperature preference of the goldfish, Carassius auratus, and the brown bullhead, Ictalurus nebulosus

  Two species of fish, Carassius auratus and Ictalurus nebulosus, were subjected to cold acclimation regimes. Acclimation temperatures were slowly lowered to 3°c, then held for a period of time. At various ...

  Citation × Citation Citation Abstract Copy Title: The effect of cold acclimation on the temperature preference of the goldfish, Carassius auratus, and the brown bullhead, Ictalurus nebulosus Author: Lord, Alfred Year: 1987 Two species of fish, Carassius auratus and Ictalurus nebulosus, were subjected to cold acclimation regimes. Acclimation temperatures were slowly lowered to 3°c, then held for a period of time. At various times during this regime, fish were taken out and allowed to spend time in a temperature gradient to determine their preferred temperatures. Carassius were left in the gradient just long enough to determine a measure of the acute temperature preference, while Ictalurus were left in the temperature gradient for longer periods of time to observe any changes that might occur as the fish adjusted to selected temperatures. In both species of fish, lower acclimation temperatures and increased time spent at low temperatures caused a preference for lower temperatures in the gradient. Title: The effect of cold acclimation on the temperature preference of the goldfish, Carassius auratus, and the brown bullhead, Ictalurus nebulosus Author: Lord, Alfred Year: 1987 Two species of fish, Carassius auratus and Ictalurus nebulosus, were subjected to cold acclimation regimes. Acclimation temperatures were slowly lowered to 3°c, then held for a period of time. At various times during this regime, fish were taken out and allowed to spend time in a temperature gradient to determine their preferred temperatures. Carassius were left in the gradient just long enough to determine a measure of the acute temperature preference, while Ictalurus were left in the temperature gradient for longer periods of time to observe any changes that might occur as the fish adjusted to selected temperatures. In both species of fish, lower acclimation temperatures and increased time spent at low temperatures caused a preference for lower temperatures in the gradient. Close

• 27. [Article] StreamNet: an integrated information system serving fisheries scientists and managers in the Columbia River Basin - or - is innovation possible when differing traditions collide?

  StreamNet is a project which brings together fisheries information collected by state agencies, federal agencies, and Indian tribes in a system of interconnected sets of data about anadromous fish in the ...

  Citation × Citation Citation Abstract Copy Title: StreamNet: an integrated information system serving fisheries scientists and managers in the Columbia River Basin - or - is innovation possible when differing traditions collide? Author: Siegel, Gretta E. Year: 1996 StreamNet is a project which brings together fisheries information collected by state agencies, federal agencies, and Indian tribes in a system of interconnected sets of data about anadromous fish in the Columbia River Basin. The data are used to observe trends in stock abundance escapement, hatchery production, etc. Each data point is linked to corresponding literature which can be searched separately in a references database. Plans are in progress to make this system available via the Internet. Data entry for the reference module is done via Microsoft Access. The application has been designed to include features of both a catalog and an index, and, through creative programming, has been successful in serving the project as both. Documents are housed in the library at the Columbia River Inter-Tribal Fish Commission. StreamNet is a cooperative project of the tribes, the state fisheries agencies of Idaho, Oregon, Washington, and Montana federal fisheries agencies, and the Pacific States Marine Fisheries Commission. The project is funded by the Bonneville Power Administration. Title: StreamNet: an integrated information system serving fisheries scientists and managers in the Columbia River Basin - or - is innovation possible when differing traditions collide? Author: Siegel, Gretta E. Year: 1996 StreamNet is a project which brings together fisheries information collected by state agencies, federal agencies, and Indian tribes in a system of interconnected sets of data about anadromous fish in the Columbia River Basin. The data are used to observe trends in stock abundance escapement, hatchery production, etc. Each data point is linked to corresponding literature which can be searched separately in a references database. Plans are in progress to make this system available via the Internet. Data entry for the reference module is done via Microsoft Access. The application has been designed to include features of both a catalog and an index, and, through creative programming, has been successful in serving the project as both. Documents are housed in the library at the Columbia River Inter-Tribal Fish Commission. StreamNet is a cooperative project of the tribes, the state fisheries agencies of Idaho, Oregon, Washington, and Montana federal fisheries agencies, and the Pacific States Marine Fisheries Commission. The project is funded by the Bonneville Power Administration. Close

• 28. [Article] Punched in the Face: Collected Essays and Reportage

  This is a diverse collection of narrative nonfiction, which includes personal essays, reportage, nature writing, and short columns. Its major themes include boxing and fly-fishing. Many of the pieces are ...

  Citation × Citation Citation Abstract Copy Title: Punched in the Face: Collected Essays and Reportage Author: Pindyck, Eben Year: 2014 This is a diverse collection of narrative nonfiction, which includes personal essays, reportage, nature writing, and short columns. Its major themes include boxing and fly-fishing. Many of the pieces are set in and around the state of Oregon. Title: Punched in the Face: Collected Essays and Reportage Author: Pindyck, Eben Year: 2014 This is a diverse collection of narrative nonfiction, which includes personal essays, reportage, nature writing, and short columns. Its major themes include boxing and fly-fishing. Many of the pieces are set in and around the state of Oregon. Close

• 29. [Article] The Dog & Pony Show (AKA Demonstrating the Value of Your Library)

  Are you interested in thinking about new ways to get people to experience the value and impact of your library? Hear how Eugene Public Library used technology to promote its value to City staff. We taught ...

  Citation × Citation Citation Abstract Copy Title: The Dog & Pony Show (AKA Demonstrating the Value of Your Library) Author: Vik, Lorie Year: 2013 Are you interested in thinking about new ways to get people to experience the value and impact of your library? Hear how Eugene Public Library used technology to promote its value to City staff. We taught them to fish, and we offered to fish. We were not surprised to find out that people like it when you save them time and money. Hear what we did and how we did it. Title: The Dog & Pony Show (AKA Demonstrating the Value of Your Library) Author: Vik, Lorie Year: 2013 Are you interested in thinking about new ways to get people to experience the value and impact of your library? Hear how Eugene Public Library used technology to promote its value to City staff. We taught them to fish, and we offered to fish. We were not surprised to find out that people like it when you save them time and money. Hear what we did and how we did it. Close

• 30. [Article] Rapid Change in Shallow Water Fish Species Composition in an Historically Stable Antarctic Environment

  McMurdo Sound, Antarctica, is home to a unique marine biota with an ecology that has evolved in this frigid environment over millions of years. The region is one of the least disturbed, and possibly the ...

  Citation × Citation Citation Abstract Copy Title: Rapid Change in Shallow Water Fish Species Composition in an Historically Stable Antarctic Environment Author: Buckley, Bradley A. Year: 2013 McMurdo Sound, Antarctica, is home to a unique marine biota with an ecology that has evolved in this frigid environment over millions of years. The region is one of the least disturbed, and possibly the last pristine, marine ecosystem on Earth. Here, the results of three seasons of fishing in the shallow nearshore waters of McMurdo Sound are reported. A shift in the composition of small fish species at one site, Inaccessible Island, has been observed in just five years. The shift in shallow water species composition occurred during a period that followed the maturation of a commercial fishery for the Antarctic toothfish, Dissostichus mawsoni Norman, a predator of smaller fish, and the presence of a large iceberg, termed B-15, at the mouth of McMurdo Sound during the early 2000s that trapped the annual sea ice in the area leading to the unusual accrual of multi-year sea ice. The data presented here provide a current record of species composition and physiological condition of small, shallow water fishes at three sites in McMurdo Sound, providing a current baseline for the assessment of future changes wrought by environmental changes and unprecedented fishery pressures in the Ross Sea. Title: Rapid Change in Shallow Water Fish Species Composition in an Historically Stable Antarctic Environment Author: Buckley, Bradley A. Year: 2013 McMurdo Sound, Antarctica, is home to a unique marine biota with an ecology that has evolved in this frigid environment over millions of years. The region is one of the least disturbed, and possibly the last pristine, marine ecosystem on Earth. Here, the results of three seasons of fishing in the shallow nearshore waters of McMurdo Sound are reported. A shift in the composition of small fish species at one site, Inaccessible Island, has been observed in just five years. The shift in shallow water species composition occurred during a period that followed the maturation of a commercial fishery for the Antarctic toothfish, Dissostichus mawsoni Norman, a predator of smaller fish, and the presence of a large iceberg, termed B-15, at the mouth of McMurdo Sound during the early 2000s that trapped the annual sea ice in the area leading to the unusual accrual of multi-year sea ice. The data presented here provide a current record of species composition and physiological condition of small, shallow water fishes at three sites in McMurdo Sound, providing a current baseline for the assessment of future changes wrought by environmental changes and unprecedented fishery pressures in the Ross Sea. Close

• 31. [Article] Defining Conservation Priorities for Freshwater Fishes According to Taxonomic, Functional, and Phylogenetic Diversity

  To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent ...

  Citation × Citation Citation Abstract Copy Title: Defining Conservation Priorities for Freshwater Fishes According to Taxonomic, Functional, and Phylogenetic Diversity Author: Strecker, Angela L., Olden, Julian D., Whittier, Joanna B., Paukert, Craig Patrick Year: 2011 To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential trade-offs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity; contemporary threats to biodiversity (including interactions with nonnative species); and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities; however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates multiple and complementary conservation values describing taxonomic, functional, and phylogenetic diversity. Title: Defining Conservation Priorities for Freshwater Fishes According to Taxonomic, Functional, and Phylogenetic Diversity Author: Strecker, Angela L., Olden, Julian D., Whittier, Joanna B., Paukert, Craig Patrick Year: 2011 To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential trade-offs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity; contemporary threats to biodiversity (including interactions with nonnative species); and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities; however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates multiple and complementary conservation values describing taxonomic, functional, and phylogenetic diversity. Close

• 32. [Article] Archaeological Data Provide Alternative Hypotheses on Pacific Herring (Clupea pallasii) Distribution, Abundance, and Variability

  Over the last century, Pacific herring, a forage fish of tremendous cultural, economic, and ecological importance, has declined in abundance over much of its range. We synthesize archaeological fisheries ...

  Citation × Citation Citation Abstract Copy Title: Archaeological Data Provide Alternative Hypotheses on Pacific Herring (Clupea pallasii) Distribution, Abundance, and Variability Author: McKechnie, Iain, Lepofsky, Dana, Moss, Madonna L., Butler, Virginia L., Orchard, Trevor J, Coupland, Gary, Foster, Frederick, Caldwell, Megan, Lertzman, Ken Year: 2014 Over the last century, Pacific herring, a forage fish of tremendous cultural, economic, and ecological importance, has declined in abundance over much of its range. We synthesize archaeological fisheries data spanning the past 10,000 y from Puget Sound in Washington to southeast Alaska to extend the ecological baseline for herring and contextualize the dynamics of modern industrial fisheries. While modern herring populations can be erratic and exhibit catastrophic declines, the archaeological record indicates a pattern of consistent abundance, providing an example of long-term sustainability and resilience in a fishery known for its modern variability. The most parsimonious explanation for the discrepancy between herring abundance in the ancient and more recent past is industrial harvesting over the last century. Title: Archaeological Data Provide Alternative Hypotheses on Pacific Herring (Clupea pallasii) Distribution, Abundance, and Variability Author: McKechnie, Iain, Lepofsky, Dana, Moss, Madonna L., Butler, Virginia L., Orchard, Trevor J, Coupland, Gary, Foster, Frederick, Caldwell, Megan, Lertzman, Ken Year: 2014 Over the last century, Pacific herring, a forage fish of tremendous cultural, economic, and ecological importance, has declined in abundance over much of its range. We synthesize archaeological fisheries data spanning the past 10,000 y from Puget Sound in Washington to southeast Alaska to extend the ecological baseline for herring and contextualize the dynamics of modern industrial fisheries. While modern herring populations can be erratic and exhibit catastrophic declines, the archaeological record indicates a pattern of consistent abundance, providing an example of long-term sustainability and resilience in a fishery known for its modern variability. The most parsimonious explanation for the discrepancy between herring abundance in the ancient and more recent past is industrial harvesting over the last century. Close

• 33. [Article] The Role of Salmon in Middle Snake River Human Economy: The Hetrick Site in Regional Contexts

  On the Columbia Plateau, the origin of the Winter Village Pattern has long been a focus of research. Intensification of resources such as salmon, roots, and local aquatic resources is often cited as the ...

  Citation × Citation Citation Abstract Copy Title: The Role of Salmon in Middle Snake River Human Economy: The Hetrick Site in Regional Contexts Author: Manning, Cassandra R. Year: 2011 On the Columbia Plateau, the origin of the Winter Village Pattern has long been a focus of research. Intensification of resources such as salmon, roots, and local aquatic resources is often cited as the cause of declining mobility. To address this question in the middle Snake River region, I have re-analyzed fish remains from the Hetrick site (10WN469; Weiser, ID), with occupations spanning the Holocene. Expectations from foraging theory and paleoclimate data are used to address whether salmon and other fish use changed over time and if such changes are correlated with the development of the Winter Village Pattern. The results of my research indicate that there is no correlation between the timing of increased salmonid use at the Hetrick site and paleoclimatic change or the earliest evidence for the Winter Village Pattern. Further, these results are very similar to patterns of fish use seen at other sites on the Snake River, particularly those from the Early and Middle Holocene. Title: The Role of Salmon in Middle Snake River Human Economy: The Hetrick Site in Regional Contexts Author: Manning, Cassandra R. Year: 2011 On the Columbia Plateau, the origin of the Winter Village Pattern has long been a focus of research. Intensification of resources such as salmon, roots, and local aquatic resources is often cited as the cause of declining mobility. To address this question in the middle Snake River region, I have re-analyzed fish remains from the Hetrick site (10WN469; Weiser, ID), with occupations spanning the Holocene. Expectations from foraging theory and paleoclimate data are used to address whether salmon and other fish use changed over time and if such changes are correlated with the development of the Winter Village Pattern. The results of my research indicate that there is no correlation between the timing of increased salmonid use at the Hetrick site and paleoclimatic change or the earliest evidence for the Winter Village Pattern. Further, these results are very similar to patterns of fish use seen at other sites on the Snake River, particularly those from the Early and Middle Holocene. Close

• 34. [Article] Aboriginal Fisheries of the Lower Columbia River

  This chapter, included in Chinookan Peoples of the Lower Columbia, published by the University of Washington Press in 2013, explores the aboriginal fisheries of the Lower Columbia River. The authors reviewed ...

  Citation × Citation Citation Abstract Copy Title: Aboriginal Fisheries of the Lower Columbia River Author: Butler, Virginia L., Martin, Michael A. Year: 2013 This chapter, included in Chinookan Peoples of the Lower Columbia, published by the University of Washington Press in 2013, explores the aboriginal fisheries of the Lower Columbia River. The authors reviewed ethnohistorical accounts and studies of archaeological sites to create a complex picture of Columbia River fisheries that challenges the prevailing view among anthropologists that salmon was the primary and predominant fishery among Chinookan peoples. The authors show that 19th century Native fishers targeted virtually all native fish species in the Lower Columbia River, and employed a wide range of strategies and tactics to acquire and process fish. Title: Aboriginal Fisheries of the Lower Columbia River Author: Butler, Virginia L., Martin, Michael A. Year: 2013 This chapter, included in Chinookan Peoples of the Lower Columbia, published by the University of Washington Press in 2013, explores the aboriginal fisheries of the Lower Columbia River. The authors reviewed ethnohistorical accounts and studies of archaeological sites to create a complex picture of Columbia River fisheries that challenges the prevailing view among anthropologists that salmon was the primary and predominant fishery among Chinookan peoples. The authors show that 19th century Native fishers targeted virtually all native fish species in the Lower Columbia River, and employed a wide range of strategies and tactics to acquire and process fish. Close

• 35. [Article] On the Validity of the Radiographic Method for Determining Age of Ancient Salmon

  White rings visible on the centrum face of salmon vertebrae with X-rays have been used since the 1980s to age Pacific salmon (Oncorhynchus spp.), which in turn have been used to determine salmon species, ...

  Citation × Citation Citation Abstract Copy Title: On the Validity of the Radiographic Method for Determining Age of Ancient Salmon Author: Hofkamp, Anthony R., Butler, Virginia L. Year: 2017 White rings visible on the centrum face of salmon vertebrae with X-rays have been used since the 1980s to age Pacific salmon (Oncorhynchus spp.), which in turn have been used to determine salmon species, season of capture and season of site occupation. This approach relies on a variety of assumptions, the most fundamental of which is that rings represent true years. Recent aDNA analysis has shown that the X-ray approach has flaws but the source of the error has been unknown. Given the value of reconstructing salmon population demographics and life history from ancient remains, establishing a valid and reliable method of ageing salmon vertebrae is extremely worthwhile. The main goal of our study was to evaluate if X-ray images of ring patterns on vertebrae provide a valid method of estimating fish age. Vertebrae from 66 adult Chinook salmon (O. tshawytscha) of known age were studied with X-rays, thin sections or low-powered (10–30 ×) magnification. We found that the white bands observed in X-rays are structural walls that do not grow annually. While X-rays are not a valid method for ageing salmonids, incremental growth seen on the surface of fish centra shows great promise for reconstructing ancient fish life history. Title: On the Validity of the Radiographic Method for Determining Age of Ancient Salmon Author: Hofkamp, Anthony R., Butler, Virginia L. Year: 2017 White rings visible on the centrum face of salmon vertebrae with X-rays have been used since the 1980s to age Pacific salmon (Oncorhynchus spp.), which in turn have been used to determine salmon species, season of capture and season of site occupation. This approach relies on a variety of assumptions, the most fundamental of which is that rings represent true years. Recent aDNA analysis has shown that the X-ray approach has flaws but the source of the error has been unknown. Given the value of reconstructing salmon population demographics and life history from ancient remains, establishing a valid and reliable method of ageing salmon vertebrae is extremely worthwhile. The main goal of our study was to evaluate if X-ray images of ring patterns on vertebrae provide a valid method of estimating fish age. Vertebrae from 66 adult Chinook salmon (O. tshawytscha) of known age were studied with X-rays, thin sections or low-powered (10–30 ×) magnification. We found that the white bands observed in X-rays are structural walls that do not grow annually. While X-rays are not a valid method for ageing salmonids, incremental growth seen on the surface of fish centra shows great promise for reconstructing ancient fish life history. Close

• 36. [Article] Desert Environments

  This is a book chapter within Extremophile Fishes. This book summarizes the key adaptations enabling extremophile fishes to survive under harsh environmental conditions. It reviews the most recent research ...

  Citation × Citation Citation Abstract Copy Title: Desert Environments Author: Hillyard, Stanley D., Podrabsky, Jason E., van Breukelen, Frank Year: 2015 This is a book chapter within Extremophile Fishes. This book summarizes the key adaptations enabling extremophile fishes to survive under harsh environmental conditions. It reviews the most recent research on acidic, Antarctic, cave, desert, hypersaline, hypoxic, temporary, and fast-flowing habitats, as well as naturally and anthropogenically toxic waters, while pointing out generalities that are evident across different study systems. Knowledge of the different adaptations that allow fish to cope with stressful environmental conditions furthers our understanding of basic physiological, ecological, and evolutionary principles. In several cases, evidence is provided for how the adaptation to extreme environments promotes the emergence of new species. Furthermore, a link is made to conservation biology, and how human activities have exacerbated existing extreme environments and created new ones. The book concludes with a discussion of major open questions in our understanding of the ecology and evolution of life in extreme environments. Title: Desert Environments Author: Hillyard, Stanley D., Podrabsky, Jason E., van Breukelen, Frank Year: 2015 This is a book chapter within Extremophile Fishes. This book summarizes the key adaptations enabling extremophile fishes to survive under harsh environmental conditions. It reviews the most recent research on acidic, Antarctic, cave, desert, hypersaline, hypoxic, temporary, and fast-flowing habitats, as well as naturally and anthropogenically toxic waters, while pointing out generalities that are evident across different study systems. Knowledge of the different adaptations that allow fish to cope with stressful environmental conditions furthers our understanding of basic physiological, ecological, and evolutionary principles. In several cases, evidence is provided for how the adaptation to extreme environments promotes the emergence of new species. Furthermore, a link is made to conservation biology, and how human activities have exacerbated existing extreme environments and created new ones. The book concludes with a discussion of major open questions in our understanding of the ecology and evolution of life in extreme environments. Close

• 37. [Article] A System Dynamics Model of the Pacific Coast Rockfish Fishery

  This paper presents a model of the dynamic behavior of the yellowtail rockfish of the Pacific Coast of the United States. The purpose of the model is to generate endogenously the historical data for fish ...

  Citation × Citation Citation Abstract Copy Title: A System Dynamics Model of the Pacific Coast Rockfish Fishery Author: Wakeland, Wayne, Cangur, Olgay, Rueda, Guillermo, Scholz, Astrid Year: 2003 This paper presents a model of the dynamic behavior of the yellowtail rockfish of the Pacific Coast of the United States. The purpose of the model is to generate endogenously the historical data for fish population, fishing vessels, regulatory parameters, and fish harvest. The model was subjected to a variety of tests to determine its sensitivity to changes in key parameters and initial values, including extreme conditions. Model results indicate that acceptable biological catch and fleet capacity must be adjusted quickly in response to changing conditions, in order to improve fishery sustainability. Additional analysis reinforces the policy of setting the maximum sustainable yield at 40%. Title: A System Dynamics Model of the Pacific Coast Rockfish Fishery Author: Wakeland, Wayne, Cangur, Olgay, Rueda, Guillermo, Scholz, Astrid Year: 2003 This paper presents a model of the dynamic behavior of the yellowtail rockfish of the Pacific Coast of the United States. The purpose of the model is to generate endogenously the historical data for fish population, fishing vessels, regulatory parameters, and fish harvest. The model was subjected to a variety of tests to determine its sensitivity to changes in key parameters and initial values, including extreme conditions. Model results indicate that acceptable biological catch and fleet capacity must be adjusted quickly in response to changing conditions, in order to improve fishery sustainability. Additional analysis reinforces the policy of setting the maximum sustainable yield at 40%. Close

• 38. [Article] Expression of Growth Arrest and DNA Damage Protein 45-alpha (gadd45-alpha) and the CCAAT/enhancer binding protein-delta (C/EBP-delta) in Fishes Exposed to Heat and Hypoxia

  The cellular stress response (CSR) is one of the most highly conserved mechanisms among all organisms. Cellular stress can be defined as damage or the threat of damage to proteins, macromolecules and/or ...

  Citation × Citation Citation Abstract Copy Title: Expression of Growth Arrest and DNA Damage Protein 45-alpha (gadd45-alpha) and the CCAAT/enhancer binding protein-delta (C/EBP-delta) in Fishes Exposed to Heat and Hypoxia Author: Hassumani, Daniel Omar Year: 2013 The cellular stress response (CSR) is one of the most highly conserved mechanisms among all organisms. Cellular stress can be defined as damage or the threat of damage to proteins, macromolecules and/or DNA. The response to damage can involve cell cycle regulation, protein chaperoning, DNA repair or, if macromolecular damage is too severe, apoptotic mechanisms can be initiated. This thesis details experiments that were designed to examine the cellular response to non-lethal environmental stressors at the protein level, using two fish species as study models. Two proteins that can cause cell cycle arrest and apoptosis mechanisms were examined. Expression of the CCAAT enhancer binding protein-delta (C/EBP-[delta]) was examined in the zebrafish, Danio rerio, exposed to acute, non-lethal hypoxic conditions. While C/EBP-[delta] was expressed constitutively in control individuals during all time points, exposure to hypoxic conditions did not have a consistent significant effect on C/EBP-[delta] expression (two-way ANOVA, P>0.05) in zebrafish white muscle tissue. In a second study, the expression of the growth arrest and DNA damage 45-alpha protein (gadd45-[alpha], a mediator of cell cycle arrest and perhaps apoptosis was examined in heat-stressed liver tissue of an extremely cold-adapted Antarctic fish, Trematomus bernacchii. Gadd45-[alpha] levels were higher in fish exposure to 2°C across all time points (one-way ANOVA; P Title: Expression of Growth Arrest and DNA Damage Protein 45-alpha (gadd45-alpha) and the CCAAT/enhancer binding protein-delta (C/EBP-delta) in Fishes Exposed to Heat and Hypoxia Author: Hassumani, Daniel Omar Year: 2013 The cellular stress response (CSR) is one of the most highly conserved mechanisms among all organisms. Cellular stress can be defined as damage or the threat of damage to proteins, macromolecules and/or DNA. The response to damage can involve cell cycle regulation, protein chaperoning, DNA repair or, if macromolecular damage is too severe, apoptotic mechanisms can be initiated. This thesis details experiments that were designed to examine the cellular response to non-lethal environmental stressors at the protein level, using two fish species as study models. Two proteins that can cause cell cycle arrest and apoptosis mechanisms were examined. Expression of the CCAAT enhancer binding protein-delta (C/EBP-[delta]) was examined in the zebrafish, Danio rerio, exposed to acute, non-lethal hypoxic conditions. While C/EBP-[delta] was expressed constitutively in control individuals during all time points, exposure to hypoxic conditions did not have a consistent significant effect on C/EBP-[delta] expression (two-way ANOVA, P>0.05) in zebrafish white muscle tissue. In a second study, the expression of the growth arrest and DNA damage 45-alpha protein (gadd45-[alpha], a mediator of cell cycle arrest and perhaps apoptosis was examined in heat-stressed liver tissue of an extremely cold-adapted Antarctic fish, Trematomus bernacchii. Gadd45-[alpha] levels were higher in fish exposure to 2°C across all time points (one-way ANOVA; P Close

• 39. [Article] Tracking Fish and Human Response to Abrupt Environmental Change at Tse-whit-zen: A Large Native American Village on the Olympic Peninsula, Washington State

  Evidence of large earthquakes occurring along the Pacific Northwest coast is reflected in coastal stratigraphy from Oregon to British Columbia, where there also exists an extensive archaeological record ...

  Citation × Citation Citation Abstract Copy Title: Tracking Fish and Human Response to Abrupt Environmental Change at Tse-whit-zen: A Large Native American Village on the Olympic Peninsula, Washington State Author: Mohlenhoff, Kathryn Anne Year: 2013 Evidence of large earthquakes occurring along the Pacific Northwest coast is reflected in coastal stratigraphy from Oregon to British Columbia, where there also exists an extensive archaeological record of Native American occupation. Tse-whit-zen, a large Native American village dating between 1824 and 54 cal B.P. located on the Olympic Peninsula of Washington State, was excavated with exceptionally fine stratigraphic control allowing for precise comparison of natural and cultural records. Here I report on the >10,000 fish remains from one 2x2 m excavation block; this assemblage spans one earthquake event, allowing study of changes in relative taxonomic abundance through time that may coincide with earthquakes or other environmental changes. Results indicate use of a wide range of marine fish taxa including various sculpins (Cottidae), flatfish (Pleuronectiformes), herring (Clupea pallasii) and salmon (Oncorhynchusspp.). This illustrates a highly diverse diet throughout occupation, though relative abundances of more offshore taxa decrease through time in favor of some nearshore taxa, possibly indicating the presence of a coseismic event. This thesis serves as part of a pilot study for a collaborative project that is underway. This larger project addresses human response to both gradual and abrupt environmental change through the analysis of all classes of Tse-whit-zen faunal remains, which provide a link to impacts on animal populations and in turn human subsistence. Title: Tracking Fish and Human Response to Abrupt Environmental Change at Tse-whit-zen: A Large Native American Village on the Olympic Peninsula, Washington State Author: Mohlenhoff, Kathryn Anne Year: 2013 Evidence of large earthquakes occurring along the Pacific Northwest coast is reflected in coastal stratigraphy from Oregon to British Columbia, where there also exists an extensive archaeological record of Native American occupation. Tse-whit-zen, a large Native American village dating between 1824 and 54 cal B.P. located on the Olympic Peninsula of Washington State, was excavated with exceptionally fine stratigraphic control allowing for precise comparison of natural and cultural records. Here I report on the >10,000 fish remains from one 2x2 m excavation block; this assemblage spans one earthquake event, allowing study of changes in relative taxonomic abundance through time that may coincide with earthquakes or other environmental changes. Results indicate use of a wide range of marine fish taxa including various sculpins (Cottidae), flatfish (Pleuronectiformes), herring (Clupea pallasii) and salmon (Oncorhynchusspp.). This illustrates a highly diverse diet throughout occupation, though relative abundances of more offshore taxa decrease through time in favor of some nearshore taxa, possibly indicating the presence of a coseismic event. This thesis serves as part of a pilot study for a collaborative project that is underway. This larger project addresses human response to both gradual and abrupt environmental change through the analysis of all classes of Tse-whit-zen faunal remains, which provide a link to impacts on animal populations and in turn human subsistence. Close

• 40. [Article] Gene Expression Life History Markers in a Hatchery and a Wild Population of Young-of-the-Year Oncorhynchus mykiss

  Life history within a single species can vary significantly. Many of these differences are associated with varying environmental conditions. Understanding what environmental conditions cue alternate life ...

  Citation × Citation Citation Abstract Copy Title: Gene Expression Life History Markers in a Hatchery and a Wild Population of Young-of-the-Year Oncorhynchus mykiss Author: Garrett, Ian D. F. Year: 2013 Life history within a single species can vary significantly. Many of these differences are associated with varying environmental conditions. Understanding what environmental conditions cue alternate life histories within a single species has been researched extensively. In salmonid fishes, more than almost any other group, varying environmental conditions give rise to individuals within species that take markedly different life history trajectories. Oncorhynchus mykissis a species of salmonid native to the Pacific Northwest region of North America. This species has two life history forms, anadromous and resident. The anadromous form spends a portion of its life in ocean while the resident life history form completes its entire life history in freshwater. Until the decision to migrate and morphological changes associated with smoltification occur, the two life history variants of this species are indistinguishable from each other. This ambiguity in juvenile O. mykiss morphology presents challenges for conservation managers charged with protecting and increasing threatened O. mykiss populations around the Pacific Northwest because conservation efforts cannot be evaluated until juvenile fish make the decision to migrate. Microarray gene expression analysis was used to profile gene expression in juvenile populations of wild and hatchery O. mykiss to identify gene expression variation associated with alternate life history variants. This analysis identified 8 DNA sequences present in both brain and gill tissues that differ in expression in rainbow trout and steelhead hatchery stocks. Differential expression as quantified by microarrays was validated with quantitative real-time PCR. Lastly, the expression of these putative life history markers was preliminarily evaluated in a wild population of O. mykiss at sample locations in the South Fork John Day River Basin, Oregon with known ratios of juvenile anadromous and resident fish. Title: Gene Expression Life History Markers in a Hatchery and a Wild Population of Young-of-the-Year Oncorhynchus mykiss Author: Garrett, Ian D. F. Year: 2013 Life history within a single species can vary significantly. Many of these differences are associated with varying environmental conditions. Understanding what environmental conditions cue alternate life histories within a single species has been researched extensively. In salmonid fishes, more than almost any other group, varying environmental conditions give rise to individuals within species that take markedly different life history trajectories. Oncorhynchus mykissis a species of salmonid native to the Pacific Northwest region of North America. This species has two life history forms, anadromous and resident. The anadromous form spends a portion of its life in ocean while the resident life history form completes its entire life history in freshwater. Until the decision to migrate and morphological changes associated with smoltification occur, the two life history variants of this species are indistinguishable from each other. This ambiguity in juvenile O. mykiss morphology presents challenges for conservation managers charged with protecting and increasing threatened O. mykiss populations around the Pacific Northwest because conservation efforts cannot be evaluated until juvenile fish make the decision to migrate. Microarray gene expression analysis was used to profile gene expression in juvenile populations of wild and hatchery O. mykiss to identify gene expression variation associated with alternate life history variants. This analysis identified 8 DNA sequences present in both brain and gill tissues that differ in expression in rainbow trout and steelhead hatchery stocks. Differential expression as quantified by microarrays was validated with quantitative real-time PCR. Lastly, the expression of these putative life history markers was preliminarily evaluated in a wild population of O. mykiss at sample locations in the South Fork John Day River Basin, Oregon with known ratios of juvenile anadromous and resident fish. Close

• 41. [Article] Scientifically Defensible Fish Conservation and Recovery Plans: Addressing Diffuse Threats and Developing Rigorous Adaptive Management Plans

  We discuss the importance of addressing diffuse threats to long-term species and habitat viability in fish conservation and recovery planning. In the Pacific Northwest, USA, salmonid management plans have ...

  Citation × Citation Citation Abstract Copy Title: Scientifically Defensible Fish Conservation and Recovery Plans: Addressing Diffuse Threats and Developing Rigorous Adaptive Management Plans Author: Maas-Hebner, Kathleen G., Schreck, Carl B., Hughes, Robert M., Yeakley, J. Alan, Molina, Nancy Year: 2016 We discuss the importance of addressing diffuse threats to long-term species and habitat viability in fish conservation and recovery planning. In the Pacific Northwest, USA, salmonid management plans have typically focused on degraded freshwater habitat, dams, fish passage, harvest rates, and hatchery releases. However, such plans inadequately address threats related to human population and economic growth, intra- and interspecific competition, and changes in climate, ocean, and estuarine conditions. Based on reviews conducted on eight conservation and/or recovery plans, we found that though threats resulting from such changes are difficult to model and/or predict, they are especially important for wide-ranging diadromous species. Adaptive management is also a critical but often inadequately constructed component of those plans. Adaptive management should be designed to respond to evolving knowledge about the fish and their supporting ecosystems; if done properly, it should help improve conservation efforts by decreasing uncertainty regarding known and diffuse threats. We conclude with a general call for environmental managers and planners to reinvigorate the adaptive management process in future management plans, including more explicitly identifying critical uncertainties, implementing monitoring programs to reduce those uncertainties, and explicitly stating what management actions will occur when pre-identified trigger points are reached. Title: Scientifically Defensible Fish Conservation and Recovery Plans: Addressing Diffuse Threats and Developing Rigorous Adaptive Management Plans Author: Maas-Hebner, Kathleen G., Schreck, Carl B., Hughes, Robert M., Yeakley, J. Alan, Molina, Nancy Year: 2016 We discuss the importance of addressing diffuse threats to long-term species and habitat viability in fish conservation and recovery planning. In the Pacific Northwest, USA, salmonid management plans have typically focused on degraded freshwater habitat, dams, fish passage, harvest rates, and hatchery releases. However, such plans inadequately address threats related to human population and economic growth, intra- and interspecific competition, and changes in climate, ocean, and estuarine conditions. Based on reviews conducted on eight conservation and/or recovery plans, we found that though threats resulting from such changes are difficult to model and/or predict, they are especially important for wide-ranging diadromous species. Adaptive management is also a critical but often inadequately constructed component of those plans. Adaptive management should be designed to respond to evolving knowledge about the fish and their supporting ecosystems; if done properly, it should help improve conservation efforts by decreasing uncertainty regarding known and diffuse threats. We conclude with a general call for environmental managers and planners to reinvigorate the adaptive management process in future management plans, including more explicitly identifying critical uncertainties, implementing monitoring programs to reduce those uncertainties, and explicitly stating what management actions will occur when pre-identified trigger points are reached. Close

• 42. [Article] A Terrestrial-Aquatic Food Web Subsidy is Potentially Mediated by Multiple Predator Effects on an Arboreal Crab

  Terrestrial-aquatic food web subsidies are known to affect food web structure, ecosystem productivity, and stability of recipient habitats. This study describes a prey flux across the land–water interface ...

  Citation × Citation Citation Abstract Copy Title: A Terrestrial-Aquatic Food Web Subsidy is Potentially Mediated by Multiple Predator Effects on an Arboreal Crab Author: Yeager, Lauren A., Stoner, Elizabeth W., Peters, Joseph R., Layman, Craig A. Year: 2015 Terrestrial-aquatic food web subsidies are known to affect food web structure, ecosystem productivity, and stability of recipient habitats. This study describes a prey flux across the land–water interface associated with a behavioral response to multiple predators. Specifically, mangrove tree crabs (Aratus pisonii, hereafter Aratus) are primarily arboreal, but may jump off mangrove trees to escape avian predators, making them vulnerable to fish predation. Mesocosm experiments, field observations, and tethering assays were used to investigate behavioral responses, habitat shifts, and risk for Aratus associated with these two predator types. In the field, Aratus spent most of their time above the water on mangroves, where risk is lowest. In response to simulated bird strikes in mesocosm trials, crabs jumped off trees to escape imminent risk, and spent more time in and near the water, enhancing risk of fish predation. Fish attacks on crabs were nearly three times greater in treatments with simulated bird attacks. In addition, empirical diet data was used to examine the importance of Aratus as a prey item for a fish predator. Aratus represented up to 29% of diet by volume for one of the most common mesopredators in the Caribbean (gray snapper Lutjanus griseus), with the proportion varying greatly across space. Because Aratus consume mangrove-derived carbon, their consumption by aquatic predators represents another pathway by which mangrove production may be incorporated into aquatic food webs. These data suggest how the nexus of behavioral and food web ecology may provide for new perspectives on energy flow between ecosystems. Title: A Terrestrial-Aquatic Food Web Subsidy is Potentially Mediated by Multiple Predator Effects on an Arboreal Crab Author: Yeager, Lauren A., Stoner, Elizabeth W., Peters, Joseph R., Layman, Craig A. Year: 2015 Terrestrial-aquatic food web subsidies are known to affect food web structure, ecosystem productivity, and stability of recipient habitats. This study describes a prey flux across the land–water interface associated with a behavioral response to multiple predators. Specifically, mangrove tree crabs (Aratus pisonii, hereafter Aratus) are primarily arboreal, but may jump off mangrove trees to escape avian predators, making them vulnerable to fish predation. Mesocosm experiments, field observations, and tethering assays were used to investigate behavioral responses, habitat shifts, and risk for Aratus associated with these two predator types. In the field, Aratus spent most of their time above the water on mangroves, where risk is lowest. In response to simulated bird strikes in mesocosm trials, crabs jumped off trees to escape imminent risk, and spent more time in and near the water, enhancing risk of fish predation. Fish attacks on crabs were nearly three times greater in treatments with simulated bird attacks. In addition, empirical diet data was used to examine the importance of Aratus as a prey item for a fish predator. Aratus represented up to 29% of diet by volume for one of the most common mesopredators in the Caribbean (gray snapper Lutjanus griseus), with the proportion varying greatly across space. Because Aratus consume mangrove-derived carbon, their consumption by aquatic predators represents another pathway by which mangrove production may be incorporated into aquatic food webs. These data suggest how the nexus of behavioral and food web ecology may provide for new perspectives on energy flow between ecosystems. Close

• 43. [Article] The Aquarium Trade as an Invasion Pathway in the Pacific Northwest

  The aquarium trade moves thousands of species around the globe, and unwanted organisms may be released into freshwaters, with adverse ecological and economic effects. We report on the first investigation ...

  Citation × Citation Citation Abstract Copy Title: The Aquarium Trade as an Invasion Pathway in the Pacific Northwest Author: Strecker, Angela L., Campbell, Philip M., Olden, Julian D. Year: 2011 The aquarium trade moves thousands of species around the globe, and unwanted organisms may be released into freshwaters, with adverse ecological and economic effects. We report on the first investigation of the ornamental pet trade as an invasion pathway in the Pacific Northwest region of the United States, where a moderate climate and a large human population present ample opportunities for the introduction and establishment of aquarium trade species. Results from a regional survey of pet stores found that the number of fish (n=400) and plant (n=124) species currently in the aquarium trade is vast. Pet stores import thousands of fish every month, the majority of which (58%) are considered to pose an ecological threat to native ecosystems. Our propagule pressure model suggests that approximately 2,500 fish (maximum 21,000 individuals) are likely released annually to the Puget Sound region by aquarists, and that water temperatures in many parts of Washington are suitable for establishment of populations. In conclusion, the aquarium trade may be a significant source of past and future invasions in the Pacific Northwest, and we recommend enhanced public education programs, greater regulation of the aquarium industry, and improved legislation of nonnative species in the ornamental trade. Title: The Aquarium Trade as an Invasion Pathway in the Pacific Northwest Author: Strecker, Angela L., Campbell, Philip M., Olden, Julian D. Year: 2011 The aquarium trade moves thousands of species around the globe, and unwanted organisms may be released into freshwaters, with adverse ecological and economic effects. We report on the first investigation of the ornamental pet trade as an invasion pathway in the Pacific Northwest region of the United States, where a moderate climate and a large human population present ample opportunities for the introduction and establishment of aquarium trade species. Results from a regional survey of pet stores found that the number of fish (n=400) and plant (n=124) species currently in the aquarium trade is vast. Pet stores import thousands of fish every month, the majority of which (58%) are considered to pose an ecological threat to native ecosystems. Our propagule pressure model suggests that approximately 2,500 fish (maximum 21,000 individuals) are likely released annually to the Puget Sound region by aquarists, and that water temperatures in many parts of Washington are suitable for establishment of populations. In conclusion, the aquarium trade may be a significant source of past and future invasions in the Pacific Northwest, and we recommend enhanced public education programs, greater regulation of the aquarium industry, and improved legislation of nonnative species in the ornamental trade. Close

• 44. [Article] Fish Species Introductions Provide Novel Insights into the Patterns and Drivers of Phylogenetic Structure in Freshwaters

  Despite long-standing interest of terrestrial ecologists, freshwater ecosystems are a fertile, yet unappreciated, testing ground for applying community phylogenetics to uncover mechanisms of species assembly. ...

  Citation × Citation Citation Abstract Copy Title: Fish Species Introductions Provide Novel Insights into the Patterns and Drivers of Phylogenetic Structure in Freshwaters Author: Strecker, Angela L., Olden, Julian D. Year: 2014 Despite long-standing interest of terrestrial ecologists, freshwater ecosystems are a fertile, yet unappreciated, testing ground for applying community phylogenetics to uncover mechanisms of species assembly. We quantify phylogenetic clustering and overdispersion of native and non-native fishes of a large river basin in the American Southwest to test for the mechanisms (environmental filtering versus competitive exclusion) and spatial scales influencing community structure. Contrary to expectations, non-native species were phylogenetically clustered and related to natural environmental conditions, whereas native species were not phylogenetically structured, likely reflecting human-related changes to the basin. The species that are most invasive (in terms of ecological impacts) tended to be the most phylogenetically divergent from natives across watersheds, but not within watersheds, supporting the hypothesis that Darwin's naturalization conundrum is driven by the spatial scale. Phylogenetic distinctiveness may facilitate non-native establishment at regional scales, but environmental filtering restricts local membership to closely related species with physiological tolerances for current environments. By contrast, native species may have been phylogenetically clustered in historical times, but species loss from contemporary populations by anthropogenic activities has likely shaped the phylogenetic signal. Our study implies that fundamental mechanisms of community assembly have changed, with fundamental consequences for the biogeography of both native and non-native species. Title: Fish Species Introductions Provide Novel Insights into the Patterns and Drivers of Phylogenetic Structure in Freshwaters Author: Strecker, Angela L., Olden, Julian D. Year: 2014 Despite long-standing interest of terrestrial ecologists, freshwater ecosystems are a fertile, yet unappreciated, testing ground for applying community phylogenetics to uncover mechanisms of species assembly. We quantify phylogenetic clustering and overdispersion of native and non-native fishes of a large river basin in the American Southwest to test for the mechanisms (environmental filtering versus competitive exclusion) and spatial scales influencing community structure. Contrary to expectations, non-native species were phylogenetically clustered and related to natural environmental conditions, whereas native species were not phylogenetically structured, likely reflecting human-related changes to the basin. The species that are most invasive (in terms of ecological impacts) tended to be the most phylogenetically divergent from natives across watersheds, but not within watersheds, supporting the hypothesis that Darwin's naturalization conundrum is driven by the spatial scale. Phylogenetic distinctiveness may facilitate non-native establishment at regional scales, but environmental filtering restricts local membership to closely related species with physiological tolerances for current environments. By contrast, native species may have been phylogenetically clustered in historical times, but species loss from contemporary populations by anthropogenic activities has likely shaped the phylogenetic signal. Our study implies that fundamental mechanisms of community assembly have changed, with fundamental consequences for the biogeography of both native and non-native species. Close

• 45. [Article] Factors Influencing the Survival of Outmigrating Juvenile Salmonids Through Multiple Dam Passages: An Individual-Based Approach

  Substantial declines of Pacific salmon populations have occurred over the past several decades related to large-scale anthropogenic and climatic changes in freshwater and marine environments. In the Columbia ...

  Citation × Citation Citation Abstract Copy Title: Factors Influencing the Survival of Outmigrating Juvenile Salmonids Through Multiple Dam Passages: An Individual-Based Approach Author: Elder, Timothy, Woodley, Christa M., Weiland, Mark A., Strecker, Angela L. Year: 2016 Substantial declines of Pacific salmon populations have occurred over the past several decades related to large-scale anthropogenic and climatic changes in freshwater and marine environments. In the Columbia River Basin, migrating juvenile salmonids may pass as many as eight large-scale hydropower projects before reaching the ocean; however, the cumulative effects of multiple dam passages are largely unknown. Using acoustic transmitters and an extensive system of hydrophone arrays in the Lower Columbia River, we calculated the survival of yearling Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) passing one, two, or three dams. We applied a unique index of biological characteristics and environmental exposures, experienced by each fish individually as it migrated downstream, in order to examine which factors most influence salmonid survival. High outflow volumes led to involuntary spill in 2011 and created an environment of supersaturated dissolved gas concentrations. In this environment, migrating smolt survival was strongly influenced by barometric pressure, fish velocity, and water temperature. The effect of these variables on survival was compounded by multiple dam passages compared to fish passing a single dam. Despite spatial isolation between dams in the Lower Columbia River hydrosystem, migrating smolt appear to experience cumulative effects akin to a press disturbance. In general, Chinook salmon and steelhead respond similarly in terms of survival rates and responses to altered environmental conditions. Management actions that limit dissolved gas concentrations in years of high flow will benefit migrating salmonids at this life stage. Title: Factors Influencing the Survival of Outmigrating Juvenile Salmonids Through Multiple Dam Passages: An Individual-Based Approach Author: Elder, Timothy, Woodley, Christa M., Weiland, Mark A., Strecker, Angela L. Year: 2016 Substantial declines of Pacific salmon populations have occurred over the past several decades related to large-scale anthropogenic and climatic changes in freshwater and marine environments. In the Columbia River Basin, migrating juvenile salmonids may pass as many as eight large-scale hydropower projects before reaching the ocean; however, the cumulative effects of multiple dam passages are largely unknown. Using acoustic transmitters and an extensive system of hydrophone arrays in the Lower Columbia River, we calculated the survival of yearling Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) passing one, two, or three dams. We applied a unique index of biological characteristics and environmental exposures, experienced by each fish individually as it migrated downstream, in order to examine which factors most influence salmonid survival. High outflow volumes led to involuntary spill in 2011 and created an environment of supersaturated dissolved gas concentrations. In this environment, migrating smolt survival was strongly influenced by barometric pressure, fish velocity, and water temperature. The effect of these variables on survival was compounded by multiple dam passages compared to fish passing a single dam. Despite spatial isolation between dams in the Lower Columbia River hydrosystem, migrating smolt appear to experience cumulative effects akin to a press disturbance. In general, Chinook salmon and steelhead respond similarly in terms of survival rates and responses to altered environmental conditions. Management actions that limit dissolved gas concentrations in years of high flow will benefit migrating salmonids at this life stage. Close

• 46. [Article] A Follow-up Study of Selected Biomarkers of Health in Cod Gadus Morhua L. Collected from the Southern Baltic off the Polish Coast

  Selected biomarkers of health were examined in 50 post-spawning cod Gadus morhua collected in November 2015 from the southern Baltic. The biomarkers included condition factor (CF), macroscopic lesions, ...

  Citation × Citation Citation Abstract Copy Title: A Follow-up Study of Selected Biomarkers of Health in Cod Gadus Morhua L. Collected from the Southern Baltic off the Polish Coast Author: Borucinska, Joanna D., Morka, Dorota, Grabowski, Zbigniew, Smith, H. Year: 2017 Selected biomarkers of health were examined in 50 post-spawning cod Gadus morhua collected in November 2015 from the southern Baltic. The biomarkers included condition factor (CF), macroscopic lesions, histopathology of spleen, liver and gonads, and morphometry of follicular atresia and hepatic and splenic melanomacrophage cells (MMC). All fish appeared in good body condition. One fish had a dermal ulcer, and in seven, macroscopic nematodes were noted within body cavity. Microscopic lesions in the liver included biliary myxozoanosis, microsporidial and necrocentric granulomas, parasitic hepatitis, multifocal necrosis, foci of cellular alterations, spongiosis, peliosis and cytoplasmic fibrillar inclusions. The spleen and gonads had microsporidial and/or necrocentric granulomas. Some of the biomarkers showed differences as compared to spawning cod collected in May from the same location in 2012, most importantly values an order of magnitude lower for splenic MMC in post-spawning fish. In post-spawning fish, there were statistically significant correlations between MMC, CF, follicular atresia, parasitic hepatitis and microsporidiosis. This is the first comparison of biomarkers of health in post-spawning and spawning Baltic cod. Future studies need to examine the relationships of biomarkers to levels of pollutants in the environment and in tissues of cod. Title: A Follow-up Study of Selected Biomarkers of Health in Cod Gadus Morhua L. Collected from the Southern Baltic off the Polish Coast Author: Borucinska, Joanna D., Morka, Dorota, Grabowski, Zbigniew, Smith, H. Year: 2017 Selected biomarkers of health were examined in 50 post-spawning cod Gadus morhua collected in November 2015 from the southern Baltic. The biomarkers included condition factor (CF), macroscopic lesions, histopathology of spleen, liver and gonads, and morphometry of follicular atresia and hepatic and splenic melanomacrophage cells (MMC). All fish appeared in good body condition. One fish had a dermal ulcer, and in seven, macroscopic nematodes were noted within body cavity. Microscopic lesions in the liver included biliary myxozoanosis, microsporidial and necrocentric granulomas, parasitic hepatitis, multifocal necrosis, foci of cellular alterations, spongiosis, peliosis and cytoplasmic fibrillar inclusions. The spleen and gonads had microsporidial and/or necrocentric granulomas. Some of the biomarkers showed differences as compared to spawning cod collected in May from the same location in 2012, most importantly values an order of magnitude lower for splenic MMC in post-spawning fish. In post-spawning fish, there were statistically significant correlations between MMC, CF, follicular atresia, parasitic hepatitis and microsporidiosis. This is the first comparison of biomarkers of health in post-spawning and spawning Baltic cod. Future studies need to examine the relationships of biomarkers to levels of pollutants in the environment and in tissues of cod. Close

• 47. [Article] Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries

  The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, ...

  Citation × Citation Citation Abstract Copy Title: Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries Author: Yildirimer, Christina Carrell Year: 2017 The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess microbial community diversity. The Cascade Mountains serve as an allopatric border between two distinct clades of steelhead that show significant differences in genomic and mitochondrial diversity. We identified differences in core microbiota of hatchery-reared fish that correlate with this divergent phylogeographic distribution. Steelhead sampled from hatcheries east of the Cascades had overall greater core gut microbiota diversity. These differences were found despite similarities in diet and rearing conditions. In addition to taxonomic variation across the geographic divide, we identified significant differences in metabolic pathways using PICRUSt gene prediction software. Our analysis revealed significant enrichment of genes associated with lipid metabolism in the gut microbiome of western fish. 8 of 19 individual lipid metabolism pathways were more prominent in western populations. Lipids are a vital nutritional component for teleost species involved in migration and subsequent return for spawning in natal environments. We hypothesize that the observed differences in lipid metabolism across this phylogenetic divide results from an increased ability of eastern Cascade (O. m. gairdneri) fish to utilize lipids taken in via the diet. This increased absorption and utilization would make lipids less available for the intestinal microbiota of the eastern fish, as evidenced by the lower abundance of lipid metabolism genes in the east. Our research utilizes information from the microbiome to understand the phenotypic implications occurring in segregated populations of hatchery-reared steelhead, further confirming elements of coevolution between an organism and its internal environment. Title: Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries Author: Yildirimer, Christina Carrell Year: 2017 The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess microbial community diversity. The Cascade Mountains serve as an allopatric border between two distinct clades of steelhead that show significant differences in genomic and mitochondrial diversity. We identified differences in core microbiota of hatchery-reared fish that correlate with this divergent phylogeographic distribution. Steelhead sampled from hatcheries east of the Cascades had overall greater core gut microbiota diversity. These differences were found despite similarities in diet and rearing conditions. In addition to taxonomic variation across the geographic divide, we identified significant differences in metabolic pathways using PICRUSt gene prediction software. Our analysis revealed significant enrichment of genes associated with lipid metabolism in the gut microbiome of western fish. 8 of 19 individual lipid metabolism pathways were more prominent in western populations. Lipids are a vital nutritional component for teleost species involved in migration and subsequent return for spawning in natal environments. We hypothesize that the observed differences in lipid metabolism across this phylogenetic divide results from an increased ability of eastern Cascade (O. m. gairdneri) fish to utilize lipids taken in via the diet. This increased absorption and utilization would make lipids less available for the intestinal microbiota of the eastern fish, as evidenced by the lower abundance of lipid metabolism genes in the east. Our research utilizes information from the microbiome to understand the phenotypic implications occurring in segregated populations of hatchery-reared steelhead, further confirming elements of coevolution between an organism and its internal environment. Close

• 48. [Article] Alagnak Wild River Visitor Use Project: Alagnak Wild River Resident User Study

  This report represents a thematic summary of findings from the Alagnak Wild River Resident Users Study, the final project in a larger series of studies conducted for the National Park Service (NPS) as ...

  Citation × Citation Citation Abstract Copy Title: Alagnak Wild River Visitor Use Project: Alagnak Wild River Resident User Study Author: Deur, Douglas Year: 2008 This report represents a thematic summary of findings from the Alagnak Wild River Resident Users Study, the final project in a larger series of studies conducted for the National Park Service (NPS) as part of the Alagnak Wild River Visitor Use Project. The National Park service administers the 56 miles of designated Wild River along the Alagnak in collaboration with the Alaska Department of Fish and Game, which manages fish and wildlife populations along the river. The NPS is charged with managing the river’s natural and cultural resources, as well as preserving the river’s lands and resources for current and future generations. Alagnak River has long served as a home and resource procurement area to Native Alaskan peoples. Though these peoples have relocated to villages nearby in the region, descendents of Alagnak’s former occupants as well as their fellow residents from nearby communities have continued to seasonally occupy Alagnak’s riparian zone and to hunt, fish, gather plant materials and participate in social activities. In recent years, non-resident visitation of Alagnak Wild River has escalated, especially for recreational fishing, but also for recreational hunting, boating, rafting, and other pursuits. In some cases, these non-resident uses of the river have been reported to conflict with Native Alaskan uses of the river. In an effort to best manage the natural and cultural resources of Alagnak Wild River, as well as to judiciously balance the needs of different visiting constituencies, the National Park Service requires additional information regarding the past and present uses of Alagnak River by Native Alaskans, as well as the observations and perspectives of Native Alaskan river users on non-resident visitation and its possible impacts. Using a variety of principally qualitative data sources, the current report seeks to thematically compile information relating to these themes. This report describes the transformation of the Alagnak River corridor from center of Native Alaskan habitation to a peripheral resource territory that is still used by descendants of its original inhabitants today. Relying primarily on ethnographic data focusing on the experiences of residents from Levelock, Igiugig, King Salmon, Naknek, South Naknek, and Kokhanok, the document also outlines the use of the Alagnak River as a place of enduring importance within Native Alaskan subsistence traditions. Individual sections provide summaries of hunting, fishing, and berry gathering, as well as trapping and other economic pursuits. In addition, this document provides an overview of concerns expressed by Native Alaskans regarding the potential impacts of visitors on the river, including: crowding, motorboat use, and their effects on public safety; the displacement of resident users and the possible cultural effects of this displacement; the possible effects of increased non-resident visitation on water quality, fish and game populations; possible increased threats associated with brown bears; and impacts on lands, allotments, and plant resources. This document also provides a an overview of what some Native Alaskans perceive as the positive effects of non-resident visitation, such as employment and land lease opportunities, as well as the availability of NPS cabins for emergencies along the Alagnak River corridor. The veracity of Native Alaskans’ claims pertaining to visitors impacts is not critically explored using biophysical methodologies, but this information is organized thematically so as to aid the National Park Service in natural and cultural resource planning for the Alagnak River corridor, to identify further research needs, and to assist that agency in anticipating concerns that may emerge in future consultation with Native Alaskan communities that are historically associated with Alagnak Wild River. Title: Alagnak Wild River Visitor Use Project: Alagnak Wild River Resident User Study Author: Deur, Douglas Year: 2008 This report represents a thematic summary of findings from the Alagnak Wild River Resident Users Study, the final project in a larger series of studies conducted for the National Park Service (NPS) as part of the Alagnak Wild River Visitor Use Project. The National Park service administers the 56 miles of designated Wild River along the Alagnak in collaboration with the Alaska Department of Fish and Game, which manages fish and wildlife populations along the river. The NPS is charged with managing the river’s natural and cultural resources, as well as preserving the river’s lands and resources for current and future generations. Alagnak River has long served as a home and resource procurement area to Native Alaskan peoples. Though these peoples have relocated to villages nearby in the region, descendents of Alagnak’s former occupants as well as their fellow residents from nearby communities have continued to seasonally occupy Alagnak’s riparian zone and to hunt, fish, gather plant materials and participate in social activities. In recent years, non-resident visitation of Alagnak Wild River has escalated, especially for recreational fishing, but also for recreational hunting, boating, rafting, and other pursuits. In some cases, these non-resident uses of the river have been reported to conflict with Native Alaskan uses of the river. In an effort to best manage the natural and cultural resources of Alagnak Wild River, as well as to judiciously balance the needs of different visiting constituencies, the National Park Service requires additional information regarding the past and present uses of Alagnak River by Native Alaskans, as well as the observations and perspectives of Native Alaskan river users on non-resident visitation and its possible impacts. Using a variety of principally qualitative data sources, the current report seeks to thematically compile information relating to these themes. This report describes the transformation of the Alagnak River corridor from center of Native Alaskan habitation to a peripheral resource territory that is still used by descendants of its original inhabitants today. Relying primarily on ethnographic data focusing on the experiences of residents from Levelock, Igiugig, King Salmon, Naknek, South Naknek, and Kokhanok, the document also outlines the use of the Alagnak River as a place of enduring importance within Native Alaskan subsistence traditions. Individual sections provide summaries of hunting, fishing, and berry gathering, as well as trapping and other economic pursuits. In addition, this document provides an overview of concerns expressed by Native Alaskans regarding the potential impacts of visitors on the river, including: crowding, motorboat use, and their effects on public safety; the displacement of resident users and the possible cultural effects of this displacement; the possible effects of increased non-resident visitation on water quality, fish and game populations; possible increased threats associated with brown bears; and impacts on lands, allotments, and plant resources. This document also provides a an overview of what some Native Alaskans perceive as the positive effects of non-resident visitation, such as employment and land lease opportunities, as well as the availability of NPS cabins for emergencies along the Alagnak River corridor. The veracity of Native Alaskans’ claims pertaining to visitors impacts is not critically explored using biophysical methodologies, but this information is organized thematically so as to aid the National Park Service in natural and cultural resource planning for the Alagnak River corridor, to identify further research needs, and to assist that agency in anticipating concerns that may emerge in future consultation with Native Alaskan communities that are historically associated with Alagnak Wild River. Close

• 49. [Article] Social-Ecological Dynamics of Coral Reef Resource Use and Management

  This dissertation investigates social and ecological factors that facilitate effective management of coral reefs as social-ecological systems. Meta-analytical and field-based methods were employed to examine ...

  Citation × Citation Citation Abstract Copy Title: Social-Ecological Dynamics of Coral Reef Resource Use and Management Author: Freed, Sarah J. Year: 2013 This dissertation investigates social and ecological factors that facilitate effective management of coral reefs as social-ecological systems. Meta-analytical and field-based methods were employed to examine current management challenges and identify strategies that improve management effectiveness and coral reef health. A meta-analysis was used to evaluate biological indicators of reef health in relation to the types of fishing regulations in place (no-take areas, gear restriction areas, and periodic closures) and the actor groups (community-based, co-management, state, private) involved in management efforts for coral reef fisheries throughout the world. Other than enhancement of fish biomass within no-take areas that was significantly greater than in gear restriction areas, most biological indicators benefitted similarly from management techniques of no-take areas and gear restriction areas. Community-based and co-management were the best performing management arrangements for some biological outcomes but require further case studies to verify findings. Investigation of management effects by region indicated that previously degraded reefs received fewer benefits from management implementation than did relatively healthier reefs. For field investigations, the Comoros islands in the Western Indian Ocean served as a model for tropical coral reefs with challenging socioeconomic contexts, high biodiversity, and high vulnerability to coral reef degradation. Empirical study at 21 sites was used to identify the relative effects of natural and anthropogenic threats to coral reefs of the Comoros. Most previous studies of reef health focus on primarily natural factors or a single anthropogenic threat. This study examined suites of natural factors and human activities to identify the relative importance of each on reef health. Human activities including fishing, sand extraction, and beachfront housing and development were the best predictors of reef health status. Most notably, human population and fishing predicted fish richness, abundance, and biomass with seasonal variation in the effects, while site orientation strongly predicted benthic cover. Field studies in the Comoros were also used to investigate the roles of community and state actors in co-management and compare effectiveness of comanagement across sites with varying levels of actor participation. Effective management was found to occur with community or `meta-community' (in this case, a Marine Protected Area in which the efforts of several communities were organized) participation in governance and support of state or external agents, while resilient management that overcame considerable challenges was found to occur only with strong community participation and leadership in governance. External agents were found to contribute to development of meta-community governance structure and initiation of community participation through education and capacity building. The findings from these studies reveal that coral reef management can be improved through context appropriate regulations that address detrimental human activities and through wide acceptance and participation in governance with cooperation among states, communities, and external agents. Title: Social-Ecological Dynamics of Coral Reef Resource Use and Management Author: Freed, Sarah J. Year: 2013 This dissertation investigates social and ecological factors that facilitate effective management of coral reefs as social-ecological systems. Meta-analytical and field-based methods were employed to examine current management challenges and identify strategies that improve management effectiveness and coral reef health. A meta-analysis was used to evaluate biological indicators of reef health in relation to the types of fishing regulations in place (no-take areas, gear restriction areas, and periodic closures) and the actor groups (community-based, co-management, state, private) involved in management efforts for coral reef fisheries throughout the world. Other than enhancement of fish biomass within no-take areas that was significantly greater than in gear restriction areas, most biological indicators benefitted similarly from management techniques of no-take areas and gear restriction areas. Community-based and co-management were the best performing management arrangements for some biological outcomes but require further case studies to verify findings. Investigation of management effects by region indicated that previously degraded reefs received fewer benefits from management implementation than did relatively healthier reefs. For field investigations, the Comoros islands in the Western Indian Ocean served as a model for tropical coral reefs with challenging socioeconomic contexts, high biodiversity, and high vulnerability to coral reef degradation. Empirical study at 21 sites was used to identify the relative effects of natural and anthropogenic threats to coral reefs of the Comoros. Most previous studies of reef health focus on primarily natural factors or a single anthropogenic threat. This study examined suites of natural factors and human activities to identify the relative importance of each on reef health. Human activities including fishing, sand extraction, and beachfront housing and development were the best predictors of reef health status. Most notably, human population and fishing predicted fish richness, abundance, and biomass with seasonal variation in the effects, while site orientation strongly predicted benthic cover. Field studies in the Comoros were also used to investigate the roles of community and state actors in co-management and compare effectiveness of comanagement across sites with varying levels of actor participation. Effective management was found to occur with community or `meta-community' (in this case, a Marine Protected Area in which the efforts of several communities were organized) participation in governance and support of state or external agents, while resilient management that overcame considerable challenges was found to occur only with strong community participation and leadership in governance. External agents were found to contribute to development of meta-community governance structure and initiation of community participation through education and capacity building. The findings from these studies reveal that coral reef management can be improved through context appropriate regulations that address detrimental human activities and through wide acceptance and participation in governance with cooperation among states, communities, and external agents. Close

• 50. [Article] Oregon's Fish and Wildlife in a Changing Climate

  Chapter 7 in: The Oregon Climate Change Assessment Report Oregon's fish and wildlife include animals on land, fish and other species in rivers and lakes, and various kinds of sea life in estuaries and ...

  Citation × Citation Citation Abstract Copy Title: Oregon's Fish and Wildlife in a Changing Climate Author: Hixon, Mark A., Gregory, Stanley V., Robinson, W. Douglas, Baker, C. Scott, Batchelder, Harold P., Epps, Clinton, Garcia, Tiffany S., Haig, Susan M., Letelier, Ricardo M., Lytle, David A., Menge, Bruce A., Miller, Jeffery C., Noakes, David L.G., Peterson, William T., Rice, James M., Rumrill, Steven S., Schreck, Carl B., Suryan, Robert M., Sytsma, Mark D., White, Angelicque E. Year: 2010 Chapter 7 in: The Oregon Climate Change Assessment Report Oregon's fish and wildlife include animals on land, fish and other species in rivers and lakes, and various kinds of sea life in estuaries and coastal ocean. Oregon is one of the most ecologically diverse states in the country. The state’s robust biodiversity, some of which is already threatened or endangered -- inhabits complex and dynamic ecosystems that we have only begun to understand, let alone examine in terms of climate change.It is clear that the abundance and distribution of species are shifting already and will shift more rapidly as habitats on land, in freshwater, and in the sea are altered due to increasing temperatures and related environmental changes. It remains to be seen if past changes are all tied to global climate change or if they are a result of some other variability, but they represent a proxy for how species may shift in a warmer climate. Among the observed species changes: Insects are moving in from the south of Oregon, frogs are reproducing earlier in the year and land birds are shifting their distributions northward and migrating earlier. Freshwater fish are losing their cool-water habitats. In the marine environment, algal blooms have increased (figure 11) and the highly predatory Humboldt squid have shifted their distribution from subtropical and tropical regions, making an appearance off the coast of Oregon in the last few years. In a warmer climate, plant and animal species may have to shift upward or northward on land or deeper at sea for survival. Rare or endangered species may become less abundant or extinct; insect pests, invasive species and harmful algal blooms may become more abundant. Declines in the abundance of species may be caused directly by physiological stress related to changes in temperature, water availability, and other environmental shifts, and/or indirectly by habitat degradation and negative interactions with species that are benefited by climate change (diseases, parasites, predators, and competitors). Understanding the responses of Oregon’s fish and wildlife to climate change will require a better understanding of smaller organisms and insects and ocean species. Knowledge of ecological interactions will be crucial for understanding the related effects of climate change (increased predation or competition, for example). Management and natural resource polices that protect intact ecosystems are a tool for adaptation; native species can live and migrate to these safe refugia. Title: Oregon's Fish and Wildlife in a Changing Climate Author: Hixon, Mark A., Gregory, Stanley V., Robinson, W. Douglas, Baker, C. Scott, Batchelder, Harold P., Epps, Clinton, Garcia, Tiffany S., Haig, Susan M., Letelier, Ricardo M., Lytle, David A., Menge, Bruce A., Miller, Jeffery C., Noakes, David L.G., Peterson, William T., Rice, James M., Rumrill, Steven S., Schreck, Carl B., Suryan, Robert M., Sytsma, Mark D., White, Angelicque E. Year: 2010 Chapter 7 in: The Oregon Climate Change Assessment Report Oregon's fish and wildlife include animals on land, fish and other species in rivers and lakes, and various kinds of sea life in estuaries and coastal ocean. Oregon is one of the most ecologically diverse states in the country. The state’s robust biodiversity, some of which is already threatened or endangered -- inhabits complex and dynamic ecosystems that we have only begun to understand, let alone examine in terms of climate change.It is clear that the abundance and distribution of species are shifting already and will shift more rapidly as habitats on land, in freshwater, and in the sea are altered due to increasing temperatures and related environmental changes. It remains to be seen if past changes are all tied to global climate change or if they are a result of some other variability, but they represent a proxy for how species may shift in a warmer climate. Among the observed species changes: Insects are moving in from the south of Oregon, frogs are reproducing earlier in the year and land birds are shifting their distributions northward and migrating earlier. Freshwater fish are losing their cool-water habitats. In the marine environment, algal blooms have increased (figure 11) and the highly predatory Humboldt squid have shifted their distribution from subtropical and tropical regions, making an appearance off the coast of Oregon in the last few years. In a warmer climate, plant and animal species may have to shift upward or northward on land or deeper at sea for survival. Rare or endangered species may become less abundant or extinct; insect pests, invasive species and harmful algal blooms may become more abundant. Declines in the abundance of species may be caused directly by physiological stress related to changes in temperature, water availability, and other environmental shifts, and/or indirectly by habitat degradation and negative interactions with species that are benefited by climate change (diseases, parasites, predators, and competitors). Understanding the responses of Oregon’s fish and wildlife to climate change will require a better understanding of smaller organisms and insects and ocean species. Knowledge of ecological interactions will be crucial for understanding the related effects of climate change (increased predation or competition, for example). Management and natural resource polices that protect intact ecosystems are a tool for adaptation; native species can live and migrate to these safe refugia. Close

• 51. [Article] "As Long as the Mighty Columbia River Flows": The Leadership and Legacy of Wilson Charley, a Yakama Indian Fisherman

  On March 10, 1957, the United States Army Corps of Engineers completed The Dalles Dam and inundated Celilo Falls, the oldest continuously inhabited site in North America and a cultural and economic hub ...

  Citation × Citation Citation Abstract Copy Title: "As Long as the Mighty Columbia River Flows": The Leadership and Legacy of Wilson Charley, a Yakama Indian Fisherman Author: Hedberg, David-Paul Brewster Year: 2017 On March 10, 1957, the United States Army Corps of Engineers completed The Dalles Dam and inundated Celilo Falls, the oldest continuously inhabited site in North America and a cultural and economic hub for Indigenous people. In the negotiation of treaties between the United States, nearly one hundred years earlier, Indigenous leaders reserved access to Columbia River fishing sites as they ceded territory and retained smaller reservations. In the years before the dam's completion, leaders, many of who were the descendants of earlier treaty signatories, attempted to stop the dam and protect both fishing sites from the encroachment of state and federal regulations and archaeological sites from destruction. This study traces the work of Wilson Charley, a Native fisherman, a member of the Yakama Nation's Tribal Council, and great-grandson of one of the 1855 treaty signatories. More broadly, this study places Indigenous actors on a twentieth-century Columbia River while demonstrating that they played active roles in the protest and management of areas affected by The Dalles Dam. Using previously untapped archival sources--a substantial cache of letters--my analysis illustrates that Charley articulated multiple strategies to fight The Dalles Dam and regulations to curtail Native's treaty fishing rights. Aiming to protect the 1855 treaty and stop The Dalles Dam, Charley created Native-centered regulatory agencies. He worked directly with politicians and supported political candidates, like Richard Neuberger, that favored Native concerns. He attempted to build partnerships with archaeologists and landscape preservationists concerned about losing the area's rich cultural sites. Even after the dam's completion, he conceptualized multiple tribal economic development plans that would allow for Natives' cultural and economic survival. Given the national rise of technological optimism and the willingness for the federal government to terminate its relationship with federally recognized tribes, Charley realized that taking the 1855 treaty to court was too risky for the political climate of the 1950s. Instead, he framed his strategies in the language of twentieth-century conservation, specifically to garner support from a national audience of non-natives interested in protecting landscapes from industrial development. While many of these non-native partners ultimately failed him, his strategies are noteworthy for three reasons. First, he cast the fight to uphold Native treaty rights in terms that were relevant to non-natives, demonstrating his complex understanding of the times in which he lived. Second, his strategies continued an ongoing struggle for Natives to fish at their treaty-protected sites, thereby documenting an overlooked period between the fishing rights cases of the turn of the twentieth century and the 1960s and 1970s. Charley left a lasting legacy that scholars have not recognized because many of his visionary ideas came to fruition decades later. Finally, my analysis of Charley's letters also documents personal details that afford readers the unique perspective of one Indigenous person navigated through a tumultuous period in the Pacific Northwest and Native American history. Title: "As Long as the Mighty Columbia River Flows": The Leadership and Legacy of Wilson Charley, a Yakama Indian Fisherman Author: Hedberg, David-Paul Brewster Year: 2017 On March 10, 1957, the United States Army Corps of Engineers completed The Dalles Dam and inundated Celilo Falls, the oldest continuously inhabited site in North America and a cultural and economic hub for Indigenous people. In the negotiation of treaties between the United States, nearly one hundred years earlier, Indigenous leaders reserved access to Columbia River fishing sites as they ceded territory and retained smaller reservations. In the years before the dam's completion, leaders, many of who were the descendants of earlier treaty signatories, attempted to stop the dam and protect both fishing sites from the encroachment of state and federal regulations and archaeological sites from destruction. This study traces the work of Wilson Charley, a Native fisherman, a member of the Yakama Nation's Tribal Council, and great-grandson of one of the 1855 treaty signatories. More broadly, this study places Indigenous actors on a twentieth-century Columbia River while demonstrating that they played active roles in the protest and management of areas affected by The Dalles Dam. Using previously untapped archival sources--a substantial cache of letters--my analysis illustrates that Charley articulated multiple strategies to fight The Dalles Dam and regulations to curtail Native's treaty fishing rights. Aiming to protect the 1855 treaty and stop The Dalles Dam, Charley created Native-centered regulatory agencies. He worked directly with politicians and supported political candidates, like Richard Neuberger, that favored Native concerns. He attempted to build partnerships with archaeologists and landscape preservationists concerned about losing the area's rich cultural sites. Even after the dam's completion, he conceptualized multiple tribal economic development plans that would allow for Natives' cultural and economic survival. Given the national rise of technological optimism and the willingness for the federal government to terminate its relationship with federally recognized tribes, Charley realized that taking the 1855 treaty to court was too risky for the political climate of the 1950s. Instead, he framed his strategies in the language of twentieth-century conservation, specifically to garner support from a national audience of non-natives interested in protecting landscapes from industrial development. While many of these non-native partners ultimately failed him, his strategies are noteworthy for three reasons. First, he cast the fight to uphold Native treaty rights in terms that were relevant to non-natives, demonstrating his complex understanding of the times in which he lived. Second, his strategies continued an ongoing struggle for Natives to fish at their treaty-protected sites, thereby documenting an overlooked period between the fishing rights cases of the turn of the twentieth century and the 1960s and 1970s. Charley left a lasting legacy that scholars have not recognized because many of his visionary ideas came to fruition decades later. Finally, my analysis of Charley's letters also documents personal details that afford readers the unique perspective of one Indigenous person navigated through a tumultuous period in the Pacific Northwest and Native American history. Close

• 52. [Article] Administrative Design for Yakima-Klickitat Production Project: Final Report

  This report provides the administrative design to implement the Yakima/Klickitat Production Project. This project is a scientifically designed salmon fishery restoration project funded by the Bonneville ...

  Citation × Citation Citation Abstract Copy Title: Administrative Design for Yakima-Klickitat Production Project: Final Report Author: Churchill, Jack, Shissler, Lee, Edner, Sheldon, Smith, Randy Year: 1990 This report provides the administrative design to implement the Yakima/Klickitat Production Project. This project is a scientifically designed salmon fishery restoration project funded by the Bonneville Power Administration in compliance with the .fishery policies established by the Northwest Power Planning Council under the authority of the Northwest Power Planning Act. This project breaks new ground in the field of fishery management. It is the first full scale application of supplementation technology directed toward maintaining and rebuilding native fish stocks and sub stocks with hatchery rearing methods. The work of the organization is an inherently more complex production function than traditional fish hatchery operations. This is in part because the project requires a high level of continuing quality control. It is also due in part because the fisheries management takes place over an extended geographical space of the watershed. The pre-design work for this project has been underway since 1987 by an ad hoc planning group composed of representative of the Yakima Indian Nation, the Washington Department of Fisheries and the Washington Department of Wildlife, and private consultants under funding of the Bonneville Power Administration. The project experimental design has been developed by the Experimental Design Work Group. The Bonneville Power Administration is contracting for design and construction of the fish rearing facilities. The research challenge was to design an organization to .implement the adaptive management concept of biological systems management. The management of complex biological systems such as salmon fish runs is character:ized by a high degree of uncertainty. Management for uncertain outcomes requires an organizational process that will induce a continuing learning atmosphere. Over time, most bureaucratic organizations suffer from inertia and are not conducive to a learning environment. Research methods involved the review of literature and related administrative experience, an interview process, a modified Delphi questionnaire, a series of group dynamic exercises, and observation of the work teams during the last six months of the planing process. The results of our research suggest that a new non-profit corporation be formed to implement the program under the direction of the three primary fish management basin agencies. The corporation should have flexibility and the organization will be phased in during the five year planning and construction cycle. A primary result of our research is the conclusion that the team management concept be the dominant organizational unit for both management of field operations and for management of scientific design and evaluation. Title: Administrative Design for Yakima-Klickitat Production Project: Final Report Author: Churchill, Jack, Shissler, Lee, Edner, Sheldon, Smith, Randy Year: 1990 This report provides the administrative design to implement the Yakima/Klickitat Production Project. This project is a scientifically designed salmon fishery restoration project funded by the Bonneville Power Administration in compliance with the .fishery policies established by the Northwest Power Planning Council under the authority of the Northwest Power Planning Act. This project breaks new ground in the field of fishery management. It is the first full scale application of supplementation technology directed toward maintaining and rebuilding native fish stocks and sub stocks with hatchery rearing methods. The work of the organization is an inherently more complex production function than traditional fish hatchery operations. This is in part because the project requires a high level of continuing quality control. It is also due in part because the fisheries management takes place over an extended geographical space of the watershed. The pre-design work for this project has been underway since 1987 by an ad hoc planning group composed of representative of the Yakima Indian Nation, the Washington Department of Fisheries and the Washington Department of Wildlife, and private consultants under funding of the Bonneville Power Administration. The project experimental design has been developed by the Experimental Design Work Group. The Bonneville Power Administration is contracting for design and construction of the fish rearing facilities. The research challenge was to design an organization to .implement the adaptive management concept of biological systems management. The management of complex biological systems such as salmon fish runs is character:ized by a high degree of uncertainty. Management for uncertain outcomes requires an organizational process that will induce a continuing learning atmosphere. Over time, most bureaucratic organizations suffer from inertia and are not conducive to a learning environment. Research methods involved the review of literature and related administrative experience, an interview process, a modified Delphi questionnaire, a series of group dynamic exercises, and observation of the work teams during the last six months of the planing process. The results of our research suggest that a new non-profit corporation be formed to implement the program under the direction of the three primary fish management basin agencies. The corporation should have flexibility and the organization will be phased in during the five year planning and construction cycle. A primary result of our research is the conclusion that the team management concept be the dominant organizational unit for both management of field operations and for management of scientific design and evaluation. Close

• 53. [Article] Developing and Calibrating the Hydrodynamic and Water Quality Model CE-QUAL-W2 for Banks Lake Washington

  Located in central Washington State, Banks Lake serves as an irrigation storage reservoir for the Columbia Basin Irrigation Project and is home to a diverse fisheries population. The current hydrologic ...

  Citation × Citation Citation Abstract Copy Title: Developing and Calibrating the Hydrodynamic and Water Quality Model CE-QUAL-W2 for Banks Lake Washington Author: McCulloch, Andrew John Year: 2011 Located in central Washington State, Banks Lake serves as an irrigation storage reservoir for the Columbia Basin Irrigation Project and is home to a diverse fisheries population. The current hydrologic management strategies used for Banks Lake have been chosen to serve two purposes: to adequately store and provide irrigation water for the Columbia Basin Irrigation Project and to maintain a healthy aquatic environment suitable for the growth and habitation of local flora and fauna. Increased needs for irrigation water within arid central Washington poses additional challenges to reservoir managers so that irrigation needs are met without damaging the present aquatic environment within Banks Lake. Future plans by the Washington Department of Ecology to use Banks Lake storage to replenish ground water reserves of the Odessa Subarea aquifer have required an investigation into how increased seasonal drawdown may affect fish growth, fish habitat and overall limnology of Banks Lake. The goal of this project is to produce a hydrodynamic and water quality model of Banks Lake that can predict the impacts of management strategies on the lake's water quality and the linkage of lake management to fish habitat. Title: Developing and Calibrating the Hydrodynamic and Water Quality Model CE-QUAL-W2 for Banks Lake Washington Author: McCulloch, Andrew John Year: 2011 Located in central Washington State, Banks Lake serves as an irrigation storage reservoir for the Columbia Basin Irrigation Project and is home to a diverse fisheries population. The current hydrologic management strategies used for Banks Lake have been chosen to serve two purposes: to adequately store and provide irrigation water for the Columbia Basin Irrigation Project and to maintain a healthy aquatic environment suitable for the growth and habitation of local flora and fauna. Increased needs for irrigation water within arid central Washington poses additional challenges to reservoir managers so that irrigation needs are met without damaging the present aquatic environment within Banks Lake. Future plans by the Washington Department of Ecology to use Banks Lake storage to replenish ground water reserves of the Odessa Subarea aquifer have required an investigation into how increased seasonal drawdown may affect fish growth, fish habitat and overall limnology of Banks Lake. The goal of this project is to produce a hydrodynamic and water quality model of Banks Lake that can predict the impacts of management strategies on the lake's water quality and the linkage of lake management to fish habitat. Close

• 54. [Article] Hydrodynamic and Water Quality Modeling of the Chehalis River in Washington

  The Chehalis River Basin is located in the southwest region of Washington and is over 125 miles long flowing through agricultural, residential, industrial, and forest land. Four major rivers, many smaller ...

  Citation × Citation Citation Abstract Copy Title: Hydrodynamic and Water Quality Modeling of the Chehalis River in Washington Author: Van Glubt, Sarah, Wells, Scott A., Berger, Chris J. Year: 2017 The Chehalis River Basin is located in the southwest region of Washington and is over 125 miles long flowing through agricultural, residential, industrial, and forest land. Four major rivers, many smaller creeks, five wastewater treatment plants, and groundwater discharge to the Chehalis River. Flooding is a major problem in the relatively flat areas surrounding the cities of Chehalis and Centralia. As a result, construction of a flood-control dam in the upper basin has been proposed. One major concern of constructing a dam is the potentially severe impacts to fish health and habitat. The Chehalis River has routinely violated water quality standards for primarily temperature and dissolved oxygen. CE-QUAL-W2, a two-dimensional (longitudinal and vertical) hydrodynamic and water quality model, was used to simulate the Chehalis River, including free flowing river stretches and stratified (in summer) lake-like stretches. The goals of this research were to assess the flood retention structure’s impacts to water quality, as well as river responses to potential climate change scenarios. In order to use the model to achieve these goals, calibration to field data for flow, temperature, and water quality constituents was performed for the years 2013 and 2014. Once calibration was complete, model scenarios for future climate conditions and dam operating regimes were conducted. Future conditions showed predictions of warmer water temperatures and slight changes to water quality conditions on the river. As fish in the area prefer cooler water temperatures, this could pose a threat to fish health and habitat. Flood retention structures with the purpose of flood retention only (only operating during times of flooding) gave model predictions for daily maximum temperature higher than structures that employed flood retention and flow augmentation (operating during all times of the year). This suggested the management of flow passage or retention by the dam is important for water quality on the river. Title: Hydrodynamic and Water Quality Modeling of the Chehalis River in Washington Author: Van Glubt, Sarah, Wells, Scott A., Berger, Chris J. Year: 2017 The Chehalis River Basin is located in the southwest region of Washington and is over 125 miles long flowing through agricultural, residential, industrial, and forest land. Four major rivers, many smaller creeks, five wastewater treatment plants, and groundwater discharge to the Chehalis River. Flooding is a major problem in the relatively flat areas surrounding the cities of Chehalis and Centralia. As a result, construction of a flood-control dam in the upper basin has been proposed. One major concern of constructing a dam is the potentially severe impacts to fish health and habitat. The Chehalis River has routinely violated water quality standards for primarily temperature and dissolved oxygen. CE-QUAL-W2, a two-dimensional (longitudinal and vertical) hydrodynamic and water quality model, was used to simulate the Chehalis River, including free flowing river stretches and stratified (in summer) lake-like stretches. The goals of this research were to assess the flood retention structure’s impacts to water quality, as well as river responses to potential climate change scenarios. In order to use the model to achieve these goals, calibration to field data for flow, temperature, and water quality constituents was performed for the years 2013 and 2014. Once calibration was complete, model scenarios for future climate conditions and dam operating regimes were conducted. Future conditions showed predictions of warmer water temperatures and slight changes to water quality conditions on the river. As fish in the area prefer cooler water temperatures, this could pose a threat to fish health and habitat. Flood retention structures with the purpose of flood retention only (only operating during times of flooding) gave model predictions for daily maximum temperature higher than structures that employed flood retention and flow augmentation (operating during all times of the year). This suggested the management of flow passage or retention by the dam is important for water quality on the river. Close

• 55. [Article] Archaeological Evidence for Resilience of Pacific Northwest Salmon Populations and the Socioecological System Over the Last ~7,500 Years

  Archaeological data on the long history of interaction between indigenous people and salmon have rarely been applied to conservation management. When joined with ethnohistoric records, archaeology provides ...

  Citation × Citation Citation Abstract Copy Title: Archaeological Evidence for Resilience of Pacific Northwest Salmon Populations and the Socioecological System Over the Last ~7,500 Years Author: Campbell, Sarah K., Butler, Virginia L. Year: 2010 Archaeological data on the long history of interaction between indigenous people and salmon have rarely been applied to conservation management. When joined with ethnohistoric records, archaeology provides an alternative conceptual view of the potential for sustainable harvests and can suggest possible social mechanisms for managing human behavior. Review of the ~7,500-year-long fish bone record from two subregions of the Pacific Northwest shows remarkable stability in salmon use. As major changes in the ecological and social system occurred over this lengthy period, persistence in the fishery is not due simply to a lack of perturbation, but rather indicates resilience in the ecological--human system. Of several factors possibly contributing to resilience, low human population size and harvesting pressure, habitat enhancement, and suppression of competing predators do not appear to be of major importance. Flexible resource use, including human use of a range of local resources, many of which are linked in a food web with salmon, likely contributed to resilience. Most important were the beliefs and social institutions (including ownership, regulation, rituals, and monitoring) that placed restraints on salmon use as a common pool resource. In contrast, only a small fraction of our modern society relies economically on or has direct interaction with the fish, which limits our concern and willingness to fundamentally change behaviors that contribute to habitat degradation and loss, the main challenges facing salmon populations today. Salmon recovery efforts may benefit substantially from investing more resources into establishing links between community groups and actual fish populations, which would create a sense of proprietorship, one of the keys to resilience in the indigenous salmon fishery. Title: Archaeological Evidence for Resilience of Pacific Northwest Salmon Populations and the Socioecological System Over the Last ~7,500 Years Author: Campbell, Sarah K., Butler, Virginia L. Year: 2010 Archaeological data on the long history of interaction between indigenous people and salmon have rarely been applied to conservation management. When joined with ethnohistoric records, archaeology provides an alternative conceptual view of the potential for sustainable harvests and can suggest possible social mechanisms for managing human behavior. Review of the ~7,500-year-long fish bone record from two subregions of the Pacific Northwest shows remarkable stability in salmon use. As major changes in the ecological and social system occurred over this lengthy period, persistence in the fishery is not due simply to a lack of perturbation, but rather indicates resilience in the ecological--human system. Of several factors possibly contributing to resilience, low human population size and harvesting pressure, habitat enhancement, and suppression of competing predators do not appear to be of major importance. Flexible resource use, including human use of a range of local resources, many of which are linked in a food web with salmon, likely contributed to resilience. Most important were the beliefs and social institutions (including ownership, regulation, rituals, and monitoring) that placed restraints on salmon use as a common pool resource. In contrast, only a small fraction of our modern society relies economically on or has direct interaction with the fish, which limits our concern and willingness to fundamentally change behaviors that contribute to habitat degradation and loss, the main challenges facing salmon populations today. Salmon recovery efforts may benefit substantially from investing more resources into establishing links between community groups and actual fish populations, which would create a sense of proprietorship, one of the keys to resilience in the indigenous salmon fishery. Close

• 56. [Article] High Mobility Group Protein 1 (HMGB1) And Its Role As A Global Transcription Regulator In Response To Temperature Fluctuations In The Annual Killifish Austrofundulus limnaeus

  As a study organism, annual killifish (Austrofundulus limnaeus) provide a well suited study system for examining the effects of environmental temperature fluctuations at the cellular level. A. limnaeus ...

  Citation × Citation Citation Abstract Copy Title: High Mobility Group Protein 1 (HMGB1) And Its Role As A Global Transcription Regulator In Response To Temperature Fluctuations In The Annual Killifish Austrofundulus limnaeus Author: Alla, Victoria Martin Year: 2011 As a study organism, annual killifish (Austrofundulus limnaeus) provide a well suited study system for examining the effects of environmental temperature fluctuations at the cellular level. A. limnaeus persist in the harsh high desert climate of the Maracaibo Basin, Venezuela where they live in small, ephemeral freshwater pools. Temperatures in these waters can vary as much as 20 degrees C daily and reach maximums of over 40 degrees C due to the semi-arid climate. Previous cDNA microarray studies on killifish revealed the mRNA pattern for High Mobility Group Protein 1 (HMGB1) to be strongly affected by temperature perturbations. Specifically, peaks in hmgb1 transcript abundance were negatively correlated with temperature during temperature cycling, and experienced over a 10 fold difference in expression in response to the temperature cycle. Using the same temperature cycling experimental setup, this study's aim was three-fold: (1) to characterize the total amount of HMGB1 protein in adult male killifish livers, (2) to describe the subcellular localization of the HMGB1 protein in adult male killifish livers and (3) to sequence the 5' upstream region of the hmgb1 gene to identify possible stress responsive elements. We detected no significant difference in total HMGB1 protein levels as a consequence of temperature cycling. The data for subcellular localization of HGMB1 protein do not support a strong change in subcellular localization of the protein in response to temperature cycling; most of the HMGB1 protein is found in the cytoplasmic compartment in liver tissue. Although overall patterns of subcellular localization did not change significantly, we found a significant difference between nuclear HMGB1 protein levels in temperature cycled fish versus control (constant temperature) fish. This could suggest a muting of the natural translocation of HMGB1 into the nucleus observed in control fish at around 9:00 at night. Finally, the upstream region of the hgmb1 gene does reveal a number of putative stress responsive transcription factor binding sites. Title: High Mobility Group Protein 1 (HMGB1) And Its Role As A Global Transcription Regulator In Response To Temperature Fluctuations In The Annual Killifish Austrofundulus limnaeus Author: Alla, Victoria Martin Year: 2011 As a study organism, annual killifish (Austrofundulus limnaeus) provide a well suited study system for examining the effects of environmental temperature fluctuations at the cellular level. A. limnaeus persist in the harsh high desert climate of the Maracaibo Basin, Venezuela where they live in small, ephemeral freshwater pools. Temperatures in these waters can vary as much as 20 degrees C daily and reach maximums of over 40 degrees C due to the semi-arid climate. Previous cDNA microarray studies on killifish revealed the mRNA pattern for High Mobility Group Protein 1 (HMGB1) to be strongly affected by temperature perturbations. Specifically, peaks in hmgb1 transcript abundance were negatively correlated with temperature during temperature cycling, and experienced over a 10 fold difference in expression in response to the temperature cycle. Using the same temperature cycling experimental setup, this study's aim was three-fold: (1) to characterize the total amount of HMGB1 protein in adult male killifish livers, (2) to describe the subcellular localization of the HMGB1 protein in adult male killifish livers and (3) to sequence the 5' upstream region of the hmgb1 gene to identify possible stress responsive elements. We detected no significant difference in total HMGB1 protein levels as a consequence of temperature cycling. The data for subcellular localization of HGMB1 protein do not support a strong change in subcellular localization of the protein in response to temperature cycling; most of the HMGB1 protein is found in the cytoplasmic compartment in liver tissue. Although overall patterns of subcellular localization did not change significantly, we found a significant difference between nuclear HMGB1 protein levels in temperature cycled fish versus control (constant temperature) fish. This could suggest a muting of the natural translocation of HMGB1 into the nucleus observed in control fish at around 9:00 at night. Finally, the upstream region of the hgmb1 gene does reveal a number of putative stress responsive transcription factor binding sites. Close

• 57. [Article] Modeling the Bull Run River-Reservoir System

  The City of Portland, Water Bureau currently operates 2 Bull Run reservoirs, Reservoir #2 and Reservoir #1 as a water supply source in the Bull Run watershed shown in Figure 1 and Figure 2. The Water Bureau ...

  Citation × Citation Citation Abstract Copy Title: Modeling the Bull Run River-Reservoir System Author: Wells, Scott A. Year: 2000 The City of Portland, Water Bureau currently operates 2 Bull Run reservoirs, Reservoir #2 and Reservoir #1 as a water supply source in the Bull Run watershed shown in Figure 1 and Figure 2. The Water Bureau wants to operate their water supply system in order to meet both water supply objectives and fish habitat objectives downstream of the Bull Run reservoirs in Bull Run River. In addition, a third Bull Run reservoir has been proposed as an additional water supply source. This reservoir also may be used to meet water supply and fish habitat objectives in Bull Run River. This proposal addresses performing the following tasks to evaluate these objectives: Gather data to construct a computer simulation model of the Bull Run system including Bull Run River, Bull Run Reservoirs #1 through #3 and the river basin without reservoirs. Ensure that the model accurately represents the system physics, chemistry and biology. Use the model to evaluate how to meet water supply and fish habitat objectives by implementation of management scenarios. Title: Modeling the Bull Run River-Reservoir System Author: Wells, Scott A. Year: 2000 The City of Portland, Water Bureau currently operates 2 Bull Run reservoirs, Reservoir #2 and Reservoir #1 as a water supply source in the Bull Run watershed shown in Figure 1 and Figure 2. The Water Bureau wants to operate their water supply system in order to meet both water supply objectives and fish habitat objectives downstream of the Bull Run reservoirs in Bull Run River. In addition, a third Bull Run reservoir has been proposed as an additional water supply source. This reservoir also may be used to meet water supply and fish habitat objectives in Bull Run River. This proposal addresses performing the following tasks to evaluate these objectives: Gather data to construct a computer simulation model of the Bull Run system including Bull Run River, Bull Run Reservoirs #1 through #3 and the river basin without reservoirs. Ensure that the model accurately represents the system physics, chemistry and biology. Use the model to evaluate how to meet water supply and fish habitat objectives by implementation of management scenarios. Close

• 58. [Article] Stable Isotope and Ancient DNA Analysis of Dog Remains From Cathlapotle (45CL1), a Contact-Era Site on the Lower Columbia River

  This study reports ancient DNA (aDNA) and stable isotope analyses of eight dog skeletal elements from the Cathlapotle site on the Lower Columbia River of the western United States. The aDNA analysis confirmed ...

  Citation × Citation Citation Abstract Copy Title: Stable Isotope and Ancient DNA Analysis of Dog Remains From Cathlapotle (45CL1), a Contact-Era Site on the Lower Columbia River Author: Ames, Kenneth M., Richards, Michael P., Speller, Camilla F., Yang, Dongya Y., Lyman, R. Lee, Butler, Virginia L. Year: 2015 This study reports ancient DNA (aDNA) and stable isotope analyses of eight dog skeletal elements from the Cathlapotle site on the Lower Columbia River of the western United States. The aDNA analysis confirmed the elements as dogs (Canis lupus familiaris). Two haplotypes were found, both of which group within dog Clade A, and have patchy distributions to the north in British Columbia and as far south as Teotihuacan (Mexico). The isotopic analysis showed that the dogs’ dietary protein was derived almost exclusively from marine sources. Lower Columbia River ethnohistoric accounts and Cathlapotle zooarchaeological records indicate that while marine fish were dietary keystones, the local diet was more diverse, and included terrestrial organisms and freshwater fishes. This apparent discrepancy raises the possibility the dogs were selectively fed. Thus their diet may not be a close proxy for human diet in this context. Title: Stable Isotope and Ancient DNA Analysis of Dog Remains From Cathlapotle (45CL1), a Contact-Era Site on the Lower Columbia River Author: Ames, Kenneth M., Richards, Michael P., Speller, Camilla F., Yang, Dongya Y., Lyman, R. Lee, Butler, Virginia L. Year: 2015 This study reports ancient DNA (aDNA) and stable isotope analyses of eight dog skeletal elements from the Cathlapotle site on the Lower Columbia River of the western United States. The aDNA analysis confirmed the elements as dogs (Canis lupus familiaris). Two haplotypes were found, both of which group within dog Clade A, and have patchy distributions to the north in British Columbia and as far south as Teotihuacan (Mexico). The isotopic analysis showed that the dogs’ dietary protein was derived almost exclusively from marine sources. Lower Columbia River ethnohistoric accounts and Cathlapotle zooarchaeological records indicate that while marine fish were dietary keystones, the local diet was more diverse, and included terrestrial organisms and freshwater fishes. This apparent discrepancy raises the possibility the dogs were selectively fed. Thus their diet may not be a close proxy for human diet in this context. Close

• 59. [Article] Sub-Antarctic and High Antarctic Notothenioid Fishes: Ecology and Adaptational Biology Revealed by the ICEFISH 2004 Cruise of RVIB Nathaniel B. Palmer

  The goal of the ICEFISH 2004 cruise, which was conducted on board RVIB Nathaniel B. Palmer and traversed the transitional zones linking the South Atlantic to the Southern Ocean, was to compare the evolution, ...

  Citation × Citation Citation Abstract Copy Title: Sub-Antarctic and High Antarctic Notothenioid Fishes: Ecology and Adaptational Biology Revealed by the ICEFISH 2004 Cruise of RVIB Nathaniel B. Palmer Author: Detrich, H. William, III, Buckley, Bradley A., Doolittle, Daniel F., Jones, Christopher D., Lockhart, Susanne J. Year: 2012 The goal of the ICEFISH 2004 cruise, which was conducted on board RVIB Nathaniel B. Palmer and traversed the transitional zones linking the South Atlantic to the Southern Ocean, was to compare the evolution, ecology, adaptational biology, community structure, and population dynamics of Antarctic notothenioid fishes relative to the cool/temperate notothenioids of the sub-Antarctic. To place this work in a comprehensive ecological context, cruise participants surveyed the benthos and geology of the biogeographic provinces and island shelves on either side of the Antarctic Polar Front (or Antarctic Convergence). Genome-enabled comparison of the responses of cold-living and temperate notothenioids to heat stress confirmed the sensitivity of the former to a warming Southern Ocean. Successful implementation of the international and interdisciplinary ICEFISH research cruise provides a model for future exploration of the sub-Antarctic sectors of the Indian and Pacific Oceans. Title: Sub-Antarctic and High Antarctic Notothenioid Fishes: Ecology and Adaptational Biology Revealed by the ICEFISH 2004 Cruise of RVIB Nathaniel B. Palmer Author: Detrich, H. William, III, Buckley, Bradley A., Doolittle, Daniel F., Jones, Christopher D., Lockhart, Susanne J. Year: 2012 The goal of the ICEFISH 2004 cruise, which was conducted on board RVIB Nathaniel B. Palmer and traversed the transitional zones linking the South Atlantic to the Southern Ocean, was to compare the evolution, ecology, adaptational biology, community structure, and population dynamics of Antarctic notothenioid fishes relative to the cool/temperate notothenioids of the sub-Antarctic. To place this work in a comprehensive ecological context, cruise participants surveyed the benthos and geology of the biogeographic provinces and island shelves on either side of the Antarctic Polar Front (or Antarctic Convergence). Genome-enabled comparison of the responses of cold-living and temperate notothenioids to heat stress confirmed the sensitivity of the former to a warming Southern Ocean. Successful implementation of the international and interdisciplinary ICEFISH research cruise provides a model for future exploration of the sub-Antarctic sectors of the Indian and Pacific Oceans. Close

• 60. [Article] Analysis and numerical simulation of the ground water system at the Bonneville navigation lock site, Oregon

  As part of the new navigation lock for Bonneville Dam a new water source for the Bonneville Fish Hatchery must be supplied. The hatchery is located on the Oregon side of the Columbia River downstream of ...

  Citation × Citation Citation Abstract Copy Title: Analysis and numerical simulation of the ground water system at the Bonneville navigation lock site, Oregon Author: Baron, Dirk Year: 1990 As part of the new navigation lock for Bonneville Dam a new water source for the Bonneville Fish Hatchery must be supplied. The hatchery is located on the Oregon side of the Columbia River downstream of the dam. It requires large quantities of water free from chemical and biological contamination. In addition, the water has to be in a narrow temperature range. Currently the fish hatchery receives its water from a well field that is located on the alluvial terrace downstream of Bonneville Dam. The well field lies in the proposed approach channel for the new lock and has to be abandoned during construction of the lock. For the continued water supply of the hatchery, a new well field will be developed north of the approach channel. Early in the planning phase for the new lock, concerns were raised about the potential impact of the relocation of the well field and the excavation of the new approach channel on the hatchery. To assess these concerns and to assure a continuous water supply during and after construction, a hydrogeologic investigation was initiated. Within the framework of the investigation this study focuses on the analysis of pumping test data and the development of a three-dimensional ground water flow model for the site. Title: Analysis and numerical simulation of the ground water system at the Bonneville navigation lock site, Oregon Author: Baron, Dirk Year: 1990 As part of the new navigation lock for Bonneville Dam a new water source for the Bonneville Fish Hatchery must be supplied. The hatchery is located on the Oregon side of the Columbia River downstream of the dam. It requires large quantities of water free from chemical and biological contamination. In addition, the water has to be in a narrow temperature range. Currently the fish hatchery receives its water from a well field that is located on the alluvial terrace downstream of Bonneville Dam. The well field lies in the proposed approach channel for the new lock and has to be abandoned during construction of the lock. For the continued water supply of the hatchery, a new well field will be developed north of the approach channel. Early in the planning phase for the new lock, concerns were raised about the potential impact of the relocation of the well field and the excavation of the new approach channel on the hatchery. To assess these concerns and to assure a continuous water supply during and after construction, a hydrogeologic investigation was initiated. Within the framework of the investigation this study focuses on the analysis of pumping test data and the development of a three-dimensional ground water flow model for the site. Close

• 61. [Article] Evaluating the Effects of Road Crossing Structures on Stream-Associated Amphibians in the Wilson River Watershed, Tillamook State Forest, Oregon

  As replacement and removal of undersized culverts gains momentum as an effective technique for restoring natural stream flows and removing fish passage barriers, it is important to evaluate the benefits ...

  Citation × Citation Citation Abstract Copy Title: Evaluating the Effects of Road Crossing Structures on Stream-Associated Amphibians in the Wilson River Watershed, Tillamook State Forest, Oregon Author: Twitchell, Sara Erin Year: 2013 As replacement and removal of undersized culverts gains momentum as an effective technique for restoring natural stream flows and removing fish passage barriers, it is important to evaluate the benefits of these efforts on the in-stream and adjacent riparian habitat for other species of potential concern. This study compares stream-associated amphibian (SAA) occurrence in streams adjacent to different road crossing structures on unpaved forest roads in the Wilson River watershed located within the Tillamook State Forest, Oregon. Surveys were conducted at road crossing structures for three taxa of SAA; Pacific giant salamander (Dicamptodon tenebrosus), coastal tailed frog (Ascaphus truei), and Columbia torrent salamander (Rhyacotriton kezeri). Statistical models were created to analyze the effect of habitat variables on SAA occupancy, and determine whether those variables changed relative to road crossing structures. Results showed that coastal tailed frog occupancy was positively associated with dissolved oxygen and crayfish presence, negatively associated with longitude, and had a slight quadratic relationship to channel confinement. Because all sites were highly saturated with oxygen, percent dissolved oxygen was likely a surrogate for one or more other covariates, such as in-stream habitat or substrate size. Detection rates of Pacific giant salamander were too high and detection rates of Columbia torrent salamander were too low to provide reliable models, but they did provide some insight into the factors affecting occupancy in the study area, including information about their interactions with road crossing structures. Occupancy rates of Pacific giant salamanders in the study area appear to be unaffected by road crossings, fish passable or otherwise. Conversely, torrent salamanders seemed to be mostly absent from the study sites altogether, but based on the one stream where they were detected, they are not excluded from occupying fish barrier culvert sites. Top weighted habitat covariates, including dissolved oxygen, channel confinement, crayfish and fish presence, and flow constriction are all indicators of disturbance that can be linked to road crossings. Although the size and structure of road crossings did not prove to significantly influence SAA occupancy, indicators of stream disturbance that can be related to road crossings were included in the best models for predicting occupancy, demonstrating the importance of reducing disturbance related to road crossings on streams. Title: Evaluating the Effects of Road Crossing Structures on Stream-Associated Amphibians in the Wilson River Watershed, Tillamook State Forest, Oregon Author: Twitchell, Sara Erin Year: 2013 As replacement and removal of undersized culverts gains momentum as an effective technique for restoring natural stream flows and removing fish passage barriers, it is important to evaluate the benefits of these efforts on the in-stream and adjacent riparian habitat for other species of potential concern. This study compares stream-associated amphibian (SAA) occurrence in streams adjacent to different road crossing structures on unpaved forest roads in the Wilson River watershed located within the Tillamook State Forest, Oregon. Surveys were conducted at road crossing structures for three taxa of SAA; Pacific giant salamander (Dicamptodon tenebrosus), coastal tailed frog (Ascaphus truei), and Columbia torrent salamander (Rhyacotriton kezeri). Statistical models were created to analyze the effect of habitat variables on SAA occupancy, and determine whether those variables changed relative to road crossing structures. Results showed that coastal tailed frog occupancy was positively associated with dissolved oxygen and crayfish presence, negatively associated with longitude, and had a slight quadratic relationship to channel confinement. Because all sites were highly saturated with oxygen, percent dissolved oxygen was likely a surrogate for one or more other covariates, such as in-stream habitat or substrate size. Detection rates of Pacific giant salamander were too high and detection rates of Columbia torrent salamander were too low to provide reliable models, but they did provide some insight into the factors affecting occupancy in the study area, including information about their interactions with road crossing structures. Occupancy rates of Pacific giant salamanders in the study area appear to be unaffected by road crossings, fish passable or otherwise. Conversely, torrent salamanders seemed to be mostly absent from the study sites altogether, but based on the one stream where they were detected, they are not excluded from occupying fish barrier culvert sites. Top weighted habitat covariates, including dissolved oxygen, channel confinement, crayfish and fish presence, and flow constriction are all indicators of disturbance that can be linked to road crossings. Although the size and structure of road crossings did not prove to significantly influence SAA occupancy, indicators of stream disturbance that can be related to road crossings were included in the best models for predicting occupancy, demonstrating the importance of reducing disturbance related to road crossings on streams. Close

• 62. [Article] A Computational Model of Adaptive Sensory Processing in the Electroreception of Mormyrid Electric Fish

  Electroreception is a sensory modality found in some fish, which enables them to sense the environment through the detection of electric fields. Biological experimentation on this ability has built an ...

  Citation × Citation Citation Abstract Copy Title: A Computational Model of Adaptive Sensory Processing in the Electroreception of Mormyrid Electric Fish Author: Agmon, Eran Year: 2011 Electroreception is a sensory modality found in some fish, which enables them to sense the environment through the detection of electric fields. Biological experimentation on this ability has built an intricate framework that has identified many of the components involved in electroreception's production, but lack the framework for bringing the details back together into a system-level model of how they operate together. This thesis builds and tests a computational model of the Electrosensory Lateral Line Lobe (ELL) in mormyrid electric fish in an attempt to bring some of electroreception's structural details together to help explain its function. The ELL is a brain region that functions as a primary processing area of electroreception. It acts as an adaptive filter that learns to predict reoccurring stimuli and removes them from its sensory stream, passing only novel inputs to other brain regions for further processing. By creating a model of the ELL, the relevant components which underlie the ELL's functional, electrophysiological patterns can be identified and scientific hypotheses regarding their behavior can be tested. Systems science's approach is adopted to identify the ELL's relevant components and bring them together into a unified conceptual framework. The methodological framework of computational neuroscience is used to create a computational model of this structure of relevant components and to simulate their interactions. Individual activation tendencies of the different included cell types are modeled with dynamical systems equations and are interconnected according to the connectivity of the real ELL. Several of the ELL's input patterns are modeled and incorporated in the model. The computational approach claims that if all of the relevant components of a system are captured and interconnected accurately in a computer program, then when provided with accurate representations of the inputs a simulation should produce functional patterns similar to those of the real system. These simulated patterns generated by the ELL model are compared to recordings from real mormyrid ELLs and their correspondences validate or nullify the model's integrity. By building a computation model that can capture the relevant components of the ELL's structure and through simulation reproduces its function, a systems-level understanding begins to emerge and leads to a description of how the ELL's structure, along with relevant inputs, generate its function. The model can be manipulated more easily than a biological ELL, and allows us to test hypotheses regarding how changes in the structures affect the function, and how different inputs propagate through the structure in a way that produces complex functional patterns. Title: A Computational Model of Adaptive Sensory Processing in the Electroreception of Mormyrid Electric Fish Author: Agmon, Eran Year: 2011 Electroreception is a sensory modality found in some fish, which enables them to sense the environment through the detection of electric fields. Biological experimentation on this ability has built an intricate framework that has identified many of the components involved in electroreception's production, but lack the framework for bringing the details back together into a system-level model of how they operate together. This thesis builds and tests a computational model of the Electrosensory Lateral Line Lobe (ELL) in mormyrid electric fish in an attempt to bring some of electroreception's structural details together to help explain its function. The ELL is a brain region that functions as a primary processing area of electroreception. It acts as an adaptive filter that learns to predict reoccurring stimuli and removes them from its sensory stream, passing only novel inputs to other brain regions for further processing. By creating a model of the ELL, the relevant components which underlie the ELL's functional, electrophysiological patterns can be identified and scientific hypotheses regarding their behavior can be tested. Systems science's approach is adopted to identify the ELL's relevant components and bring them together into a unified conceptual framework. The methodological framework of computational neuroscience is used to create a computational model of this structure of relevant components and to simulate their interactions. Individual activation tendencies of the different included cell types are modeled with dynamical systems equations and are interconnected according to the connectivity of the real ELL. Several of the ELL's input patterns are modeled and incorporated in the model. The computational approach claims that if all of the relevant components of a system are captured and interconnected accurately in a computer program, then when provided with accurate representations of the inputs a simulation should produce functional patterns similar to those of the real system. These simulated patterns generated by the ELL model are compared to recordings from real mormyrid ELLs and their correspondences validate or nullify the model's integrity. By building a computation model that can capture the relevant components of the ELL's structure and through simulation reproduces its function, a systems-level understanding begins to emerge and leads to a description of how the ELL's structure, along with relevant inputs, generate its function. The model can be manipulated more easily than a biological ELL, and allows us to test hypotheses regarding how changes in the structures affect the function, and how different inputs propagate through the structure in a way that produces complex functional patterns. Close

• 63. [Article] The Response of Zooplankton Communities in Montane Lakes of Different Fish Stocking Histories to Atmospheric Nitrogen Deposition Simulations

  Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number ...

  Citation × Citation Citation Abstract Copy Title: The Response of Zooplankton Communities in Montane Lakes of Different Fish Stocking Histories to Atmospheric Nitrogen Deposition Simulations Author: Brittain, Jeffrey Thomas Year: 2015 Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number of naturally fishless lakes and have resulted in cascading food web repercussions in aquatic and terrestrial habitats. Additional anthropogenic influences that result from increases in global airborne emissions also threaten wildlife habitat. Atmospheric nitrogen deposition has been recognized as an anthropogenic contributor to acidification and eutrophication of wilderness ecosystems. Planktonic communities have shown declines in response to predation and shifts in composition as a result of nutrient inputs and acidification, both of which are potential fates of nitrogen deposition. This study identified the response of zooplankton communities from two lakes (fish present vs. absent) in Mount Rainier National Park to manipulations simulating an episodic disturbance event in mesocosms. The experiment used a 2 x 2 factorial design with acid and nitrogen treatments. Treatments resulted in significantly elevated nitrogen and decreased pH conditions from control mesocosms over 42 days, indicating that the treatment effects were achieved. Results indicate that zooplankton communities from lakes with different food web structure respond differently to the singular effects of acid and nitrogen addition. Surprisingly, the interaction of the two stressors was related to increases in community metrics (e.g., abundance, biomass, body size, richness, and Shannon-Weiner diversity) for both lake types. This work can aid management decisions as agencies look to restore more aquatic montane habitats to their historic fishless states, and assess their abilities to recover and afford resistance to atmospheric pollution. Title: The Response of Zooplankton Communities in Montane Lakes of Different Fish Stocking Histories to Atmospheric Nitrogen Deposition Simulations Author: Brittain, Jeffrey Thomas Year: 2015 Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number of naturally fishless lakes and have resulted in cascading food web repercussions in aquatic and terrestrial habitats. Additional anthropogenic influences that result from increases in global airborne emissions also threaten wildlife habitat. Atmospheric nitrogen deposition has been recognized as an anthropogenic contributor to acidification and eutrophication of wilderness ecosystems. Planktonic communities have shown declines in response to predation and shifts in composition as a result of nutrient inputs and acidification, both of which are potential fates of nitrogen deposition. This study identified the response of zooplankton communities from two lakes (fish present vs. absent) in Mount Rainier National Park to manipulations simulating an episodic disturbance event in mesocosms. The experiment used a 2 x 2 factorial design with acid and nitrogen treatments. Treatments resulted in significantly elevated nitrogen and decreased pH conditions from control mesocosms over 42 days, indicating that the treatment effects were achieved. Results indicate that zooplankton communities from lakes with different food web structure respond differently to the singular effects of acid and nitrogen addition. Surprisingly, the interaction of the two stressors was related to increases in community metrics (e.g., abundance, biomass, body size, richness, and Shannon-Weiner diversity) for both lake types. This work can aid management decisions as agencies look to restore more aquatic montane habitats to their historic fishless states, and assess their abilities to recover and afford resistance to atmospheric pollution. Close

• 64. [Article] On the Integrability of Orthogonal Distributions in Poisson Manifolds

  We study conditions for the integrability of the distribution defined on a regular Poisson manifold as the orthogonal complement (with respect to some (pseudo)-Riemannian metric) to the tangent spaces ...

  Citation × Citation Citation Abstract Copy Title: On the Integrability of Orthogonal Distributions in Poisson Manifolds Author: Fish, Daniel, Preston, Serge Year: 2010 We study conditions for the integrability of the distribution defined on a regular Poisson manifold as the orthogonal complement (with respect to some (pseudo)-Riemannian metric) to the tangent spaces of the leaves of a symplectic foliation. Examples of integrability and non-integrability of this distribution are provided. Title: On the Integrability of Orthogonal Distributions in Poisson Manifolds Author: Fish, Daniel, Preston, Serge Year: 2010 We study conditions for the integrability of the distribution defined on a regular Poisson manifold as the orthogonal complement (with respect to some (pseudo)-Riemannian metric) to the tangent spaces of the leaves of a symplectic foliation. Examples of integrability and non-integrability of this distribution are provided. Close

• 65. [Article] A readership study of Oregon wildlife magazine

  The purpose of this study was to determine the extent and frequency of readership of the Oregon Wildlife magazine and this relationship to Klapper's reinforcing hypothesis. The basic question posed was: ...

  Citation × Citation Citation Abstract Copy Title: A readership study of Oregon wildlife magazine Author: Sullivan, Deborah C. Year: 1978 The purpose of this study was to determine the extent and frequency of readership of the Oregon Wildlife magazine and this relationship to Klapper's reinforcing hypothesis. The basic question posed was: What population of individuals in Oregon read which types of fish and wildlife articles in the Oregon Wildlife magazine, and how do these respondents assess the readability and accuracy of the magazine? Title: A readership study of Oregon wildlife magazine Author: Sullivan, Deborah C. Year: 1978 The purpose of this study was to determine the extent and frequency of readership of the Oregon Wildlife magazine and this relationship to Klapper's reinforcing hypothesis. The basic question posed was: What population of individuals in Oregon read which types of fish and wildlife articles in the Oregon Wildlife magazine, and how do these respondents assess the readability and accuracy of the magazine? Close

• 66. [Article] Review of The Tragedy of the Commodity: Oceans, Fisheries, and Aquaculture

  Book review of, The Tragedy of the Commodity: Oceans, Fisheries, and Aquaculture By Stefano B. Longo, Rebecca Clausen, and Brett Clark. Rutgers University Press (June 25, 2015).

  Citation × Citation Citation Abstract Copy Title: Review of The Tragedy of the Commodity: Oceans, Fisheries, and Aquaculture Author: McGee, Julius Year: 2016 Book review of, The Tragedy of the Commodity: Oceans, Fisheries, and Aquaculture By Stefano B. Longo, Rebecca Clausen, and Brett Clark. Rutgers University Press (June 25, 2015). Title: Review of The Tragedy of the Commodity: Oceans, Fisheries, and Aquaculture Author: McGee, Julius Year: 2016 Book review of, The Tragedy of the Commodity: Oceans, Fisheries, and Aquaculture By Stefano B. Longo, Rebecca Clausen, and Brett Clark. Rutgers University Press (June 25, 2015). Close

• 67. [Article] Reefscapes of Fear: Predation Risk and Reef Hetero-Geneity Interact to Shape Herbivore Foraging Behaviour

  Predators can exert strong direct and indirect effects on ecological communities by intimidating their prey. The nature of predation risk effects is often context dependent, but in some ecosystems these ...

  Citation × Citation Citation Abstract Copy Title: Reefscapes of Fear: Predation Risk and Reef Hetero-Geneity Interact to Shape Herbivore Foraging Behaviour Author: Catano, Laura B., Rojas, Maria C., Malossi, Ryan J., Peters, Joseph R., Heathaus, Michael R., Fourquren, James W., Burkepile, Deron E. Year: 2016 Predators can exert strong direct and indirect effects on ecological communities by intimidating their prey. The nature of predation risk effects is often context dependent, but in some ecosystems these contingencies are often overlooked. Risk effects are often not uniform across landscapes or among species. Indeed, they can vary widely across gradients of habitat complexity and with different prey escape tactics. These context dependencies may be especially important for ecosystems such as coral reefs that vary widely in habitat complexity and have species-rich predator and prey communities. With field experiments using predator decoys of the black grouper (Mycteroperca bonaci), we investigated how reef complexity interacts with predation risk to affect the foraging behaviour and herbivory rates of large herbivorous fishes (e.g. parrotfishes and surgeonfishes) across four coral reefs in the Florida Keys (USA). In both high and low complexity areas of the reef, we measured how herbivory changed with increasing distance from the predator decoy to examine how herbivorous fishes reconcile the conflicting demands of avoiding predation vs. foraging within a reefscape context. We show that with increasing risk, herbivorous fishes consumed dramatically less food (ca. 90%) but fed at a faster rate when they did feed (ca. 26%). Furthermore, we show that fishes foraging closest to the predator decoy were 40% smaller than those that foraged at further distances. Thus, smaller individuals showed muted response to predation risk compared to their larger counterparts, potentially due to their decreased risk to predation or lower reproductive value (i.e. the asset protection principle). Habitat heterogeneity mediated risk effects differently for different species of herbivores, with predation risk more strongly suppressing herbivore feeding in more complex areas and for individuals at higher risk of predation. Predators appear to create a reefscape of fear that changes the size structure of herbivores towards smaller individuals, increases individual feeding rates, but suppresses overall amounts of primary producers consumed, potentially altering patterns of herbivory, an ecosystem process critical for healthy coral reefs. Title: Reefscapes of Fear: Predation Risk and Reef Hetero-Geneity Interact to Shape Herbivore Foraging Behaviour Author: Catano, Laura B., Rojas, Maria C., Malossi, Ryan J., Peters, Joseph R., Heathaus, Michael R., Fourquren, James W., Burkepile, Deron E. Year: 2016 Predators can exert strong direct and indirect effects on ecological communities by intimidating their prey. The nature of predation risk effects is often context dependent, but in some ecosystems these contingencies are often overlooked. Risk effects are often not uniform across landscapes or among species. Indeed, they can vary widely across gradients of habitat complexity and with different prey escape tactics. These context dependencies may be especially important for ecosystems such as coral reefs that vary widely in habitat complexity and have species-rich predator and prey communities. With field experiments using predator decoys of the black grouper (Mycteroperca bonaci), we investigated how reef complexity interacts with predation risk to affect the foraging behaviour and herbivory rates of large herbivorous fishes (e.g. parrotfishes and surgeonfishes) across four coral reefs in the Florida Keys (USA). In both high and low complexity areas of the reef, we measured how herbivory changed with increasing distance from the predator decoy to examine how herbivorous fishes reconcile the conflicting demands of avoiding predation vs. foraging within a reefscape context. We show that with increasing risk, herbivorous fishes consumed dramatically less food (ca. 90%) but fed at a faster rate when they did feed (ca. 26%). Furthermore, we show that fishes foraging closest to the predator decoy were 40% smaller than those that foraged at further distances. Thus, smaller individuals showed muted response to predation risk compared to their larger counterparts, potentially due to their decreased risk to predation or lower reproductive value (i.e. the asset protection principle). Habitat heterogeneity mediated risk effects differently for different species of herbivores, with predation risk more strongly suppressing herbivore feeding in more complex areas and for individuals at higher risk of predation. Predators appear to create a reefscape of fear that changes the size structure of herbivores towards smaller individuals, increases individual feeding rates, but suppresses overall amounts of primary producers consumed, potentially altering patterns of herbivory, an ecosystem process critical for healthy coral reefs. Close

• 68. [Article] The Resurrection of a River: The Umatilla and its Salmon

  Until the 1990s, salmon had been extinct from the Umatilla River for over 70 years. The struggle to bring salmon back to this river is a compelling story that exemplifies some of the new relationships ...

  Citation × Citation Citation Abstract Copy Title: The Resurrection of a River: The Umatilla and its Salmon Author: Shelley, Christopher Ward Year: 2002 Until the 1990s, salmon had been extinct from the Umatilla River for over 70 years. The struggle to bring salmon back to this river is a compelling story that exemplifies some of the new relationships in Columbia River Basin salmon management. The Umatilla River and the disappearance of its salmon was a local issue. Irrigation interests had used the river so thoroughly it ceased to flow during the late summer and fall months-precisely when salmon needed it for migration. The Confederated Tribes of the Umatilla Indian Reservation saw decided that they would change that: they would figure out a way to put both salmon and water back into the river. This thesis examines this process. First, it contextualizes the Umatilla River within the Columbia River Basin and Columbia Basin salmon management, and shows how a local salmon issue became a regional salmon issue. It then discusses the triangle of relationships that Indians, salmon, and hatcheries have come to form. Chapter III discusses the formation of the unique Umatilla Fish Restoration Program, which reintroduced fish into the river, and was paid for by the Bonneville Power Administration (BPA), as per the Northwest Power Act. Key elements within BPA's Fish and Wildlife Division resisted complying with the directives of the Northwest Power Planning Council to pay for the Program, setting the Program back years. I argue that this comes from two clashing ways of seeing the River: "cost-benefit analysis" versus "least cost." Chapter IV looks at the new partnerships formed in the Umatilla River Basin by the Tribes and irrigation districts in order to encourage the U.S. Bureau of Reclamation to construct a water delivery system that would satisfy irrigators while allowing most of the Umatilla to flow freely. The last Chapter suggests that these new and somewhat ironic partnerships between federal and state governments, private irrigators and landowners, nongovernmental organizations, and Indian tribes are key to restoring ecosystems in the Columbia River Basin. It further argues that without tribal nations playing an active role and exerting their treaty rights, restoring rivers like the Umatilla is impossible. Title: The Resurrection of a River: The Umatilla and its Salmon Author: Shelley, Christopher Ward Year: 2002 Until the 1990s, salmon had been extinct from the Umatilla River for over 70 years. The struggle to bring salmon back to this river is a compelling story that exemplifies some of the new relationships in Columbia River Basin salmon management. The Umatilla River and the disappearance of its salmon was a local issue. Irrigation interests had used the river so thoroughly it ceased to flow during the late summer and fall months-precisely when salmon needed it for migration. The Confederated Tribes of the Umatilla Indian Reservation saw decided that they would change that: they would figure out a way to put both salmon and water back into the river. This thesis examines this process. First, it contextualizes the Umatilla River within the Columbia River Basin and Columbia Basin salmon management, and shows how a local salmon issue became a regional salmon issue. It then discusses the triangle of relationships that Indians, salmon, and hatcheries have come to form. Chapter III discusses the formation of the unique Umatilla Fish Restoration Program, which reintroduced fish into the river, and was paid for by the Bonneville Power Administration (BPA), as per the Northwest Power Act. Key elements within BPA's Fish and Wildlife Division resisted complying with the directives of the Northwest Power Planning Council to pay for the Program, setting the Program back years. I argue that this comes from two clashing ways of seeing the River: "cost-benefit analysis" versus "least cost." Chapter IV looks at the new partnerships formed in the Umatilla River Basin by the Tribes and irrigation districts in order to encourage the U.S. Bureau of Reclamation to construct a water delivery system that would satisfy irrigators while allowing most of the Umatilla to flow freely. The last Chapter suggests that these new and somewhat ironic partnerships between federal and state governments, private irrigators and landowners, nongovernmental organizations, and Indian tribes are key to restoring ecosystems in the Columbia River Basin. It further argues that without tribal nations playing an active role and exerting their treaty rights, restoring rivers like the Umatilla is impossible. Close

• 69. [Article] Prohibiting Certain Fishing in Coastal Stream (State Measure 7); City Services, Salaries (Portland Measure 55); Legislator's Salaries (State Measure 5); Tax Emergency Clause (State Measure 1)

  Citation × Citation Citation Abstract Copy Title: Prohibiting Certain Fishing in Coastal Stream (State Measure 7); City Services, Salaries (Portland Measure 55); Legislator's Salaries (State Measure 5); Tax Emergency Clause (State Measure 1) Author: City Club of Portland (Portland, Or.) Year: 1956 Title: Prohibiting Certain Fishing in Coastal Stream (State Measure 7); City Services, Salaries (Portland Measure 55); Legislator's Salaries (State Measure 5); Tax Emergency Clause (State Measure 1) Author: City Club of Portland (Portland, Or.) Year: 1956 Close

• 70. [Article] City Club of Portland Information Report: Endangered Fish Species in Portland

  Citation × Citation Citation Abstract Copy Title: City Club of Portland Information Report: Endangered Fish Species in Portland Author: City Club of Portland (Portland, Or.) Year: 1999 Title: City Club of Portland Information Report: Endangered Fish Species in Portland Author: City Club of Portland (Portland, Or.) Year: 1999 Close

• 71. [Article] Report on Use of State Bond Proceeds to Finance Fish Protection and Watershed Restoration Projects (State Ballot Measure No. 1)

  Citation × Citation Citation Abstract Copy Title: Report on Use of State Bond Proceeds to Finance Fish Protection and Watershed Restoration Projects (State Ballot Measure No. 1) Author: City Club of Portland (Portland, Or.) Year: 1988 Title: Report on Use of State Bond Proceeds to Finance Fish Protection and Watershed Restoration Projects (State Ballot Measure No. 1) Author: City Club of Portland (Portland, Or.) Year: 1988 Close

• 72. [Article] Report on Prohibiting Commercial Fishing for Salmon, Steelhead (State Measure No. 4)

  Citation × Citation Citation Abstract Copy Title: Report on Prohibiting Commercial Fishing for Salmon, Steelhead (State Measure No. 4) Author: City Club of Portland (Portland, Or.) Year: 1964 Title: Report on Prohibiting Commercial Fishing for Salmon, Steelhead (State Measure No. 4) Author: City Club of Portland (Portland, Or.) Year: 1964 Close

• 73. [Article] Modeling the Impact of Water Quality and Food Web Structure on Bull Trout in Two Washington Reservoirs

  Mechanistic models of the hydrodynamics and water quality were developed for Lake Kachess and Lake Keechelus in the Yakima River basin of Eastern Washington. These models were coupled to a fish bioenergetics ...

  Citation × Citation Citation Abstract Copy Title: Modeling the Impact of Water Quality and Food Web Structure on Bull Trout in Two Washington Reservoirs Author: Berger, Chris J., Wells, Scott A. Year: 2017 Mechanistic models of the hydrodynamics and water quality were developed for Lake Kachess and Lake Keechelus in the Yakima River basin of Eastern Washington. These models were coupled to a fish bioenergetics model and used to explore management strategies to improve water quality in the reservoirs affecting kokanee production. The models were also applied to evaluate the impacts of the proposed implementation of the Kachess Drought Relief Pumping Plant (KDRPP) projects. The public domain model, CEQUAL-W2 Version 4 (Cole and Wells, 2016) was adapted to model the reservoirs. CEQUAL-W2 is a 2-dimensional (longitudinal-vertical) hydrodynamic and water quality model capable of predicting water surface, velocity, temperature, nutrients, multiple algae, zooplankton, periphyton, and macrophyte species, fish bioenergetics, sediment diagenesis, dissolved oxygen, pH, alkalinity, multiple CBOD groups, multiple suspended solids groups, multiple generic constituents (such as tracer, bacteria, toxics), and multiple organic matter groups, both dissolved and particulate. The model is set up to predict these state variables at longitudinal segments and vertical layers. Comparisons of field data to model predictions were made for water level, temperature, NH4-N, NO3-N, PO4-P, total N, Total P, total organic carbon, alkalinity, zooplankton, pH, chlorophyll a, and dissolved oxygen at multiple reservoir sites at various depths. Title: Modeling the Impact of Water Quality and Food Web Structure on Bull Trout in Two Washington Reservoirs Author: Berger, Chris J., Wells, Scott A. Year: 2017 Mechanistic models of the hydrodynamics and water quality were developed for Lake Kachess and Lake Keechelus in the Yakima River basin of Eastern Washington. These models were coupled to a fish bioenergetics model and used to explore management strategies to improve water quality in the reservoirs affecting kokanee production. The models were also applied to evaluate the impacts of the proposed implementation of the Kachess Drought Relief Pumping Plant (KDRPP) projects. The public domain model, CEQUAL-W2 Version 4 (Cole and Wells, 2016) was adapted to model the reservoirs. CEQUAL-W2 is a 2-dimensional (longitudinal-vertical) hydrodynamic and water quality model capable of predicting water surface, velocity, temperature, nutrients, multiple algae, zooplankton, periphyton, and macrophyte species, fish bioenergetics, sediment diagenesis, dissolved oxygen, pH, alkalinity, multiple CBOD groups, multiple suspended solids groups, multiple generic constituents (such as tracer, bacteria, toxics), and multiple organic matter groups, both dissolved and particulate. The model is set up to predict these state variables at longitudinal segments and vertical layers. Comparisons of field data to model predictions were made for water level, temperature, NH4-N, NO3-N, PO4-P, total N, Total P, total organic carbon, alkalinity, zooplankton, pH, chlorophyll a, and dissolved oxygen at multiple reservoir sites at various depths. Close

• 74. [Article] Mechanisms of Animal Diapause: Recent Developments from Nematodes, Crustaceans, Insects, and Fish

  Life cycle delays are beneficial for opportunistic species encountering suboptimal environments. Many animals display a programmed arrest of development (diapause) at some stage(s) of their development, ...

  Citation × Citation Citation Abstract Copy Title: Mechanisms of Animal Diapause: Recent Developments from Nematodes, Crustaceans, Insects, and Fish Author: Hand, Steven C., Denlinger, David L., Podrabsky, Jason E., Roy, Richard Year: 2016 Life cycle delays are beneficial for opportunistic species encountering suboptimal environments. Many animals display a programmed arrest of development (diapause) at some stage(s) of their development, and the diapause state may or may not be associated with some degree of metabolic depression. In this review, we will evaluate current advancements in our understanding of the mechanisms responsible for the remarkable phenotype, as well as environmental cues that signal entry and termination of the state. The developmental stage at which diapause occurs dictates and constrains the mechanisms governing diapause. Considerable progress has been made in clarifying proximal mechanisms of metabolic arrest and the signaling pathways like insulin/Foxo that control gene expression patterns. Overlapping themes are also seen in mechanisms that control cell cycle arrest. Evidence is emerging for epigenetic contributions to diapause regulation via small RNAs in nematodes, crustaceans, insects, and fish. Knockdown of circadian clock genes in selected insect species supports the importance of clock genes in the photoperiodic response that cues diapause. A large suite of chaperone-like proteins, expressed during diapause, protects biological structures during long periods of energy-limited stasis. More information is needed to paint a complete picture of how environmental cues are coupled to the signal transduction that initiates the complex diapause phenotype, as well as molecular explanations for how the state is terminated. Excellent examples of molecular memory in post-dauer animals have been documented in Caenorhabditis elegans It is clear that a single suite of mechanisms does not regulate diapause across all species and developmental stages. Title: Mechanisms of Animal Diapause: Recent Developments from Nematodes, Crustaceans, Insects, and Fish Author: Hand, Steven C., Denlinger, David L., Podrabsky, Jason E., Roy, Richard Year: 2016 Life cycle delays are beneficial for opportunistic species encountering suboptimal environments. Many animals display a programmed arrest of development (diapause) at some stage(s) of their development, and the diapause state may or may not be associated with some degree of metabolic depression. In this review, we will evaluate current advancements in our understanding of the mechanisms responsible for the remarkable phenotype, as well as environmental cues that signal entry and termination of the state. The developmental stage at which diapause occurs dictates and constrains the mechanisms governing diapause. Considerable progress has been made in clarifying proximal mechanisms of metabolic arrest and the signaling pathways like insulin/Foxo that control gene expression patterns. Overlapping themes are also seen in mechanisms that control cell cycle arrest. Evidence is emerging for epigenetic contributions to diapause regulation via small RNAs in nematodes, crustaceans, insects, and fish. Knockdown of circadian clock genes in selected insect species supports the importance of clock genes in the photoperiodic response that cues diapause. A large suite of chaperone-like proteins, expressed during diapause, protects biological structures during long periods of energy-limited stasis. More information is needed to paint a complete picture of how environmental cues are coupled to the signal transduction that initiates the complex diapause phenotype, as well as molecular explanations for how the state is terminated. Excellent examples of molecular memory in post-dauer animals have been documented in Caenorhabditis elegans It is clear that a single suite of mechanisms does not regulate diapause across all species and developmental stages. Close

• 75. [Article] Working for the "Working River": Willamette River Water Pollution, 1926 to 1962

  Efforts to abate Willamette River pollution between 1926 and 1962 centered on a struggle between abatement advocates and the two primary polluters in the watershed, the City of Portland and the pulp and ...

  Citation × Citation Citation Abstract Copy Title: Working for the "Working River": Willamette River Water Pollution, 1926 to 1962 Author: Hillegas, James Vincent Year: 2009 Efforts to abate Willamette River pollution between 1926 and 1962 centered on a struggle between abatement advocates and the two primary polluters in the watershed, the City of Portland and the pulp and paper industry. Throughout the twentieth century, the Willamette was by far the most heavily populated and industrialized watershed in Oregon. Like many other of the world's rivers, the Willamette was an integral part of municipal and industrial waste removal systems. As such, the main stem of the river carried the combined wastes from sewage outfalls serving hundreds of thousands of people and millions of gallons daily of pulp and paper making effluents. Exacerbating the impacts of these pollutants on the Willamette were unavoidable geologic and hydrologic constraints impacting the river's flow and, therefore, the river's ability to dilute wastes. As the pollution load in the Willamette River increased throughout the twentieth century, accustomed activities such as recreation, sports fishing, and commercial fishing, were constrained. The polluted water also threatened potential uses of the river, such as tourism and expanded recreation after World War II. To address these concerns, beginning in 1926 clean streams advocates created ad hoc groups of public health experts, sanitary engineers, conservationists, sportsmen, and others to pressure Portland officials and industry representatives to cease polluting the river. In November 1938, continued activism and lobbying from these groups led to the passage of a citizen's initiative creating the Oregon State Sanitary Authority (OSSA). From 1939 to 1962, the OSSA took the lead in the water pollution abatement issue and realized some limited successes including pushing Portland and other cities to build sewage treatment plants and regulating pulp and paper mill discharges. However, in spite of these accomplishments, the issue of water quality grew more complex and difficult through the 1950s, as reflected in Tom McCall's November 1962 television documentary Pollution in Paradise. Title: Working for the "Working River": Willamette River Water Pollution, 1926 to 1962 Author: Hillegas, James Vincent Year: 2009 Efforts to abate Willamette River pollution between 1926 and 1962 centered on a struggle between abatement advocates and the two primary polluters in the watershed, the City of Portland and the pulp and paper industry. Throughout the twentieth century, the Willamette was by far the most heavily populated and industrialized watershed in Oregon. Like many other of the world's rivers, the Willamette was an integral part of municipal and industrial waste removal systems. As such, the main stem of the river carried the combined wastes from sewage outfalls serving hundreds of thousands of people and millions of gallons daily of pulp and paper making effluents. Exacerbating the impacts of these pollutants on the Willamette were unavoidable geologic and hydrologic constraints impacting the river's flow and, therefore, the river's ability to dilute wastes. As the pollution load in the Willamette River increased throughout the twentieth century, accustomed activities such as recreation, sports fishing, and commercial fishing, were constrained. The polluted water also threatened potential uses of the river, such as tourism and expanded recreation after World War II. To address these concerns, beginning in 1926 clean streams advocates created ad hoc groups of public health experts, sanitary engineers, conservationists, sportsmen, and others to pressure Portland officials and industry representatives to cease polluting the river. In November 1938, continued activism and lobbying from these groups led to the passage of a citizen's initiative creating the Oregon State Sanitary Authority (OSSA). From 1939 to 1962, the OSSA took the lead in the water pollution abatement issue and realized some limited successes including pushing Portland and other cities to build sewage treatment plants and regulating pulp and paper mill discharges. However, in spite of these accomplishments, the issue of water quality grew more complex and difficult through the 1950s, as reflected in Tom McCall's November 1962 television documentary Pollution in Paradise. Close

• 76. [Article] Life Cycle, Additions to Biology, and New Hosts of Apophallus Donicus (Trematoda: Heterophyidae) in Oregon

  Apophallus donicus is examined, its life cycle is described, and certain additions are made to its biology. It is thought, but not proven, that eggs are eaten by the first.intermediate host, the local ...

  Citation × Citation Citation Abstract Copy Title: Life Cycle, Additions to Biology, and New Hosts of Apophallus Donicus (Trematoda: Heterophyidae) in Oregon Author: Niemi, Delbert Raymond Year: 1973 Apophallus donicus is examined, its life cycle is described, and certain additions are made to its biology. It is thought, but not proven, that eggs are eaten by the first.intermediate host, the local stream snail FluI menicola virens, and the miracidia escape internally. Mother and daughter rediae stages result, the later producing cercariae which are shed into the water. After burrowing just beneath the skin in suckers (Catostomus macrocheilus Girard), rainbow trout (Salmo 9airdneri Richardson), coho salmon (Oncorhynchus kisutch (Walbaum) squawfish (Ptychocheilus oregonensis Richardson), blackside dace (Rhinichthys osculus nubilus (Girard), redside shiners (Richardsonius balteatus balteatus (Richardson),and possibly other fish, the cercariae encyst and the resulting metacercariae cause black-spot disease in the host. Natural definitive hosts were not found, but laboratory infections included gerbils, white rats, golden hamsters, chickens, catfish (Ictalurus punctatus (Rafinesque), cats, and the author. A rainbow trout was found which had 33 immature Apophallus in its small intestine. All were alive and active, but their entire posterior ends, including all the sex organs, were degenerate and poorly formed compared to the anterior halves of their bodies, and there was no evidence that adults with eggs would have resulted. This trematode is very hardy and adaptable in all stages of its life cycle, e.g., cercariae lived and were active up until eight days after being shed, metacercariae remained infective in fish which had been dead and out of water for 60 hours, and adults lived in tap water at room temperature for 72 hours. Title: Life Cycle, Additions to Biology, and New Hosts of Apophallus Donicus (Trematoda: Heterophyidae) in Oregon Author: Niemi, Delbert Raymond Year: 1973 Apophallus donicus is examined, its life cycle is described, and certain additions are made to its biology. It is thought, but not proven, that eggs are eaten by the first.intermediate host, the local stream snail FluI menicola virens, and the miracidia escape internally. Mother and daughter rediae stages result, the later producing cercariae which are shed into the water. After burrowing just beneath the skin in suckers (Catostomus macrocheilus Girard), rainbow trout (Salmo 9airdneri Richardson), coho salmon (Oncorhynchus kisutch (Walbaum) squawfish (Ptychocheilus oregonensis Richardson), blackside dace (Rhinichthys osculus nubilus (Girard), redside shiners (Richardsonius balteatus balteatus (Richardson),and possibly other fish, the cercariae encyst and the resulting metacercariae cause black-spot disease in the host. Natural definitive hosts were not found, but laboratory infections included gerbils, white rats, golden hamsters, chickens, catfish (Ictalurus punctatus (Rafinesque), cats, and the author. A rainbow trout was found which had 33 immature Apophallus in its small intestine. All were alive and active, but their entire posterior ends, including all the sex organs, were degenerate and poorly formed compared to the anterior halves of their bodies, and there was no evidence that adults with eggs would have resulted. This trematode is very hardy and adaptable in all stages of its life cycle, e.g., cercariae lived and were active up until eight days after being shed, metacercariae remained infective in fish which had been dead and out of water for 60 hours, and adults lived in tap water at room temperature for 72 hours. Close

• 77. [Article] Investigating a Role for the CCAAT/Enhancer-Binding Protein δ in the Developing Zebrafish

  The CCAAT/enhancer-binding protein delta (C/EBPδ) is a highly conserved transcription factor capable of regulating numerous cell fate processes, such as cell growth, differentiation, proliferation and ...

  Citation × Citation Citation Abstract Copy Title: Investigating a Role for the CCAAT/Enhancer-Binding Protein δ in the Developing Zebrafish Author: Beirl, Alisha Jennifer Year: 2014 The CCAAT/enhancer-binding protein delta (C/EBPδ) is a highly conserved transcription factor capable of regulating numerous cell fate processes, such as cell growth, differentiation, proliferation and apoptosis. C/EBPδ is inducible during cellular stress responses, including inflammation and responses to growth factor deprivation or thermal stress. C/EBPδ is stress-inducible in a diversity of fishes, including the zebrafish Danio rerio; however, little is known about its role in fish development. Here I show that overexpression of C/EBPδ leads to severe developmental defects, including reduced body length, edema, liver malformation and retinal abnormalities. The proportion of individuals that display developmental abnormalities is significantly greater in C/EBPδ-overexpressing embryos compared to control embryos and overexpression significantly reduces survival of larvae over time. TUNEL analysis suggests C/EBPδ-overexpressing embryos exhibit a pattern of apoptotic cell death which is spatially distinct from control embryos. These data support a critical role for C/EBPδ in numerous developmental processes, including promoting programmed cell death during development. Mutations in C/EBPδ have been implicated in the progression of human tumors, including those of myeloid, hepatocellular and breast cancers. Therefore, the C/EBPδ-overexpressing zebrafish will serve as a valuable model for examining the role of this gene during development, as a part of the cellular response to stress and in pathological states such as tumor progression. Title: Investigating a Role for the CCAAT/Enhancer-Binding Protein δ in the Developing Zebrafish Author: Beirl, Alisha Jennifer Year: 2014 The CCAAT/enhancer-binding protein delta (C/EBPδ) is a highly conserved transcription factor capable of regulating numerous cell fate processes, such as cell growth, differentiation, proliferation and apoptosis. C/EBPδ is inducible during cellular stress responses, including inflammation and responses to growth factor deprivation or thermal stress. C/EBPδ is stress-inducible in a diversity of fishes, including the zebrafish Danio rerio; however, little is known about its role in fish development. Here I show that overexpression of C/EBPδ leads to severe developmental defects, including reduced body length, edema, liver malformation and retinal abnormalities. The proportion of individuals that display developmental abnormalities is significantly greater in C/EBPδ-overexpressing embryos compared to control embryos and overexpression significantly reduces survival of larvae over time. TUNEL analysis suggests C/EBPδ-overexpressing embryos exhibit a pattern of apoptotic cell death which is spatially distinct from control embryos. These data support a critical role for C/EBPδ in numerous developmental processes, including promoting programmed cell death during development. Mutations in C/EBPδ have been implicated in the progression of human tumors, including those of myeloid, hepatocellular and breast cancers. Therefore, the C/EBPδ-overexpressing zebrafish will serve as a valuable model for examining the role of this gene during development, as a part of the cellular response to stress and in pathological states such as tumor progression. Close

• 78. [Article] Event Ecology: An Analysis of Discourses Surrounding the Disappearance of the Kah Shakes Cove Herring (Clupea pallasi)

  The conflict over the herring run at Kah Shakes is complicated. In 1991, the Alaska Department of Fish and Game (ADFG) expanded the commercial herring sac roe fishing boundary in the Revillagigedo Channel ...

  Citation × Citation Citation Abstract Copy Title: Event Ecology: An Analysis of Discourses Surrounding the Disappearance of the Kah Shakes Cove Herring (Clupea pallasi) Author: Hebert, Jamie Sue Year: 2011 The conflict over the herring run at Kah Shakes is complicated. In 1991, the Alaska Department of Fish and Game (ADFG) expanded the commercial herring sac roe fishing boundary in the Revillagigedo Channel to include Cat and Dog Islands. Native and non-Native local residents of Ketchikan protested the boundary expansion, as did managers of the neighboring Annette Island Fishery managed by the local reservation. Using cultural anthropological research methods that include ethnographic data, semi-structured, qualitative interviews gathered in southeast Alaska in 2008, and a comprehensive literature review of historic data culled from newspapers and other texts, I examine the many political factors that contribute to this conflict, including the contest between anecdotal and scientific data, the construction of fisheries management boundaries, and issues of collective memory. Using Vayda and Walters' event ecology methodology, bolstered by discourse analysis, I identify three discourses (local ecological knowledge, management and environmental). I use these discourses as comparative units to show that little coincident data can be identified between these discourses. I examine two areas of dissident data, stock definition and measures of abundance, and recommend that local ecological knowledge (LEK) be used to expand the scientific database on which current management techniques depend, to question the accuracy of current ADFG management boundaries and stock identification, and to recalibrate guideline harvest levels by exposing the effects of shifting baselines. I then outline how Geographic Information Systems (GIS) may assist in the validation and integration of LEK into the current fisheries management paradigm to create a more holistic narrative of ecological change. Title: Event Ecology: An Analysis of Discourses Surrounding the Disappearance of the Kah Shakes Cove Herring (Clupea pallasi) Author: Hebert, Jamie Sue Year: 2011 The conflict over the herring run at Kah Shakes is complicated. In 1991, the Alaska Department of Fish and Game (ADFG) expanded the commercial herring sac roe fishing boundary in the Revillagigedo Channel to include Cat and Dog Islands. Native and non-Native local residents of Ketchikan protested the boundary expansion, as did managers of the neighboring Annette Island Fishery managed by the local reservation. Using cultural anthropological research methods that include ethnographic data, semi-structured, qualitative interviews gathered in southeast Alaska in 2008, and a comprehensive literature review of historic data culled from newspapers and other texts, I examine the many political factors that contribute to this conflict, including the contest between anecdotal and scientific data, the construction of fisheries management boundaries, and issues of collective memory. Using Vayda and Walters' event ecology methodology, bolstered by discourse analysis, I identify three discourses (local ecological knowledge, management and environmental). I use these discourses as comparative units to show that little coincident data can be identified between these discourses. I examine two areas of dissident data, stock definition and measures of abundance, and recommend that local ecological knowledge (LEK) be used to expand the scientific database on which current management techniques depend, to question the accuracy of current ADFG management boundaries and stock identification, and to recalibrate guideline harvest levels by exposing the effects of shifting baselines. I then outline how Geographic Information Systems (GIS) may assist in the validation and integration of LEK into the current fisheries management paradigm to create a more holistic narrative of ecological change. Close

• 79. [Article] Engaging Recreational Fishers in Management and Conservation: Global Case Studies

  Globally, the number of recreational fishers is sizeable and increasing in many countries. Associated with this trend is the potential for negative impacts on fish stocks through exploitation or management ...

  Citation × Citation Citation Abstract Copy Title: Engaging Recreational Fishers in Management and Conservation: Global Case Studies Author: Granek, Elise F., Madin, Elizabeth M.P., Brown, M. A., Figueira, Will F., Cameron, Darren S., Hogan, Zeb, Kristianson, Gerry, de Villiers, Pierre, Williams, Jack E., Post, John R., Zahn, S., Arlinghaus, R. Year: 2008 Globally, the number of recreational fishers is sizeable and increasing in many countries. Associated with this trend is the potential for negative impacts on fish stocks through exploitation or management measures such as stocking and introduction of non-native fishes. Nevertheless, recreational fishers can be instrumental in successful fisheries conservation through active involvement in, or initiation of, conservation projects to reduce both direct and external stressors contributing to fishery declines. Understanding fishers’ concerns for sustained access to the resource and developing methods for their meaningful participation can have positive impacts on conservation efforts. We examined a suite of case studies that demonstrate successful involvement of recreational fishers in conservation and management activities that span developed and developing countries, temperate and tropical regions, marine and freshwater systems, and open- and closedaccess fisheries. To illustrate potential benefits and challenges of involving recreational fishers in fisheries management and conservation, we examined the socioeconomic and ecological contexts of each case study. We devised a conceptual framework for the engagement of recreational fishers that targets particular types of involvement (enforcement, advocacy, conservation, management design [type and location], research, and monitoring) on the basis of degree of stakeholder stewardship, scale of the fishery, and source of impacts (internal or external). These activities can be enhanced by incorporating local knowledge and traditions, taking advantage of leadership and regional networks, and creating collaborations among various stakeholder groups, scientists, and agencies to maximize the probability of recreational fisher involvement and project success. Title: Engaging Recreational Fishers in Management and Conservation: Global Case Studies Author: Granek, Elise F., Madin, Elizabeth M.P., Brown, M. A., Figueira, Will F., Cameron, Darren S., Hogan, Zeb, Kristianson, Gerry, de Villiers, Pierre, Williams, Jack E., Post, John R., Zahn, S., Arlinghaus, R. Year: 2008 Globally, the number of recreational fishers is sizeable and increasing in many countries. Associated with this trend is the potential for negative impacts on fish stocks through exploitation or management measures such as stocking and introduction of non-native fishes. Nevertheless, recreational fishers can be instrumental in successful fisheries conservation through active involvement in, or initiation of, conservation projects to reduce both direct and external stressors contributing to fishery declines. Understanding fishers’ concerns for sustained access to the resource and developing methods for their meaningful participation can have positive impacts on conservation efforts. We examined a suite of case studies that demonstrate successful involvement of recreational fishers in conservation and management activities that span developed and developing countries, temperate and tropical regions, marine and freshwater systems, and open- and closedaccess fisheries. To illustrate potential benefits and challenges of involving recreational fishers in fisheries management and conservation, we examined the socioeconomic and ecological contexts of each case study. We devised a conceptual framework for the engagement of recreational fishers that targets particular types of involvement (enforcement, advocacy, conservation, management design [type and location], research, and monitoring) on the basis of degree of stakeholder stewardship, scale of the fishery, and source of impacts (internal or external). These activities can be enhanced by incorporating local knowledge and traditions, taking advantage of leadership and regional networks, and creating collaborations among various stakeholder groups, scientists, and agencies to maximize the probability of recreational fisher involvement and project success. Close

• 80. [Article] Stranding Mortality Patterns in California Sea Lions and Steller Sea Lions in Oregon and Southern Washington, 2006 to 2014

  As changing ocean conditions lead to declining fish stocks and movement of forage fish, sea lions on the Oregon coast are subject to the pressures of declining prey availability and increasing conflicts ...

  Citation × Citation Citation Abstract Copy Title: Stranding Mortality Patterns in California Sea Lions and Steller Sea Lions in Oregon and Southern Washington, 2006 to 2014 Author: Lee, Kessina Year: 2016 As changing ocean conditions lead to declining fish stocks and movement of forage fish, sea lions on the Oregon coast are subject to the pressures of declining prey availability and increasing conflicts with commercial and recreational fisheries. An analysis of strandings of California sea lions, Zalophus californianus, and Steller sea lions, Eumetopias jubatus, from 2006 to 2014, included cause of death, changing ocean conditions, and anthropogenic activity. Causes of death included disease, injury, and human interaction, such as gunshot wounds, fisheries net entanglements and boat strikes. Oregon and Washington strandings of California sea lions are primarily adult and subadult males that migrate north from California rookeries, while Steller sea lions are year-round residents and strandings are comprised of males and females of all ages. While the California sea lion population is currently at or near carrying capacity, the Eastern Pacific population of Steller sea lions was designated as Threatened under the Endangered Species Act until October 2013. Understanding impacts to these two pinniped species is vital to implementing effective management and conservation policies. Oregon and southern Washington strandings of California sea lions and Steller sea lions from 2006 to 2014 were analyzed spatially using the geographic information system (GIS), and temporally to identify possible correlations with prey availability and human interaction. Strandings were found to follow seasonal patterns from year to year: Steller sea lion strandings were highest from May to July, California sea lions peaked in September, October, and November. There was a correlation between significantly high numbers of strandings and the three largest commercial fisheries in Oregon: Chinook salmon, Coho salmon, and Dungeness crab. This analysis provides a format for continuing to monitor primary ecological and anthropogenic drivers of pinniped mortality in Oregon and southern Washington. Title: Stranding Mortality Patterns in California Sea Lions and Steller Sea Lions in Oregon and Southern Washington, 2006 to 2014 Author: Lee, Kessina Year: 2016 As changing ocean conditions lead to declining fish stocks and movement of forage fish, sea lions on the Oregon coast are subject to the pressures of declining prey availability and increasing conflicts with commercial and recreational fisheries. An analysis of strandings of California sea lions, Zalophus californianus, and Steller sea lions, Eumetopias jubatus, from 2006 to 2014, included cause of death, changing ocean conditions, and anthropogenic activity. Causes of death included disease, injury, and human interaction, such as gunshot wounds, fisheries net entanglements and boat strikes. Oregon and Washington strandings of California sea lions are primarily adult and subadult males that migrate north from California rookeries, while Steller sea lions are year-round residents and strandings are comprised of males and females of all ages. While the California sea lion population is currently at or near carrying capacity, the Eastern Pacific population of Steller sea lions was designated as Threatened under the Endangered Species Act until October 2013. Understanding impacts to these two pinniped species is vital to implementing effective management and conservation policies. Oregon and southern Washington strandings of California sea lions and Steller sea lions from 2006 to 2014 were analyzed spatially using the geographic information system (GIS), and temporally to identify possible correlations with prey availability and human interaction. Strandings were found to follow seasonal patterns from year to year: Steller sea lion strandings were highest from May to July, California sea lions peaked in September, October, and November. There was a correlation between significantly high numbers of strandings and the three largest commercial fisheries in Oregon: Chinook salmon, Coho salmon, and Dungeness crab. This analysis provides a format for continuing to monitor primary ecological and anthropogenic drivers of pinniped mortality in Oregon and southern Washington. Close

• 81. [Article] A Statistical Investigation of Lower Columbia River Water Temperature, 1915-2003

  The Columbia River is home to anadromous salmon populations that migrate upriver every year to spawn. These fish require cool water temperatures (Tw) to survive. In recent years, high summer Tw in the ...

  Citation × Citation Citation Abstract Copy Title: A Statistical Investigation of Lower Columbia River Water Temperature, 1915-2003 Author: Overman, Corina Christina Mae Year: 2017 The Columbia River is home to anadromous salmon populations that migrate upriver every year to spawn. These fish require cool water temperatures (Tw) to survive. In recent years, high summer Tw in the Columbia River has caused increased mortality of salmon. Different possible explanations for increased Tw include climate change, deforestation, and decreased summertime streamflow (Q) due to dams. In this study, robust linear regression models of Tw based on air temperature (Ta) and Q were developed to examine the change in Tw over time. The data was separated into an historical period (1938-1956) and a modern period (1977-2003). Seasonal regression models were used for May through October (summer) and November through April (winter) for each period. Comparison of these models showed that Tw has become less sensitive to recent atmospheric heating and cooling. By contrast, analysis suggested that Tw has become more sensitive to variations in Q. Of the 1.5ºC increase in maximum summertime Tw, approximately 1.3ºC was due to dams and reservoir management based on changes in regression coefficients and average Q. A smaller, 0.2ºC change was estimated to be caused by increasing Ta since the mid-20th century. While average maximum Tw has increased, both the statistical model and data suggest that the variability in Tw from its climatological average has decreased, probably due to reservoir management. Title: A Statistical Investigation of Lower Columbia River Water Temperature, 1915-2003 Author: Overman, Corina Christina Mae Year: 2017 The Columbia River is home to anadromous salmon populations that migrate upriver every year to spawn. These fish require cool water temperatures (Tw) to survive. In recent years, high summer Tw in the Columbia River has caused increased mortality of salmon. Different possible explanations for increased Tw include climate change, deforestation, and decreased summertime streamflow (Q) due to dams. In this study, robust linear regression models of Tw based on air temperature (Ta) and Q were developed to examine the change in Tw over time. The data was separated into an historical period (1938-1956) and a modern period (1977-2003). Seasonal regression models were used for May through October (summer) and November through April (winter) for each period. Comparison of these models showed that Tw has become less sensitive to recent atmospheric heating and cooling. By contrast, analysis suggested that Tw has become more sensitive to variations in Q. Of the 1.5ºC increase in maximum summertime Tw, approximately 1.3ºC was due to dams and reservoir management based on changes in regression coefficients and average Q. A smaller, 0.2ºC change was estimated to be caused by increasing Ta since the mid-20th century. While average maximum Tw has increased, both the statistical model and data suggest that the variability in Tw from its climatological average has decreased, probably due to reservoir management. Close

• 82. [Article] A Metabolic Hypothesis for the Evolution of Temperature Effects on the Arterial PCO2 and pH of Vertebrate Ectotherms

  Body temperature increases in ectothermic vertebrates characteristically lead to both increases in arterial PCO2 (PaCO2) and declines in resting arterial pH (pHa) of about 0.017 pH units/°C increase in ...

  Citation × Citation Citation Abstract Copy Title: A Metabolic Hypothesis for the Evolution of Temperature Effects on the Arterial PCO2 and pH of Vertebrate Ectotherms Author: Hillman, Stanley S., Hedrick, Michael Scott Year: 2017 Body temperature increases in ectothermic vertebrates characteristically lead to both increases in arterial PCO2 (PaCO2) and declines in resting arterial pH (pHa) of about 0.017 pH units/°C increase in temperature. This ‘alphastat’ pH pattern has previously been interpreted as being evolutionarily-driven by the maintenance of a constant protonation state on the imidazole moiety of histidine protein residues, hence stabilizing protein structure-function. Analysis of the existing data for interclass responses of ectothermic vertebrates show different degrees of PaCO2 increases and pH declines with temperature between the classes with reptiles>amphibians>fish. The PaCO2 at the temperature where maximal aerobic metabolism (VO2max) is achieved is significantly and positively correlated with temperature for all vertebrate classes. For ectotherms, the PaCO2 where VO2max is greatest is also correlated with VO2max indicating there is an increased driving force for CO2 efflux that is lowest in fish, intermediate in amphibians and highest in reptiles. The pattern of increased PaCO2 and the resultant reduction of pHa to increased body temperature would serve to increase CO2 efflux, O2 delivery, blood buffering capacity and maintain ventilatory scope. This represents a new hypothesis for the selective advantage of arterial pH regulation from a systems physiology perspective in addition to the advantages of maintenance of protein structure-function. Title: A Metabolic Hypothesis for the Evolution of Temperature Effects on the Arterial PCO2 and pH of Vertebrate Ectotherms Author: Hillman, Stanley S., Hedrick, Michael Scott Year: 2017 Body temperature increases in ectothermic vertebrates characteristically lead to both increases in arterial PCO2 (PaCO2) and declines in resting arterial pH (pHa) of about 0.017 pH units/°C increase in temperature. This ‘alphastat’ pH pattern has previously been interpreted as being evolutionarily-driven by the maintenance of a constant protonation state on the imidazole moiety of histidine protein residues, hence stabilizing protein structure-function. Analysis of the existing data for interclass responses of ectothermic vertebrates show different degrees of PaCO2 increases and pH declines with temperature between the classes with reptiles>amphibians>fish. The PaCO2 at the temperature where maximal aerobic metabolism (VO2max) is achieved is significantly and positively correlated with temperature for all vertebrate classes. For ectotherms, the PaCO2 where VO2max is greatest is also correlated with VO2max indicating there is an increased driving force for CO2 efflux that is lowest in fish, intermediate in amphibians and highest in reptiles. The pattern of increased PaCO2 and the resultant reduction of pHa to increased body temperature would serve to increase CO2 efflux, O2 delivery, blood buffering capacity and maintain ventilatory scope. This represents a new hypothesis for the selective advantage of arterial pH regulation from a systems physiology perspective in addition to the advantages of maintenance of protein structure-function. Close

• 83. [Article] Aquatic Vegetation in Irrigation Canals

  Preparation of this guidance manual for integrated aquatic vegetation management in irrigation canals was stimulated, in large part, by the accidental release of acrolein-treated irrigation water into ...

  Citation × Citation Citation Abstract Copy Title: Aquatic Vegetation in Irrigation Canals Author: Sytsma, Mark, Parker, Michael Year: 1999 Preparation of this guidance manual for integrated aquatic vegetation management in irrigation canals was stimulated, in large part, by the accidental release of acrolein-treated irrigation water into Bear Creek in southern Oregon. The resulting fish kill brought into focus the need to examine the methods available for managing aquatic vegetation in flowing water. Furthermore, it demonstrated the need for technical assistance on aquatic vegetation management in Oregon. Vegetation management in flowing water is a difficult undertaking. The interconnectedness of natural and manmade water conveyance systems, the tenuous status of many aquatic species, and the necessity of water delivery for profitable and productive agriculture in Oregon and much of the Northwest interact to focus attention on the way that aquatic vegetation management is conducted. Endangerment of fish species in the Pacific Northwest requires a detailed examination of agricultural operations. This manual is intended to provide water conveyance system managers a summary of available technologies for aquatic vegetation management and to outline the concepts and procedures necessary for development of an integrated management plan for vegetation growing in canals. With the adoption of a thoughtful approach to aquatic vegetation management, and with technical assistance and research on the problem plants and control techniques, aquatic vegetation can be managed without severe off-site and non-target impacts. It is hoped that this manual will assist in reaching that goal. Title: Aquatic Vegetation in Irrigation Canals Author: Sytsma, Mark, Parker, Michael Year: 1999 Preparation of this guidance manual for integrated aquatic vegetation management in irrigation canals was stimulated, in large part, by the accidental release of acrolein-treated irrigation water into Bear Creek in southern Oregon. The resulting fish kill brought into focus the need to examine the methods available for managing aquatic vegetation in flowing water. Furthermore, it demonstrated the need for technical assistance on aquatic vegetation management in Oregon. Vegetation management in flowing water is a difficult undertaking. The interconnectedness of natural and manmade water conveyance systems, the tenuous status of many aquatic species, and the necessity of water delivery for profitable and productive agriculture in Oregon and much of the Northwest interact to focus attention on the way that aquatic vegetation management is conducted. Endangerment of fish species in the Pacific Northwest requires a detailed examination of agricultural operations. This manual is intended to provide water conveyance system managers a summary of available technologies for aquatic vegetation management and to outline the concepts and procedures necessary for development of an integrated management plan for vegetation growing in canals. With the adoption of a thoughtful approach to aquatic vegetation management, and with technical assistance and research on the problem plants and control techniques, aquatic vegetation can be managed without severe off-site and non-target impacts. It is hoped that this manual will assist in reaching that goal. Close

• 84. [Article] Assessing Reproducibility in Faunal Analysis Using Blind Tests: A case Study From Northwestern North America

  Zooarchaeologists have long recognized that assigning taxonomic identifications to animal remains is a subjective process, and recent studies have highlighted the need for data quality assurance standards ...

  Citation × Citation Citation Abstract Copy Title: Assessing Reproducibility in Faunal Analysis Using Blind Tests: A case Study From Northwestern North America Author: Nims, Reno, Butler, Virginia L. Year: 2017 Zooarchaeologists have long recognized that assigning taxonomic identifications to animal remains is a subjective process, and recent studies have highlighted the need for data quality assurance standards in archaeofaunal research. Our study contributes to this growing interest in quality assurance by presenting simple quantitative methods for assessing the reproducibility of analytic results through blind reanalysis of animal remains that we developed during analysis of fishbone from Čḯxwicən, a large Native American village on the coast of Washington State, U.S.A. Given the large scale of the Čḯxwicən project – over 112,000 fish remains were documented by five different analysts over three years – there was a real possibility that inconsistencies in laboratory practices affected analytic results (e.g., number of identified specimens, taxa present and relative abundance, elements identified, burning frequencies). To evaluate the reproducibility of the Čḯxwicən fishbone data, and the possibility of “protocol drift” – changes in how specimens and bone modifications were identified over the course of analysis – we reanalyzed samples of fish remains that were previously documented during three discrete stages (beginning, middle, and end) of the Čḯxwicən project. The original data and the reanalysis results show close agreement in each stage, with only minor differences in the numbers of recorded specimens, taxonomic representation at family- and finer taxonomic levels, and body part representation assessed for a single taxonomic order. Identifying burning on bone was not very reproducible. Reproducibility studies such as this are useful for highlighting ambiguous identification criteria (e.g., in taxonomic assignment, bone modification), and could stimulate dialog among researchers about ways to address such issues in future studies. Increasing the implementation of these, and other, widely applicable methods should improve zooarchaeological data quality and stimulate further research on quality assurance in archaeology overall. Title: Assessing Reproducibility in Faunal Analysis Using Blind Tests: A case Study From Northwestern North America Author: Nims, Reno, Butler, Virginia L. Year: 2017 Zooarchaeologists have long recognized that assigning taxonomic identifications to animal remains is a subjective process, and recent studies have highlighted the need for data quality assurance standards in archaeofaunal research. Our study contributes to this growing interest in quality assurance by presenting simple quantitative methods for assessing the reproducibility of analytic results through blind reanalysis of animal remains that we developed during analysis of fishbone from Čḯxwicən, a large Native American village on the coast of Washington State, U.S.A. Given the large scale of the Čḯxwicən project – over 112,000 fish remains were documented by five different analysts over three years – there was a real possibility that inconsistencies in laboratory practices affected analytic results (e.g., number of identified specimens, taxa present and relative abundance, elements identified, burning frequencies). To evaluate the reproducibility of the Čḯxwicən fishbone data, and the possibility of “protocol drift” – changes in how specimens and bone modifications were identified over the course of analysis – we reanalyzed samples of fish remains that were previously documented during three discrete stages (beginning, middle, and end) of the Čḯxwicən project. The original data and the reanalysis results show close agreement in each stage, with only minor differences in the numbers of recorded specimens, taxonomic representation at family- and finer taxonomic levels, and body part representation assessed for a single taxonomic order. Identifying burning on bone was not very reproducible. Reproducibility studies such as this are useful for highlighting ambiguous identification criteria (e.g., in taxonomic assignment, bone modification), and could stimulate dialog among researchers about ways to address such issues in future studies. Increasing the implementation of these, and other, widely applicable methods should improve zooarchaeological data quality and stimulate further research on quality assurance in archaeology overall. Close

• 85. [Article] Euryhelmis cotti N. Sp. (Trematoda: Heterophyidae) with observations on its life cycle

  Fish of the genus Cottus were found infected with heterophyid metacercariae. Laboratory animals were infected with the metacercariae, and adult heterophid trematodes were recovered. These flukes were found ...

  Citation × Citation Citation Abstract Copy Title: Euryhelmis cotti N. Sp. (Trematoda: Heterophyidae) with observations on its life cycle Author: Simon, Michael Joseph Year: 1972 Fish of the genus Cottus were found infected with heterophyid metacercariae. Laboratory animals were infected with the metacercariae, and adult heterophid trematodes were recovered. These flukes were found to represent an undescribed species of the genus Euryhelmis. Various streams in the Willamette Valley and coastal areas were sampled for infected Cottus sp. Snails of the genera Oxytrema and Fluminicola were collected. Several possible definitive hosts were examined. A partial review of the subfamily Apophallinae and a complete review of the genus Euryhelmis are presented. Euryhelmis cotti n. sp. is placed in the subfamily Apophallinae, and its life cycle is partially described. Title: Euryhelmis cotti N. Sp. (Trematoda: Heterophyidae) with observations on its life cycle Author: Simon, Michael Joseph Year: 1972 Fish of the genus Cottus were found infected with heterophyid metacercariae. Laboratory animals were infected with the metacercariae, and adult heterophid trematodes were recovered. These flukes were found to represent an undescribed species of the genus Euryhelmis. Various streams in the Willamette Valley and coastal areas were sampled for infected Cottus sp. Snails of the genera Oxytrema and Fluminicola were collected. Several possible definitive hosts were examined. A partial review of the subfamily Apophallinae and a complete review of the genus Euryhelmis are presented. Euryhelmis cotti n. sp. is placed in the subfamily Apophallinae, and its life cycle is partially described. Close

• 86. [Article] Multiplex SNP Discrimination

  Multiplex hybridization reactions of perfectly matched duplexes and duplexes containing a single basepair mismatch (SNPs) were investigated on DNA microarrays. Effects of duplex length, G-C percentage, ...

  Citation × Citation Citation Abstract Copy Title: Multiplex SNP Discrimination Author: Fish, Daniel J., Horne, M. Todd, Searles, Robert P., Brewood, Greg P., Benight, Albert S. Year: 2007 Multiplex hybridization reactions of perfectly matched duplexes and duplexes containing a single basepair mismatch (SNPs) were investigated on DNA microarrays. Effects of duplex length, G-C percentage, and relative position of the SNP on duplex hybridization and SNP resolution were determined. Our theoretical model of multiplex hybridization accurately predicts observed results and implicates target concentration as a critical variable in multiplex SNP detection. Title: Multiplex SNP Discrimination Author: Fish, Daniel J., Horne, M. Todd, Searles, Robert P., Brewood, Greg P., Benight, Albert S. Year: 2007 Multiplex hybridization reactions of perfectly matched duplexes and duplexes containing a single basepair mismatch (SNPs) were investigated on DNA microarrays. Effects of duplex length, G-C percentage, and relative position of the SNP on duplex hybridization and SNP resolution were determined. Our theoretical model of multiplex hybridization accurately predicts observed results and implicates target concentration as a critical variable in multiplex SNP detection. Close

• 87. [Article] Alaska Aquatic Plant Survey Report 2005

  Invasive, non-indigenous plants can degrade water quality and fish habitat when they invade lakes, ponds, and streams. Changes in plant community architecture in lakes due to invasion by canopy-forming ...

  Citation × Citation Citation Abstract Copy Title: Alaska Aquatic Plant Survey Report 2005 Author: Pfauth, Mary, Sytsma, Mark Year: 2005 Invasive, non-indigenous plants can degrade water quality and fish habitat when they invade lakes, ponds, and streams. Changes in plant community architecture in lakes due to invasion by canopy-forming invasive aquatic plants can result in loss of native plant biodiversity and reduction of the structural complexity of the underwater habitat. Title: Alaska Aquatic Plant Survey Report 2005 Author: Pfauth, Mary, Sytsma, Mark Year: 2005 Invasive, non-indigenous plants can degrade water quality and fish habitat when they invade lakes, ponds, and streams. Changes in plant community architecture in lakes due to invasion by canopy-forming invasive aquatic plants can result in loss of native plant biodiversity and reduction of the structural complexity of the underwater habitat. Close

• 88. [Article] Final Coastal Lakes Aquatic Plant Survey Report

  Invasive, non-indigenous plants can degrade water quality and fish habitat when they invade lakes, ponds, and streams. Changes in plant community architecture in lakes due to invasion by canopy-forming ...

  Citation × Citation Citation Abstract Copy Title: Final Coastal Lakes Aquatic Plant Survey Report Author: Pfauth, Mary, Sytsma, Mark Year: 2013 Invasive, non-indigenous plants can degrade water quality and fish habitat when they invade lakes, ponds, and streams. Changes in plant community architecture in lakes due to invasion by canopy-forming invasive aquatic plants can result in loss of native plant biodiversity and reduction of the structural complexity of the underwater habitat. Title: Final Coastal Lakes Aquatic Plant Survey Report Author: Pfauth, Mary, Sytsma, Mark Year: 2013 Invasive, non-indigenous plants can degrade water quality and fish habitat when they invade lakes, ponds, and streams. Changes in plant community architecture in lakes due to invasion by canopy-forming invasive aquatic plants can result in loss of native plant biodiversity and reduction of the structural complexity of the underwater habitat. Close

• 89. [Article] Saving the Yellowstone

  The Yellowstone River remains the only major free-flowing stream in the lower 48 states. Defenders of free-flowing status argue that benefits derived from maintaining the historic river surpass those gained ...

  Citation × Citation Citation Abstract Copy Title: Saving the Yellowstone Author: Lang, William L. Year: 1985 The Yellowstone River remains the only major free-flowing stream in the lower 48 states. Defenders of free-flowing status argue that benefits derived from maintaining the historic river surpass those gained through dams. The 1973 Montana Water Use Act placed water allocation in the state's hands, and the 1974 Yellowstone Moratorium gave the state three years to determine the Yellowstone's future. The Montana Fish and Game Department requested maintenance of the instream flow to protect the fisheries and the river, and the state Natural Resources board partially granted the request, thereby preventing dams on the Yellowstone. Title: Saving the Yellowstone Author: Lang, William L. Year: 1985 The Yellowstone River remains the only major free-flowing stream in the lower 48 states. Defenders of free-flowing status argue that benefits derived from maintaining the historic river surpass those gained through dams. The 1973 Montana Water Use Act placed water allocation in the state's hands, and the 1974 Yellowstone Moratorium gave the state three years to determine the Yellowstone's future. The Montana Fish and Game Department requested maintenance of the instream flow to protect the fisheries and the river, and the state Natural Resources board partially granted the request, thereby preventing dams on the Yellowstone. Close

• 90. [Article] The Mechanics of Flycasting: The Flyline

  In order to propel a fishing fly through the air toward the distant quarry, a rather massive line, to which the fly is attached, is cast. As the cast line rolls out, the fly actually accelerates horizontally ...

  Citation × Citation Citation Abstract Copy Title: The Mechanics of Flycasting: The Flyline Author: Spolek, Graig A. Year: 1986 In order to propel a fishing fly through the air toward the distant quarry, a rather massive line, to which the fly is attached, is cast. As the cast line rolls out, the fly actually accelerates horizontally and seems to defy physical law. The phenomenon is modeled simplistically to determine the magnitude of this effect. In the absence of air drag, the fly can accelerate to increase its velocity by an order of magnitude. Air friction dramatically decreases the effect, but some fly accelerationis still predicted. By tapering the flyline in various ways, the fly velocity history can be significantly modified, and some tapers are predicted to perform better than others. Title: The Mechanics of Flycasting: The Flyline Author: Spolek, Graig A. Year: 1986 In order to propel a fishing fly through the air toward the distant quarry, a rather massive line, to which the fly is attached, is cast. As the cast line rolls out, the fly actually accelerates horizontally and seems to defy physical law. The phenomenon is modeled simplistically to determine the magnitude of this effect. In the absence of air drag, the fly can accelerate to increase its velocity by an order of magnitude. Air friction dramatically decreases the effect, but some fly accelerationis still predicted. By tapering the flyline in various ways, the fly velocity history can be significantly modified, and some tapers are predicted to perform better than others. Close

• 91. [Article] Coastal Lakes Aquatic Plant Survey Report

  Invasive, non-indigenous plants can degrade water quality and fish habitat when they invade lakes, ponds, and streams. Changes in plant community architecture in lakes due to invasion by canopy-forming ...

  Citation × Citation Citation Abstract Copy Title: Coastal Lakes Aquatic Plant Survey Report Author: Pfauth, Mary, Sytsma, Mark Year: 2004 Invasive, non-indigenous plants can degrade water quality and fish habitat when they invade lakes, ponds, and streams. Changes in plant community architecture in lakes due to invasion by canopy-forming invasive aquatic plants can result in loss of native plant biodiversity and reduction of the structural complexity of the underwater habitat. Differences in photosynthetic biochemistry between non-indigenous and native plants can result in large diurnal pH and dissolved oxygen concentrations. Title: Coastal Lakes Aquatic Plant Survey Report Author: Pfauth, Mary, Sytsma, Mark Year: 2004 Invasive, non-indigenous plants can degrade water quality and fish habitat when they invade lakes, ponds, and streams. Changes in plant community architecture in lakes due to invasion by canopy-forming invasive aquatic plants can result in loss of native plant biodiversity and reduction of the structural complexity of the underwater habitat. Differences in photosynthetic biochemistry between non-indigenous and native plants can result in large diurnal pH and dissolved oxygen concentrations. Close

• 92. [Article] Emerging Contaminants in Oregon Coastal Waters: Hotspots, Landscape Drivers and Synergistic Effects on Bivalves

  This presentation focuses on the following research questions: Types and levels of contaminants of emerging concern (CECs) in Oregon’s coastal ocean? Levels of CECs in native and commercial oysters? ...

  Citation × Citation Citation Abstract Copy Title: Emerging Contaminants in Oregon Coastal Waters: Hotspots, Landscape Drivers and Synergistic Effects on Bivalves Author: Granek, Elise F., Fish, William, Strecker, Angela L. Year: 2013 This presentation focuses on the following research questions: Types and levels of contaminants of emerging concern (CECs) in Oregon’s coastal ocean? Levels of CECs in native and commercial oysters? Ecological effects (growth, reproductive output, etc.) of these contaminants in marine bivalves? Title: Emerging Contaminants in Oregon Coastal Waters: Hotspots, Landscape Drivers and Synergistic Effects on Bivalves Author: Granek, Elise F., Fish, William, Strecker, Angela L. Year: 2013 This presentation focuses on the following research questions: Types and levels of contaminants of emerging concern (CECs) in Oregon’s coastal ocean? Levels of CECs in native and commercial oysters? Ecological effects (growth, reproductive output, etc.) of these contaminants in marine bivalves? Close

• 93. [Article] Fostering Intelligent Moderation in the Next Generation: Insights from Remida-Inspired Reuse Materials Education

  Ecologically minded leaders and early childhood teacher educators offer a culturally significant shiny fish project in their community as a way to launch an environmental-material reuse project. Questioning ...

  Citation × Citation Citation Abstract Copy Title: Fostering Intelligent Moderation in the Next Generation: Insights from Remida-Inspired Reuse Materials Education Author: Parnell, William A., Downs, Christine, Cullen, Julianne Year: 2017 Ecologically minded leaders and early childhood teacher educators offer a culturally significant shiny fish project in their community as a way to launch an environmental-material reuse project. Questioning if environmental collapse is imminent, their project investigation of developing a locally relevant Remida Reggio-inspired center serves as hope for reconceptualizing early childhood practices, offering innovations, and fostering intelligent moderation of earthly resources. Finding widening circles of influence and engaging participants are key to nurturing hope, and these educators draw implications to manifest a large and impactful vision and call to action. Title: Fostering Intelligent Moderation in the Next Generation: Insights from Remida-Inspired Reuse Materials Education Author: Parnell, William A., Downs, Christine, Cullen, Julianne Year: 2017 Ecologically minded leaders and early childhood teacher educators offer a culturally significant shiny fish project in their community as a way to launch an environmental-material reuse project. Questioning if environmental collapse is imminent, their project investigation of developing a locally relevant Remida Reggio-inspired center serves as hope for reconceptualizing early childhood practices, offering innovations, and fostering intelligent moderation of earthly resources. Finding widening circles of influence and engaging participants are key to nurturing hope, and these educators draw implications to manifest a large and impactful vision and call to action. Close

• 94. [Article] Stream Temperature Management in the Tualatin Watershed: Is it Improving Salmonid Habitat?

  The purpose of this paper is to examine the literature from scientific and governmental entities that describes the problems with elevated stream temperatures in the Tualatin basin, the actions being taken ...

  Citation × Citation Citation Abstract Copy Title: Stream Temperature Management in the Tualatin Watershed: Is it Improving Salmonid Habitat? Author: Hennings, Raymond Banks Year: 2014 The purpose of this paper is to examine the literature from scientific and governmental entities that describes the problems with elevated stream temperatures in the Tualatin basin, the actions being taken to resolve those problems, and to assess whether these actions are meeting the goal of improving salmonid habitat in the basin. Elevated stream temperatures are considered a pollutant under the US Clean Water Act (Clean Water Act 1972, as amended) because increased stream temperatures can be harmful to native aquatic biota, particularly salmonid fish species that have evolved to use cold water (IMST 2004). Title: Stream Temperature Management in the Tualatin Watershed: Is it Improving Salmonid Habitat? Author: Hennings, Raymond Banks Year: 2014 The purpose of this paper is to examine the literature from scientific and governmental entities that describes the problems with elevated stream temperatures in the Tualatin basin, the actions being taken to resolve those problems, and to assess whether these actions are meeting the goal of improving salmonid habitat in the basin. Elevated stream temperatures are considered a pollutant under the US Clean Water Act (Clean Water Act 1972, as amended) because increased stream temperatures can be harmful to native aquatic biota, particularly salmonid fish species that have evolved to use cold water (IMST 2004). Close

• 95. [Article] Album 1, Photo #25

  Fishing outing

  Citation × Citation Citation Abstract Copy Title: Album 1, Photo #25 Author: Watson, Edward Year: 1916 Fishing outing Title: Album 1, Photo #25 Author: Watson, Edward Year: 1916 Fishing outing Close

• 96. [Article] Cascades Island Lamprey Passage Structure: Evaluating Passage and Migration Following Structure Modifications

  Pacific lamprey (Entosphenus tridentatus), an endemic species to the Columbia River Basin, U.S.A, has experienced staggering decreases in returns to spawning territories in recent decades. As lamprey are ...

  Citation × Citation Citation Abstract Copy Title: Cascades Island Lamprey Passage Structure: Evaluating Passage and Migration Following Structure Modifications Author: Lopez-Johnston, Siena Marie Year: 2014 Pacific lamprey (Entosphenus tridentatus), an endemic species to the Columbia River Basin, U.S.A, has experienced staggering decreases in returns to spawning territories in recent decades. As lamprey are threatened severely by a lack of passage at mainstem dams, lamprey specific passage structures have been designed and constructed to address the problem. The Cascades Island Lamprey Passage Structure (LPS) at Bonneville Dam is the longest and steepest structure of its type, following the addition of an exit pipe which allows lampreys to travel from the tailrace of the dam to the forebay. The intent of this study was to assess lamprey use of the structure and whether the structure hinders lamprey migration to subsequent dams. The study was carried out during the 2013 migration season. The study used three different treatment groups of lampreys released on five dates spanning the migration season (n=75 lamprey). Two of these groups (n=50), with different tagging methods, were released directly into the LPS to assess passage success, travel time, and tagging effect. The third group (n=25) was released into the forebay to test whether the structure impedes migration upstream. Fish were monitored via receiver arrays on the LPS and at dams on the river system. Overall passage efficiency was 74% (37 of 50 used the CI LPS successfully). Mean travel time to navigate the structure was 12 h. Fish size had no significant effect on travel time in the LPS. Water temperature had a significant effect on travel time in the LPS. There was no statistically significant effect of tagging on passage efficiency or travel time. The groups that used the LPS performed slightly better migrating upstream to the next dam than the group that bypassed the structure, but the difference was not significant. The groups that used the LPS traveled to more subsequent dams upstream than did the group that bypassed the LPS. It can be concluded that lamprey passed the structure successfully. Temperature (proxy for seasonality) had an effect on travel time in the LPS; however fish size and tagging had no effect. The LPS does not affect the ability of migrating lampreys to continue migration to subsequent dams. Such findings have important implications for management of lamprey in the region. Title: Cascades Island Lamprey Passage Structure: Evaluating Passage and Migration Following Structure Modifications Author: Lopez-Johnston, Siena Marie Year: 2014 Pacific lamprey (Entosphenus tridentatus), an endemic species to the Columbia River Basin, U.S.A, has experienced staggering decreases in returns to spawning territories in recent decades. As lamprey are threatened severely by a lack of passage at mainstem dams, lamprey specific passage structures have been designed and constructed to address the problem. The Cascades Island Lamprey Passage Structure (LPS) at Bonneville Dam is the longest and steepest structure of its type, following the addition of an exit pipe which allows lampreys to travel from the tailrace of the dam to the forebay. The intent of this study was to assess lamprey use of the structure and whether the structure hinders lamprey migration to subsequent dams. The study was carried out during the 2013 migration season. The study used three different treatment groups of lampreys released on five dates spanning the migration season (n=75 lamprey). Two of these groups (n=50), with different tagging methods, were released directly into the LPS to assess passage success, travel time, and tagging effect. The third group (n=25) was released into the forebay to test whether the structure impedes migration upstream. Fish were monitored via receiver arrays on the LPS and at dams on the river system. Overall passage efficiency was 74% (37 of 50 used the CI LPS successfully). Mean travel time to navigate the structure was 12 h. Fish size had no significant effect on travel time in the LPS. Water temperature had a significant effect on travel time in the LPS. There was no statistically significant effect of tagging on passage efficiency or travel time. The groups that used the LPS performed slightly better migrating upstream to the next dam than the group that bypassed the structure, but the difference was not significant. The groups that used the LPS traveled to more subsequent dams upstream than did the group that bypassed the LPS. It can be concluded that lamprey passed the structure successfully. Temperature (proxy for seasonality) had an effect on travel time in the LPS; however fish size and tagging had no effect. The LPS does not affect the ability of migrating lampreys to continue migration to subsequent dams. Such findings have important implications for management of lamprey in the region. Close

• 97. [Article] The Spatial Distribution of Ground Stone Tools as a Marker of Status Differentials in a Chinookan Plank House on the Lower Columbia River

  Social status was an integral part of the social structure of Northwest Coast societies. The presence of ranked social structures and household space based on rank is reported in the ethnographic literature. ...

  Citation × Citation Citation Abstract Copy Title: The Spatial Distribution of Ground Stone Tools as a Marker of Status Differentials in a Chinookan Plank House on the Lower Columbia River Author: Wolf, John William Year: 1994 Social status was an integral part of the social structure of Northwest Coast societies. The presence of ranked social structures and household space based on rank is reported in the ethnographic literature. Archaeologists have long searched for independent and verifiable means to infer social structure from archaeological deposits. Burial goods have been used to identify status differences. Do other items of material culture also reflect such differences? The purpose of this study was to ascertain whether or not the distribution of certain tools recovered from a Chinookan plank house on the lower Columbia River paralleled the household residence location that was keyed to social status. Among Northwest Coast societies the household was the basic social and economic unit. Ground stone tools were selected for study because they include tools which were instrumental parts of a technology that depended upon highly organized and scheduled activities, i.e. fishing and house construction. If these tools were controlled by particular individuals or families within the household, their archaeological deposition might reflect social status differences. Two questions were asked in this study. (1) What is the correlation between the volume of sediment excavated and the number of ground stone artifacts recovered from the house? (2) What is the relationship between residence location and the density of ground stone artifacts recovered from the house? The ground stone artifacts were identified, classified and counted. Correlation coefficients between the volumes of sediment excavated and the number of ground stone artifacts recovered showed that the correlation was suspiciously weak, in general, and not correlated for fishing net weights. Some factor other than solely excavation volumes was affecting ground stone artifact counts. To answer the second question linear regressions were performed. They revealed that although location was to some degree a function of the density of ground stone artifacts, that relationship was weak at the .05 significance level. However, the relationship was stronger for fishing net weights. It is likely that there are multiple reasons for ground stone tool distributions and sites must be excavated with broad exposures in order to understand the relationship between residence location and artifact densities. Title: The Spatial Distribution of Ground Stone Tools as a Marker of Status Differentials in a Chinookan Plank House on the Lower Columbia River Author: Wolf, John William Year: 1994 Social status was an integral part of the social structure of Northwest Coast societies. The presence of ranked social structures and household space based on rank is reported in the ethnographic literature. Archaeologists have long searched for independent and verifiable means to infer social structure from archaeological deposits. Burial goods have been used to identify status differences. Do other items of material culture also reflect such differences? The purpose of this study was to ascertain whether or not the distribution of certain tools recovered from a Chinookan plank house on the lower Columbia River paralleled the household residence location that was keyed to social status. Among Northwest Coast societies the household was the basic social and economic unit. Ground stone tools were selected for study because they include tools which were instrumental parts of a technology that depended upon highly organized and scheduled activities, i.e. fishing and house construction. If these tools were controlled by particular individuals or families within the household, their archaeological deposition might reflect social status differences. Two questions were asked in this study. (1) What is the correlation between the volume of sediment excavated and the number of ground stone artifacts recovered from the house? (2) What is the relationship between residence location and the density of ground stone artifacts recovered from the house? The ground stone artifacts were identified, classified and counted. Correlation coefficients between the volumes of sediment excavated and the number of ground stone artifacts recovered showed that the correlation was suspiciously weak, in general, and not correlated for fishing net weights. Some factor other than solely excavation volumes was affecting ground stone artifact counts. To answer the second question linear regressions were performed. They revealed that although location was to some degree a function of the density of ground stone artifacts, that relationship was weak at the .05 significance level. However, the relationship was stronger for fishing net weights. It is likely that there are multiple reasons for ground stone tool distributions and sites must be excavated with broad exposures in order to understand the relationship between residence location and artifact densities. Close

• 98. [Article] Age Determination of Modern and Archaeological Chinook Salmon (Oncorhynchus tshawytcha) Using Vertebrae

  Incremental growth rings in X-rays of salmon vertebrae have been used since the 1980s to age Pacific salmon (Oncorhynchus spp.) remains from archaeological sites in the Pacific Northwest. These age estimates, ...

  Citation × Citation Citation Abstract Copy Title: Age Determination of Modern and Archaeological Chinook Salmon (Oncorhynchus tshawytcha) Using Vertebrae Author: Hofkamp, Anthony Raymond Year: 2015 Incremental growth rings in X-rays of salmon vertebrae have been used since the 1980s to age Pacific salmon (Oncorhynchus spp.) remains from archaeological sites in the Pacific Northwest. These age estimates, paired with generalized life history patterns, have been used to determine salmon species, season of capture and in turn season of site occupation. This approach relies on a variety of assumptions, the most fundamental of which is that rings represent true years. Archaeologists using vertebral age determination techniques have failed to adequately test this assumption and present their methodologies. This thesis assesses the validity of using incremental growth structures in Chinook salmon (Oncorhynchus tshawytscha) vertebrae to determine the age at death of fish represented in archaeological sites. This project develops criteria and a protocol for the identification of true annuli and tests these identifications on a collection of modern Chinook salmon of known age. Finally, this protocol is applied to archaeological remains of Chinook from Cathlapotle (45CL1). Three collections of modern known age fish (N=121) were used to evaluate and test approaches to aging Chinook salmon with vertebrae. These collections contained juvenile and adult Chinook from throughout Washington and Oregon. I evaluated a variety of methods for viewing rings including magnified surface images, X-ray images and thin sections to determine which is the most accurate, reliable and efficient, also considering the extent of specimen destruction. Rings visible in X-rays were found to reflect the internal structure of vertebrae rather than annular growth. The number of these internal walls did not correspond to the known ages of fish and are therefore not true annuli. Criteria previously described by salmon fisheries biologist were used to isolate annuli (on the centrum surface) on the Hanford reach collection (N=46). In a test for accuracy 39 (85%) were aged correctly. In a test of reliability utilizing five additional readers all but 14 cases showed discrepancies among readers. Results of the test of reliability were not as successful as other researchers in fisheries biology but given the high accuracy rate the method remains valid. The final goal of this project was to determine the feasibility of applying the surface ring method of age determination to archaeological collections. Archaeological salmon vertebrae from Cathlapotle (45CL1) on the lower Columbia River, Washington state were utilized. One hundred salmon vertebrae were selected and classified to species according to Huber et al. (2011); 89 were identified as Chinook. Of these, 39 had sufficient preservation of the surface to view and interpret incremental rings. Three ages were identified 3, 4 and 5 year olds. This ageing protocol can be applied to archaeological Chinook salmon vertebrae to estimate age of ancient Chinook salmon. Additional work is needed on other salmon species to demonstrate the methods validity across all salmonid species. This analysis has great potential for modeling salmon paleo-life history by contributing data from salmon populations prior to the major impacts of the 19th and 20th century. This is particularly valuable for salmon conservation because information on size, the timing and duration of freshwater emigration as well as the age of spawning and death is critical to the management of hatchery and wild salmon populations. Title: Age Determination of Modern and Archaeological Chinook Salmon (Oncorhynchus tshawytcha) Using Vertebrae Author: Hofkamp, Anthony Raymond Year: 2015 Incremental growth rings in X-rays of salmon vertebrae have been used since the 1980s to age Pacific salmon (Oncorhynchus spp.) remains from archaeological sites in the Pacific Northwest. These age estimates, paired with generalized life history patterns, have been used to determine salmon species, season of capture and in turn season of site occupation. This approach relies on a variety of assumptions, the most fundamental of which is that rings represent true years. Archaeologists using vertebral age determination techniques have failed to adequately test this assumption and present their methodologies. This thesis assesses the validity of using incremental growth structures in Chinook salmon (Oncorhynchus tshawytscha) vertebrae to determine the age at death of fish represented in archaeological sites. This project develops criteria and a protocol for the identification of true annuli and tests these identifications on a collection of modern Chinook salmon of known age. Finally, this protocol is applied to archaeological remains of Chinook from Cathlapotle (45CL1). Three collections of modern known age fish (N=121) were used to evaluate and test approaches to aging Chinook salmon with vertebrae. These collections contained juvenile and adult Chinook from throughout Washington and Oregon. I evaluated a variety of methods for viewing rings including magnified surface images, X-ray images and thin sections to determine which is the most accurate, reliable and efficient, also considering the extent of specimen destruction. Rings visible in X-rays were found to reflect the internal structure of vertebrae rather than annular growth. The number of these internal walls did not correspond to the known ages of fish and are therefore not true annuli. Criteria previously described by salmon fisheries biologist were used to isolate annuli (on the centrum surface) on the Hanford reach collection (N=46). In a test for accuracy 39 (85%) were aged correctly. In a test of reliability utilizing five additional readers all but 14 cases showed discrepancies among readers. Results of the test of reliability were not as successful as other researchers in fisheries biology but given the high accuracy rate the method remains valid. The final goal of this project was to determine the feasibility of applying the surface ring method of age determination to archaeological collections. Archaeological salmon vertebrae from Cathlapotle (45CL1) on the lower Columbia River, Washington state were utilized. One hundred salmon vertebrae were selected and classified to species according to Huber et al. (2011); 89 were identified as Chinook. Of these, 39 had sufficient preservation of the surface to view and interpret incremental rings. Three ages were identified 3, 4 and 5 year olds. This ageing protocol can be applied to archaeological Chinook salmon vertebrae to estimate age of ancient Chinook salmon. Additional work is needed on other salmon species to demonstrate the methods validity across all salmonid species. This analysis has great potential for modeling salmon paleo-life history by contributing data from salmon populations prior to the major impacts of the 19th and 20th century. This is particularly valuable for salmon conservation because information on size, the timing and duration of freshwater emigration as well as the age of spawning and death is critical to the management of hatchery and wild salmon populations. Close

• 99. [Article] Lake Roosevelt Water Quality and Hydrodynamic Model Calibration with Fish Bioenergetics

  An understanding of the effects of hydrodynamics and reservoir operations on the Franklin D. Roosevelt Lake (Lake Roosevelt) aquatic food web allows for better management of the reservoir. A CE-QUAL-W2, ...

  Citation × Citation Citation Abstract Copy Title: Lake Roosevelt Water Quality and Hydrodynamic Model Calibration with Fish Bioenergetics Author: McKillip, Michael Lee Year: 2007 An understanding of the effects of hydrodynamics and reservoir operations on the Franklin D. Roosevelt Lake (Lake Roosevelt) aquatic food web allows for better management of the reservoir. A CE-QUAL-W2, v.3.5, hydrodynamic and water quality model (Cole and Wells, 20061) is being applied to the reservoir. The models zooplankton algorithms are expanded and a fish bioenergetics model is incorporated. The Lake Roosevelt model extent is shown in Figure 1. The model includes the lacustrine arms up to full pool on the Sanpoil, Kettle, and Colville Rivers; the Spokane River arm up to Little Falls Dam; and the Columbia River from Grand Coulee Dam to the U.S.-Canadian border. The previous companion report, “Boundary Conditions and Set-up” (McKillip, Annear, and Wells, 2006), covered • A limnological overview • Hydrodynamic boundary condition data and model inputs • Grand Coulee Dam structures (powerhouse and spillway characteristics) • Water temperature boundary condition data and model inputs • Meteorological data and model inputs • Water quality boundary condition data • Model bathymetry data and model grid development • Topographic shading • Primary and secondary production data • Kokanee hatchery release data This report discusses the model calibration and issues related to the calibration. This report discusses the topics of: 1) Hydrodynamic calibration: Hydrodynamic calibration focuses on matching the water surface elevation at Grand Coulee Dam. 2) Temperature calibration: Temperature calibration focuses on matching temperature profiles throughout the reservoir and continuous data below Grand Coulee Dam. Many of the calibration issues centered on properly characterizing the localized wind and powerhouse withdrawals. 3) Abiotic water quality calibration: Abiotic water quality calibration focused on matching water quality profile data in the reservoir. The selection of proper rate kinetics and understanding the impact of hydrodynamics on water quality state variables was critical to proper calibration. 4) Bioenergetic (algae, zooplankton, kokanee) modeling approach and calibration 5) Sensitivity analyses Title: Lake Roosevelt Water Quality and Hydrodynamic Model Calibration with Fish Bioenergetics Author: McKillip, Michael Lee Year: 2007 An understanding of the effects of hydrodynamics and reservoir operations on the Franklin D. Roosevelt Lake (Lake Roosevelt) aquatic food web allows for better management of the reservoir. A CE-QUAL-W2, v.3.5, hydrodynamic and water quality model (Cole and Wells, 20061) is being applied to the reservoir. The models zooplankton algorithms are expanded and a fish bioenergetics model is incorporated. The Lake Roosevelt model extent is shown in Figure 1. The model includes the lacustrine arms up to full pool on the Sanpoil, Kettle, and Colville Rivers; the Spokane River arm up to Little Falls Dam; and the Columbia River from Grand Coulee Dam to the U.S.-Canadian border. The previous companion report, “Boundary Conditions and Set-up” (McKillip, Annear, and Wells, 2006), covered • A limnological overview • Hydrodynamic boundary condition data and model inputs • Grand Coulee Dam structures (powerhouse and spillway characteristics) • Water temperature boundary condition data and model inputs • Meteorological data and model inputs • Water quality boundary condition data • Model bathymetry data and model grid development • Topographic shading • Primary and secondary production data • Kokanee hatchery release data This report discusses the model calibration and issues related to the calibration. This report discusses the topics of: 1) Hydrodynamic calibration: Hydrodynamic calibration focuses on matching the water surface elevation at Grand Coulee Dam. 2) Temperature calibration: Temperature calibration focuses on matching temperature profiles throughout the reservoir and continuous data below Grand Coulee Dam. Many of the calibration issues centered on properly characterizing the localized wind and powerhouse withdrawals. 3) Abiotic water quality calibration: Abiotic water quality calibration focused on matching water quality profile data in the reservoir. The selection of proper rate kinetics and understanding the impact of hydrodynamics on water quality state variables was critical to proper calibration. 4) Bioenergetic (algae, zooplankton, kokanee) modeling approach and calibration 5) Sensitivity analyses Close

• 100. [Article] Hydrodynamic and Water Quality Modeling of the Chehalis River Using CE-QUAL-W2

  The Chehalis River Basin is located in the southwest region of Washington State, originating in the Olympic Mountains and flowing to Grays Harbor and the Pacific Ocean. The Chehalis River is over 125 miles, ...

  Citation × Citation Citation Abstract Copy Title: Hydrodynamic and Water Quality Modeling of the Chehalis River Using CE-QUAL-W2 Author: Van Glubt, Sarah Year: 2017 The Chehalis River Basin is located in the southwest region of Washington State, originating in the Olympic Mountains and flowing to Grays Harbor and the Pacific Ocean. The Chehalis River is over 125 miles, exists within five counties, and flows through agricultural, residential, industrial, and forest land areas. Four major rivers discharge to the Chehalis River, as well as many smaller creeks, five wastewater treatment plants, and groundwater flows. Flooding is a major problem in the relatively flat areas surrounding the cities of Chehalis and Centralia, with severe consequences for property, safety and transportation. As a result, construction of a flood-control dam in the upper basin has been proposed. One major concern of constructing a dam is the potentially severe impacts to fish health and habitat. The Chehalis River has routinely violated water quality standards for primarily temperature and dissolved oxygen, and has had multiple water quality and Total Maximum Daily Load studies beginning in 1990. CE-QUAL-W2, a two-dimensional (longitudinal and vertical) hydrodynamic and water quality model, was used to simulate the Chehalis River, including free flowing river stretches and stratified (in summer) lake-like stretches. The goals of this research were to assess the flood retention structure's impacts to water quality, as well as river responses to potential climate change scenarios. In order to use the model to achieve these goals, calibration to field data for flow, temperature, and water quality constituents was performed. This involved developing meteorological data, riparian shading data, and flow, temperature, water quality records for all tributaries during the calibration period of January 1, 2013 to December 31, 2014. System cross-sectional geometry data were also required for the model grid. Because of the short travel time in the river, the model was sensitive to boundary condition data, wind speed, bathymetry, nutrient kinetics, and algae, epiphyton, and zooplankton kinetics. Future conditions showed predictions of warmer water temperatures and slight changes to water quality conditions on the river. As fish in the area prefer cooler water temperatures, this could pose a threat to fish health and habitat. Flood retention structures also showed impacts to river temperature and water quality. Structures with the purpose of flood retention only (only operating during times of flooding) gave model predictions for daily maximum temperature higher than structures that employed flood retention and flow augmentation (operating during all times of the year). This suggested the management of flow passage or retention by the dam is important for water quality on the river. As this research continues improvements will be made, particularly to temperature and water quality constituents. Additional data for the system would be beneficial to this process. Model predictions of temperature were sensitive to meteorological data, including cloud cover, which were largely estimated based on solar radiation. Additional meteorological data throughout the basin would be useful to temperature results. Temperature results were also sensitive to the model bathymetry, and additional investigations into segments widths and water depths may improve temperature predictions. Water quality constituent data were largely lacking for the system. Many estimation techniques and approximations were used for input water quality constituents for the model upstream boundary and tributaries when little or no data were available, introducing uncertainty to the model. It was not possible to calibrate pH to field data because alkalinity data were essentially unavailable. However, other constituents had good agreement between model predictions and field data, including dissolved oxygen, nitrates, total phosphorus, and total suspended solids. Title: Hydrodynamic and Water Quality Modeling of the Chehalis River Using CE-QUAL-W2 Author: Van Glubt, Sarah Year: 2017 The Chehalis River Basin is located in the southwest region of Washington State, originating in the Olympic Mountains and flowing to Grays Harbor and the Pacific Ocean. The Chehalis River is over 125 miles, exists within five counties, and flows through agricultural, residential, industrial, and forest land areas. Four major rivers discharge to the Chehalis River, as well as many smaller creeks, five wastewater treatment plants, and groundwater flows. Flooding is a major problem in the relatively flat areas surrounding the cities of Chehalis and Centralia, with severe consequences for property, safety and transportation. As a result, construction of a flood-control dam in the upper basin has been proposed. One major concern of constructing a dam is the potentially severe impacts to fish health and habitat. The Chehalis River has routinely violated water quality standards for primarily temperature and dissolved oxygen, and has had multiple water quality and Total Maximum Daily Load studies beginning in 1990. CE-QUAL-W2, a two-dimensional (longitudinal and vertical) hydrodynamic and water quality model, was used to simulate the Chehalis River, including free flowing river stretches and stratified (in summer) lake-like stretches. The goals of this research were to assess the flood retention structure's impacts to water quality, as well as river responses to potential climate change scenarios. In order to use the model to achieve these goals, calibration to field data for flow, temperature, and water quality constituents was performed. This involved developing meteorological data, riparian shading data, and flow, temperature, water quality records for all tributaries during the calibration period of January 1, 2013 to December 31, 2014. System cross-sectional geometry data were also required for the model grid. Because of the short travel time in the river, the model was sensitive to boundary condition data, wind speed, bathymetry, nutrient kinetics, and algae, epiphyton, and zooplankton kinetics. Future conditions showed predictions of warmer water temperatures and slight changes to water quality conditions on the river. As fish in the area prefer cooler water temperatures, this could pose a threat to fish health and habitat. Flood retention structures also showed impacts to river temperature and water quality. Structures with the purpose of flood retention only (only operating during times of flooding) gave model predictions for daily maximum temperature higher than structures that employed flood retention and flow augmentation (operating during all times of the year). This suggested the management of flow passage or retention by the dam is important for water quality on the river. As this research continues improvements will be made, particularly to temperature and water quality constituents. Additional data for the system would be beneficial to this process. Model predictions of temperature were sensitive to meteorological data, including cloud cover, which were largely estimated based on solar radiation. Additional meteorological data throughout the basin would be useful to temperature results. Temperature results were also sensitive to the model bathymetry, and additional investigations into segments widths and water depths may improve temperature predictions. Water quality constituent data were largely lacking for the system. Many estimation techniques and approximations were used for input water quality constituents for the model upstream boundary and tributaries when little or no data were available, introducing uncertainty to the model. It was not possible to calibrate pH to field data because alkalinity data were essentially unavailable. However, other constituents had good agreement between model predictions and field data, including dissolved oxygen, nitrates, total phosphorus, and total suspended solids. Close