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• 31. [Article] Coastal cutthroat trout : life in the watershed

  Citation × Citation Citation Abstract Copy Title: Coastal cutthroat trout : life in the watershed Author: Fitzpatrick, Martin S., Oregon State University. Sea Grant College Program Title: Coastal cutthroat trout : life in the watershed Author: Fitzpatrick, Martin S., Oregon State University. Sea Grant College Program Close

• 32. [Article] Ecological baselines for Oregon's coast: a report for agencies that manage Oregon's coastal habitats for ecological and economic sustainability, and for all who are interested in the welfare of wildlife that inhabit our coast and its estuaries

  Against the backdrop of growing concern about dead zones, rare and endangered sea mammals, depletion of Oregon’s once‐abundant fish stocks, acidification threatening coastal molluscs, and proposals for ...

  Citation × Citation Citation Abstract Copy Title: Ecological baselines for Oregon's coast: a report for agencies that manage Oregon's coastal habitats for ecological and economic sustainability, and for all who are interested in the welfare of wildlife that inhabit our coast and its estuaries Author: Mrakovcich, Karina Lorenz, Gilden, Jennifer S., Hall, Roberta L., Ebert, Thomas A., Hatch, David R., Smith, Courtland L. Against the backdrop of growing concern about dead zones, rare and endangered sea mammals, depletion of Oregon’s once‐abundant fish stocks, acidification threatening coastal molluscs, and proposals for marine reserves along Oregon’s coastline, a multidisciplinary group of scientists was called together in 2008 to discuss what is known about Oregon’s coastal resources at specific points in the past. They agreed that knowing more about the condition of resources in the past could help state resource agencies understand its ecological potential and such information would be useful in planning restoration projects as well as determining gaps in knowledge that need to be filled. Called together by John Meyer, representing Communication Partnership for Science and the Sea (COMPASS), the group decided to develop an “Ecological Baselines” report on past coastal resources at whatever times empirical data exist. We begin this report with a chapter reviewing archaeological, ethnographic, and historic materials to provide a picture of Oregon’s coastal resources before 1750. Subsequent chapters consider salmon, sea otters, and sub‐tidal sea urchins. The salmon chapter provides details on twentieth century abundance and decline of one of Oregon’s most charismatic and economically important ocean resources. This chapter’s authors also evaluate remedies that have attempted to restore salmon species. Next, the sea otter chapter describes a mammal once abundant but no longer present on the Oregon coast, and discusses what the coast has lost by its demise. A decade ago, the author, a descendant of Aleut and Coos/Siuslaw natives, organized a multi‐disciplinary project, named The Elakha Alliance, to study and consider restoration of this keystone species. The sub‐tidal purple sea urchin, described in our fourth chapter, in contrast to salmon and otter, is so small that the intense labor required to harvest it has protected it from commercial harvesting. However, the urchin is affected by all the forces that impinge on the coast’s ecological web, and warming seas could affect its ability to survive along Oregon’s coast. Not all developments in the past decades have been negative. We discuss major estuary restoration projects on the Salmon River and the Coquille River that show how restoration is working in these areas and that suggest how other estuary restorations could proceed. On Tuesday Feb. 22, 2012, the Oregon legislature passed a bill that will add 38 square miles of marine reserves in Oregon’s territorial waters at five locations. And in our final section, the epilogue discusses a significant new paradigm for understanding the process of ecological collapse, beginning with the removal of top consumers – keystone predators. This multi‐authored review, published in Science in 2011, thereby suggests ecosystem wide strategies for restoration and stability (Estes et al., 2011). Our report on historical, ecological baselines is only a first step in a compilation of information on significant coastal resources that we believe could encourage additional research and longterm strategies for restoration. Title: Ecological baselines for Oregon's coast: a report for agencies that manage Oregon's coastal habitats for ecological and economic sustainability, and for all who are interested in the welfare of wildlife that inhabit our coast and its estuaries Author: Mrakovcich, Karina Lorenz, Gilden, Jennifer S., Hall, Roberta L., Ebert, Thomas A., Hatch, David R., Smith, Courtland L. Against the backdrop of growing concern about dead zones, rare and endangered sea mammals, depletion of Oregon’s once‐abundant fish stocks, acidification threatening coastal molluscs, and proposals for marine reserves along Oregon’s coastline, a multidisciplinary group of scientists was called together in 2008 to discuss what is known about Oregon’s coastal resources at specific points in the past. They agreed that knowing more about the condition of resources in the past could help state resource agencies understand its ecological potential and such information would be useful in planning restoration projects as well as determining gaps in knowledge that need to be filled. Called together by John Meyer, representing Communication Partnership for Science and the Sea (COMPASS), the group decided to develop an “Ecological Baselines” report on past coastal resources at whatever times empirical data exist. We begin this report with a chapter reviewing archaeological, ethnographic, and historic materials to provide a picture of Oregon’s coastal resources before 1750. Subsequent chapters consider salmon, sea otters, and sub‐tidal sea urchins. The salmon chapter provides details on twentieth century abundance and decline of one of Oregon’s most charismatic and economically important ocean resources. This chapter’s authors also evaluate remedies that have attempted to restore salmon species. Next, the sea otter chapter describes a mammal once abundant but no longer present on the Oregon coast, and discusses what the coast has lost by its demise. A decade ago, the author, a descendant of Aleut and Coos/Siuslaw natives, organized a multi‐disciplinary project, named The Elakha Alliance, to study and consider restoration of this keystone species. The sub‐tidal purple sea urchin, described in our fourth chapter, in contrast to salmon and otter, is so small that the intense labor required to harvest it has protected it from commercial harvesting. However, the urchin is affected by all the forces that impinge on the coast’s ecological web, and warming seas could affect its ability to survive along Oregon’s coast. Not all developments in the past decades have been negative. We discuss major estuary restoration projects on the Salmon River and the Coquille River that show how restoration is working in these areas and that suggest how other estuary restorations could proceed. On Tuesday Feb. 22, 2012, the Oregon legislature passed a bill that will add 38 square miles of marine reserves in Oregon’s territorial waters at five locations. And in our final section, the epilogue discusses a significant new paradigm for understanding the process of ecological collapse, beginning with the removal of top consumers – keystone predators. This multi‐authored review, published in Science in 2011, thereby suggests ecosystem wide strategies for restoration and stability (Estes et al., 2011). Our report on historical, ecological baselines is only a first step in a compilation of information on significant coastal resources that we believe could encourage additional research and longterm strategies for restoration. Close

• 33. [Article] Biological opinion: Morse Brothers Habitat Restoration Project

  On October 16, 2000, the National Marine Fisheries Service (NMFS) received a request from Portland District Army Corps of Engineers (COE) for Endangered Species Act (ESA) section 7 consultation for issuance ...

  Citation × Citation Citation Abstract Copy Title: Biological opinion: Morse Brothers Habitat Restoration Project Author: National Marine Fisheries Service, Northwest Region On October 16, 2000, the National Marine Fisheries Service (NMFS) received a request from Portland District Army Corps of Engineers (COE) for Endangered Species Act (ESA) section 7 consultation for issuance of a Corps permit to Morse Brothers (Corps No. 2000-00844) for a habitat restoration project that will connect an abandoned gravel mining pit and pond with the Willamette River near Harrisburg, Linn County, Oregon. In the October 16, 2000 letter, the COE determined that the Upper Willamette River (UWR) chinook salmon (Oncorhynchus tshawytscha) may occur within the project area and that this species may be affected by the proposed project. Because the proposed action would provide seasonal access to a floodplain pond and back water slough that may entrap, or take, the indicated listed fish, the COE determined that the proposed action may adversely affect these species and requested formal consultation. The NMFS was contacted by Jeff Steyaert, Morse Brothers, and Dr. Peter Bayley, Oregon State University who is conducting a research project related to the proposed activity. Mr. Steyaert and Dr. Bayley provided detailed information regarding the proposed action and the ongoing research. The baseline conditions for the Willamette River in the action area, the immediate location of the proposed action, have been generally described and understood from previous study and analysis. References to this work were noted in the documents provided. The objective of this Opinion is to determine whether the action to restore habitat by modifying the floodplain pond and constructing a channel to connect the pond with the Willamette River is likely to jeopardize the continued existence of UWR or destroy or adversely modify critical habitat. Title: Biological opinion: Morse Brothers Habitat Restoration Project Author: National Marine Fisheries Service, Northwest Region On October 16, 2000, the National Marine Fisheries Service (NMFS) received a request from Portland District Army Corps of Engineers (COE) for Endangered Species Act (ESA) section 7 consultation for issuance of a Corps permit to Morse Brothers (Corps No. 2000-00844) for a habitat restoration project that will connect an abandoned gravel mining pit and pond with the Willamette River near Harrisburg, Linn County, Oregon. In the October 16, 2000 letter, the COE determined that the Upper Willamette River (UWR) chinook salmon (Oncorhynchus tshawytscha) may occur within the project area and that this species may be affected by the proposed project. Because the proposed action would provide seasonal access to a floodplain pond and back water slough that may entrap, or take, the indicated listed fish, the COE determined that the proposed action may adversely affect these species and requested formal consultation. The NMFS was contacted by Jeff Steyaert, Morse Brothers, and Dr. Peter Bayley, Oregon State University who is conducting a research project related to the proposed activity. Mr. Steyaert and Dr. Bayley provided detailed information regarding the proposed action and the ongoing research. The baseline conditions for the Willamette River in the action area, the immediate location of the proposed action, have been generally described and understood from previous study and analysis. References to this work were noted in the documents provided. The objective of this Opinion is to determine whether the action to restore habitat by modifying the floodplain pond and constructing a channel to connect the pond with the Willamette River is likely to jeopardize the continued existence of UWR or destroy or adversely modify critical habitat. Close

• 34. [Article] Coastal steelhead trout : life in the watershed

  Citation × Citation Citation Abstract Copy Title: Coastal steelhead trout : life in the watershed Author: Fitzpatrick, Martin S., Oregon State University. Sea Grant College Program Title: Coastal steelhead trout : life in the watershed Author: Fitzpatrick, Martin S., Oregon State University. Sea Grant College Program Close

• 35. [Article] Stream habitat classification and restoration in the Blue Mountians of northeast Oregon

  The restoration of rivers and streams should be based on a strong conceptual framework. Streams are developing systems. As such, streams exhibit temporal behaviors that change with changing stream environments. ...

  Citation × Citation Citation Abstract Copy Title: Stream habitat classification and restoration in the Blue Mountians of northeast Oregon Author: Ebersole, Joseph Lamar The restoration of rivers and streams should be based on a strong conceptual framework. Streams are developing systems. As such, streams exhibit temporal behaviors that change with changing stream environments. Underlying the dynamic development of streams is potential capacity. Streams express this capacity as an array of habitats over time and across the landscape. Human land uses in the western United States have rapidly altered aquatic habitats as well as the processes that shape habitat. As a result, the diversity of native fishes and their habitats has been suppressed. Restoration is fundamentally about allowing stream systems to re-express their capacities. Four steps are provided to guide stream restoration activities. Key tasks include: identification of the historic patterns of habitat development; protection of the developmental diversity that remains; local application of specific knowledge about suppressive factors; classification of sensitive, critical or refugium habitats; release of anthropogenic suppression; and monitoring of biotic response to habitat change. Applying these concepts, I describe potential habitat refugia for aquatic organisms in the Joseph Creek basin in the Blue Mountains of northeast Oregon. Five valley segment classes, differing in valley corridor landforms, are described. Of these, low-gradient wide alluvial valleys have been most altered by human land use. Riparian vegetation has been extensively removed or altered in alluvial valleys. Currently, stream habitats are structurally depauperate, and warm to temperatures well above thermal tolerances of native salmonids. Potential refugia for native coldwater fishes in these valleys include patches of complex habitat within stream reaches. Reaches fenced to exclude domestic livestock exhibit narrower channels, more pools, and higher frequencies of stable vegetated banks than nearby unfenced reaches. During summer low flow periods, cold groundwater seeping into and accumulating in stream channels forms "cold pools". Cold pools provide potential seasonal refuge for coldwater fish at microhabitat scales. Cold pools are associated with channel complexity, and are more frequent in reaches with vigorous riparian vegetation. Seven classes of cold pools are described. Cold pool classes differ in minimum temperature, maximum depth and volume. Distributions of cold pool classes between valley segment classes suggest that valley geomorphology in addition to local channel form may influence development of certain cold pool types. Although refugia at the microhabitat to reach scales are important, the context within which remnant or refugium habitats and associated relict populations are maintained may ultimately determine the persistence of those species and habitats. In managed landscapes, protection and restoration of habitats at many scales may be necessary if we are to best insure the persistence of native species. Title: Stream habitat classification and restoration in the Blue Mountians of northeast Oregon Author: Ebersole, Joseph Lamar The restoration of rivers and streams should be based on a strong conceptual framework. Streams are developing systems. As such, streams exhibit temporal behaviors that change with changing stream environments. Underlying the dynamic development of streams is potential capacity. Streams express this capacity as an array of habitats over time and across the landscape. Human land uses in the western United States have rapidly altered aquatic habitats as well as the processes that shape habitat. As a result, the diversity of native fishes and their habitats has been suppressed. Restoration is fundamentally about allowing stream systems to re-express their capacities. Four steps are provided to guide stream restoration activities. Key tasks include: identification of the historic patterns of habitat development; protection of the developmental diversity that remains; local application of specific knowledge about suppressive factors; classification of sensitive, critical or refugium habitats; release of anthropogenic suppression; and monitoring of biotic response to habitat change. Applying these concepts, I describe potential habitat refugia for aquatic organisms in the Joseph Creek basin in the Blue Mountains of northeast Oregon. Five valley segment classes, differing in valley corridor landforms, are described. Of these, low-gradient wide alluvial valleys have been most altered by human land use. Riparian vegetation has been extensively removed or altered in alluvial valleys. Currently, stream habitats are structurally depauperate, and warm to temperatures well above thermal tolerances of native salmonids. Potential refugia for native coldwater fishes in these valleys include patches of complex habitat within stream reaches. Reaches fenced to exclude domestic livestock exhibit narrower channels, more pools, and higher frequencies of stable vegetated banks than nearby unfenced reaches. During summer low flow periods, cold groundwater seeping into and accumulating in stream channels forms "cold pools". Cold pools provide potential seasonal refuge for coldwater fish at microhabitat scales. Cold pools are associated with channel complexity, and are more frequent in reaches with vigorous riparian vegetation. Seven classes of cold pools are described. Cold pool classes differ in minimum temperature, maximum depth and volume. Distributions of cold pool classes between valley segment classes suggest that valley geomorphology in addition to local channel form may influence development of certain cold pool types. Although refugia at the microhabitat to reach scales are important, the context within which remnant or refugium habitats and associated relict populations are maintained may ultimately determine the persistence of those species and habitats. In managed landscapes, protection and restoration of habitats at many scales may be necessary if we are to best insure the persistence of native species. Close

• 36. [Article] Nehalem River watershed assessment

  Watershed assessment is a process for evaluating how well a watershed is working. The purpose of this assessment was to determine how natural and human-induced changes have impacted the sustainability ...

  Citation × Citation Citation Abstract Copy Title: Nehalem River watershed assessment Author: Maser, Jospeh, Johnson, Jill Watershed assessment is a process for evaluating how well a watershed is working. The purpose of this assessment was to determine how natural and human-induced changes have impacted the sustainability of salmon populations in the Nehalem River Watershed. Both historical and current information is included regarding the watershed’s ability to produce clean water and healthy salmon habitat. The assessment was prepared for the Upper and Lower Nehalem River Watershed Councils. It will be a baseline for developing and prioritizing potential restoration projects in terms of fish habitat. Geographic Information Systems (GIS) was used for much of the analysis and has been provided to the watershed councils. Title: Nehalem River watershed assessment Author: Maser, Jospeh, Johnson, Jill Watershed assessment is a process for evaluating how well a watershed is working. The purpose of this assessment was to determine how natural and human-induced changes have impacted the sustainability of salmon populations in the Nehalem River Watershed. Both historical and current information is included regarding the watershed’s ability to produce clean water and healthy salmon habitat. The assessment was prepared for the Upper and Lower Nehalem River Watershed Councils. It will be a baseline for developing and prioritizing potential restoration projects in terms of fish habitat. Geographic Information Systems (GIS) was used for much of the analysis and has been provided to the watershed councils. Close

• 37. [Article] Reconnecting aquatic habitats : validating historical habitat use by anadromous fishes using telemetry and stable isotope analysis above barriers

  I conducted a study to identify potential spawning habitat for anadromous salmonids above a 60-year-old hydropower dam in the headwaters of the North Umpqua River in Oregon. Like many other historical ...

  Citation × Citation Citation Abstract Copy Title: Reconnecting aquatic habitats : validating historical habitat use by anadromous fishes using telemetry and stable isotope analysis above barriers Author: Lewis, Sierra Koch I conducted a study to identify potential spawning habitat for anadromous salmonids above a 60-year-old hydropower dam in the headwaters of the North Umpqua River in Oregon. Like many other historical salmonid-bearing rivers, little documentation exists for anadromous fish presence above potential natural obstacles upstream of Soda Springs Dam. My prediction was that if migratory salmonids are allowed to move upstream of the dam using a new fish ladder they would utilize available upstream spawning habitat. I captured, radio-tagged, and transplanted wild adult summer steelhead, O. mykiss, above Soda Springs Dam and tracked daily movements for 1 year to observe habitat preferences. I also investigated evidence of historical anadromy throughout the North Umpqua River basin using stable isotope analysis of salmon-derived nitrogen (¹⁵N) in foliar samples from Douglas fir trees, P. menziesii, (>100 years old). I tested the hypothesis that I could identify undocumented, historical salmon spawning reaches above natural and anthropogenic obstacles based solely upon δ¹⁵N foliar deposition patterns. While tracking radio-tagged steelhead, I documented holding locations, the timing of spawning activities, and the outmigration of kelts. Tagged fish did not show any extensive movement in the river or tributaries above the dam. Most of the tagged adults showed incremental daily movements near the release site or downstream into the hydropower reservoir but did not travel further than 1 kilometer upstream in the main river channel. I recorded movements and localized activities that suggested some of the fish spawned and subsequently moved downstream towards the Pacific Ocean. My observations indicated that spawning behavior of tagged fish above Soda Springs Dam was delayed several weeks relative to fish spawning below the dam. There was no evidence from telemetry that any fish moved upstream in Fish Creek, the newly accessible habitat of interest in this project. My data suggest that steelhead will use restored habitat above dams, but that re-colonization activities are variable and may be affected by altered flow regimes within the restored habitat upstream of the dam and intra-specific density dependence. My stable isotope data indicated that the foliar δ¹⁵N deposition patterns were confounded with elevation. I documented potential "salmon-derived" false positives on the Umpqua National Forest above impassable waterfalls. Overall I found that foliar δ¹⁵N deposition patterns were highly variable and unexpectedly indicated a statistically significant negative correlation of foliar δ¹⁵N values with historical salmon presence. My linear mixed-effects modeling suggests that the presence of salmon is the most important indicator of foliar δ¹⁵N values, rather than the proximity of a sampled tree to stream flow above or below migratory barriers. I was not able to use the mixed effects model to identify previously undocumented salmon spawning habitat. My results from the foliar technique suggest that the method may not be universally applicable as has been previously suggested in the literature. Title: Reconnecting aquatic habitats : validating historical habitat use by anadromous fishes using telemetry and stable isotope analysis above barriers Author: Lewis, Sierra Koch I conducted a study to identify potential spawning habitat for anadromous salmonids above a 60-year-old hydropower dam in the headwaters of the North Umpqua River in Oregon. Like many other historical salmonid-bearing rivers, little documentation exists for anadromous fish presence above potential natural obstacles upstream of Soda Springs Dam. My prediction was that if migratory salmonids are allowed to move upstream of the dam using a new fish ladder they would utilize available upstream spawning habitat. I captured, radio-tagged, and transplanted wild adult summer steelhead, O. mykiss, above Soda Springs Dam and tracked daily movements for 1 year to observe habitat preferences. I also investigated evidence of historical anadromy throughout the North Umpqua River basin using stable isotope analysis of salmon-derived nitrogen (¹⁵N) in foliar samples from Douglas fir trees, P. menziesii, (>100 years old). I tested the hypothesis that I could identify undocumented, historical salmon spawning reaches above natural and anthropogenic obstacles based solely upon δ¹⁵N foliar deposition patterns. While tracking radio-tagged steelhead, I documented holding locations, the timing of spawning activities, and the outmigration of kelts. Tagged fish did not show any extensive movement in the river or tributaries above the dam. Most of the tagged adults showed incremental daily movements near the release site or downstream into the hydropower reservoir but did not travel further than 1 kilometer upstream in the main river channel. I recorded movements and localized activities that suggested some of the fish spawned and subsequently moved downstream towards the Pacific Ocean. My observations indicated that spawning behavior of tagged fish above Soda Springs Dam was delayed several weeks relative to fish spawning below the dam. There was no evidence from telemetry that any fish moved upstream in Fish Creek, the newly accessible habitat of interest in this project. My data suggest that steelhead will use restored habitat above dams, but that re-colonization activities are variable and may be affected by altered flow regimes within the restored habitat upstream of the dam and intra-specific density dependence. My stable isotope data indicated that the foliar δ¹⁵N deposition patterns were confounded with elevation. I documented potential "salmon-derived" false positives on the Umpqua National Forest above impassable waterfalls. Overall I found that foliar δ¹⁵N deposition patterns were highly variable and unexpectedly indicated a statistically significant negative correlation of foliar δ¹⁵N values with historical salmon presence. My linear mixed-effects modeling suggests that the presence of salmon is the most important indicator of foliar δ¹⁵N values, rather than the proximity of a sampled tree to stream flow above or below migratory barriers. I was not able to use the mixed effects model to identify previously undocumented salmon spawning habitat. My results from the foliar technique suggest that the method may not be universally applicable as has been previously suggested in the literature. Close

• 38. [Article] Aspects of the early life history of juvenile salmonids in the Dungeness River Estuary

  The decline of many Pacific salmon stocks has stimulated interest in the early life history and habitat requirements of juvenile salmon. Although estuarine habitat associations of juvenile salmon have ...

  Citation × Citation Citation Abstract Copy Title: Aspects of the early life history of juvenile salmonids in the Dungeness River Estuary Author: Sather, Nichole K. The decline of many Pacific salmon stocks has stimulated interest in the early life history and habitat requirements of juvenile salmon. Although estuarine habitat associations of juvenile salmon have been investigated in many coastal areas of the eastern Pacific Ocean, until recently, little was known about juvenile salmonid ecology within the Straits of Juan de Fuca. During the Spring/Summer outmigration period in 2006 and 2007, I examined the early life history of the five species of anadromous salmon in the Dungeness River estuary on the north Olympic Peninsula, Washington. I sampled multiple spatial scales within several habitat types to characterize salmon distribution and habitat use. My results presented in this thesis are segregated into two components: 1) tidal marsh ecology of juvenile salmonids in the Dungeness River estuary, and 2) the landscape-scale distribution of juvenile salmonids within the Dungeness River estuary. I examined the population of juvenile salmonids within blind tidal sloughs near the vicinity of the Dungeness River delta. Salmonids were present within the tidal marshes throughout the entire outmigration period (e.g., March through July). Juvenile Chinook salmon (Oncorhynchus tshawytscha) were the most abundant salmonid species within the marshes. Based on the temporal distribution and size structure of juvenile Chinook salmon in the estuary I identified at least four life history types: 1) a fry strategy included a large pulse of fish emigrating from the river at a small size (e.g., 35-45mm FL) during late winter and early spring months; 2) the second group of fish was the least abundant group emigrating from the river from April through mid May at sizes ranging from 50-75mm FL; 3) the third group of migrants entered the estuary between from late spring through the summer months at larger sizes than the initial groups (e.g., 60-90mm FL); and 4) the final group of Chinook salmon included a stream-type yearling strategy. In addition to the four life history strategies identified for Chinook salmon, I detected at least three groups of chum salmon migrating into the estuary. These groups were distinguished by their size and timing of migration and are further described according to different rearing strategies. The distribution of juvenile salmonids was most strongly influenced by the degree of connectivity (i.e., distance) between the tidal marshes and the mouth of the Dungeness River. Habitat complexity and opportunity also governed the distribution of juvenile salmonids within the tidal marshes. I also sampled three regions of the estuary with a beach seine to investigate the nearshore distribution of juvenile salmonids within the Dungeness River estuary: the delta face, inner Bay, and outer Bay. Among the three regions, species composition was highly variable between 2006 and 2007. The most common salmonids encountered within the beach seine sites included Chinook salmon, chum salmon (O. kisutch), and pink salmon (O. gorbuscha). The relative abundance of salmonids was highest near the delta face and lowest within the outer bay area. The landscape-scale distribution and habitat use of juvenile salmonids within the Dungeness River estuary is largely influenced by ecosystem connectivity, but is also linked to biotic characteristics of the fish (e.g., life history type and fish size). Although the Dungeness includes hydrogeomorphic characteristics (e.g., steep river gradient, composition of sand spits in the estuary) unique to other Pacific Northwest watersheds, this system produces a variety of life history types comparable to other estuaries. Understanding the mechanisms that drive the distribution of juvenile salmonids within the Dungeness will supply local resource managers with a baseline with which to establish ecosystem restoration goals. Title: Aspects of the early life history of juvenile salmonids in the Dungeness River Estuary Author: Sather, Nichole K. The decline of many Pacific salmon stocks has stimulated interest in the early life history and habitat requirements of juvenile salmon. Although estuarine habitat associations of juvenile salmon have been investigated in many coastal areas of the eastern Pacific Ocean, until recently, little was known about juvenile salmonid ecology within the Straits of Juan de Fuca. During the Spring/Summer outmigration period in 2006 and 2007, I examined the early life history of the five species of anadromous salmon in the Dungeness River estuary on the north Olympic Peninsula, Washington. I sampled multiple spatial scales within several habitat types to characterize salmon distribution and habitat use. My results presented in this thesis are segregated into two components: 1) tidal marsh ecology of juvenile salmonids in the Dungeness River estuary, and 2) the landscape-scale distribution of juvenile salmonids within the Dungeness River estuary. I examined the population of juvenile salmonids within blind tidal sloughs near the vicinity of the Dungeness River delta. Salmonids were present within the tidal marshes throughout the entire outmigration period (e.g., March through July). Juvenile Chinook salmon (Oncorhynchus tshawytscha) were the most abundant salmonid species within the marshes. Based on the temporal distribution and size structure of juvenile Chinook salmon in the estuary I identified at least four life history types: 1) a fry strategy included a large pulse of fish emigrating from the river at a small size (e.g., 35-45mm FL) during late winter and early spring months; 2) the second group of fish was the least abundant group emigrating from the river from April through mid May at sizes ranging from 50-75mm FL; 3) the third group of migrants entered the estuary between from late spring through the summer months at larger sizes than the initial groups (e.g., 60-90mm FL); and 4) the final group of Chinook salmon included a stream-type yearling strategy. In addition to the four life history strategies identified for Chinook salmon, I detected at least three groups of chum salmon migrating into the estuary. These groups were distinguished by their size and timing of migration and are further described according to different rearing strategies. The distribution of juvenile salmonids was most strongly influenced by the degree of connectivity (i.e., distance) between the tidal marshes and the mouth of the Dungeness River. Habitat complexity and opportunity also governed the distribution of juvenile salmonids within the tidal marshes. I also sampled three regions of the estuary with a beach seine to investigate the nearshore distribution of juvenile salmonids within the Dungeness River estuary: the delta face, inner Bay, and outer Bay. Among the three regions, species composition was highly variable between 2006 and 2007. The most common salmonids encountered within the beach seine sites included Chinook salmon, chum salmon (O. kisutch), and pink salmon (O. gorbuscha). The relative abundance of salmonids was highest near the delta face and lowest within the outer bay area. The landscape-scale distribution and habitat use of juvenile salmonids within the Dungeness River estuary is largely influenced by ecosystem connectivity, but is also linked to biotic characteristics of the fish (e.g., life history type and fish size). Although the Dungeness includes hydrogeomorphic characteristics (e.g., steep river gradient, composition of sand spits in the estuary) unique to other Pacific Northwest watersheds, this system produces a variety of life history types comparable to other estuaries. Understanding the mechanisms that drive the distribution of juvenile salmonids within the Dungeness will supply local resource managers with a baseline with which to establish ecosystem restoration goals. Close

• 39. [Article] Recovery of Wild Salmonids in Western Oregon Lowlands

  This report was prepared by the Independent Multidisciplinary Science Team to the Oregon Plan for Salmon and watersheds.

  Citation × Citation Citation Abstract Copy Title: Recovery of Wild Salmonids in Western Oregon Lowlands Author: Independent Multidisciplinary Science Team (Or.) This report was prepared by the Independent Multidisciplinary Science Team to the Oregon Plan for Salmon and watersheds. Title: Recovery of Wild Salmonids in Western Oregon Lowlands Author: Independent Multidisciplinary Science Team (Or.) This report was prepared by the Independent Multidisciplinary Science Team to the Oregon Plan for Salmon and watersheds. Close

• 40. [Article] Breeding site selection by coho salmon (Oncorhynchus kisutch) in relation to large wood additions and factors that drive reproductive success

  The fitness of female Pacific salmon (Oncorhynchus spp.) with respect to breeding behavior can be partitioned into at least four components: survival to reproduction, competition for breeding sites, success ...

  Citation × Citation Citation Abstract Copy Title: Breeding site selection by coho salmon (Oncorhynchus kisutch) in relation to large wood additions and factors that drive reproductive success Author: Clark, Steven (Steven Michael) The fitness of female Pacific salmon (Oncorhynchus spp.) with respect to breeding behavior can be partitioned into at least four components: survival to reproduction, competition for breeding sites, success of egg incubation, and suitability of the local environment near breeding sites for early rearing of juveniles. Accordingly, breeding sites should exhibit predictable habitat features linked to these components. In this study, I evaluated the relative influences of habitat features linked to fitness components on selection of breeding sites by coho salmon (Oncorhynchus kisutch). I also evaluated associations between breeding site selection and additions of large wood, as the latter were introduced into the study system as a means of restoring habitat conditions to benefit coho salmon. I used a model selection approach to organize specific habitat features into groupings reflecting fitness components and influences of large wood. The relative likelihood of each of these models was then evaluated based on how coho salmon were observed to select breeding sites. Specific variables examined within these models included depth at the redd, width to depth ratio, stream network location, proximity to other redds, maximum depth, proximity to a pool tail, and the count of naturally occurring and artificially placed large wood. Results of this work suggest that female coho salmon most likely select breeding sites based on habitat features linked to all four hypothesized fitness components. Linkages between large wood and breeding site selection were less clear, likely due to mismatches between the scale at which availability was quantified relative to the geomorphic influences of wood, insufficient time for wood to have geomorphic influences on habitat, or the directionality in which geomorphic effects are currently manifested (i.e., upstream, downstream, or bi-directional influences). Future work focused on geomorphic processes in this system could reveal stronger linkages between instream wood and the habitat features that coho salmon select for breeding. Title: Breeding site selection by coho salmon (Oncorhynchus kisutch) in relation to large wood additions and factors that drive reproductive success Author: Clark, Steven (Steven Michael) The fitness of female Pacific salmon (Oncorhynchus spp.) with respect to breeding behavior can be partitioned into at least four components: survival to reproduction, competition for breeding sites, success of egg incubation, and suitability of the local environment near breeding sites for early rearing of juveniles. Accordingly, breeding sites should exhibit predictable habitat features linked to these components. In this study, I evaluated the relative influences of habitat features linked to fitness components on selection of breeding sites by coho salmon (Oncorhynchus kisutch). I also evaluated associations between breeding site selection and additions of large wood, as the latter were introduced into the study system as a means of restoring habitat conditions to benefit coho salmon. I used a model selection approach to organize specific habitat features into groupings reflecting fitness components and influences of large wood. The relative likelihood of each of these models was then evaluated based on how coho salmon were observed to select breeding sites. Specific variables examined within these models included depth at the redd, width to depth ratio, stream network location, proximity to other redds, maximum depth, proximity to a pool tail, and the count of naturally occurring and artificially placed large wood. Results of this work suggest that female coho salmon most likely select breeding sites based on habitat features linked to all four hypothesized fitness components. Linkages between large wood and breeding site selection were less clear, likely due to mismatches between the scale at which availability was quantified relative to the geomorphic influences of wood, insufficient time for wood to have geomorphic influences on habitat, or the directionality in which geomorphic effects are currently manifested (i.e., upstream, downstream, or bi-directional influences). Future work focused on geomorphic processes in this system could reveal stronger linkages between instream wood and the habitat features that coho salmon select for breeding. Close