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• 491. [Article] Identification of optimal broodstock for Pacific Northwest oysters

  The United States Pacific Northwest is well known for its shellfish farming. Historically, commercial harvests were dominated by the native Olympia oyster, Ostrea lurida, but over-exploitation, habitat ...

  Citation × Citation Citation Abstract Copy Title: Identification of optimal broodstock for Pacific Northwest oysters Author: Stick, David A. The United States Pacific Northwest is well known for its shellfish farming. Historically, commercial harvests were dominated by the native Olympia oyster, Ostrea lurida, but over-exploitation, habitat degradation, and competition and predation by non-native species has drastically depleted their densities and extirpated many local populations. As a result, shellfish aquaculture production has shifted to the introduced Pacific oyster, Crassostrea gigas. An underlying objective of this dissertation is the use of molecular genetics to improve our ability to accurately identifying optimal oyster broodstock for either restoration of Olympia oysters or farming of Pacific oysters. The ecological benefits provided by oysters as well as the Olympia oyster's historical significance, has motivated numerous restoration/supplementation efforts but these efforts are proceeding without a clear understanding of the genetic structure among extant populations, which could be substantial as a consequence of limited dispersal, local adaptation and/or anthropogenic impacts. To facilitate this understanding, we isolated and characterized 19 polymorphic microsatellites and used 8 of these to study the genetic structure of 2,712 individuals collected from 25 remnant Olympia oyster populations between the northern tip of Vancouver Island BC and Elkhorn Slough CA. Gene flow among geographically separated extant Olympia oyster populations is surprisingly limited for a marine invertebrate species whose free-swimming larvae are capable of planktonic dispersal as long as favorable water conditions exist. We found a significant correlation between geographic and genetic distances supporting the premise that coastal populations are isolated by distance. Genetic structure among remnant populations was not limited to broad geographic regions but was also present at sub-regional scales in both Puget Sound WA and San Francisco Bay CA. Until it can be determined whether genetically differentiated O. lurida populations are locally adapted, restoration projects and resource managers should be cautious of random mixing or transplantation of stocks where gene flow is restricted. As we transition from our Olympia oyster population analysis to our Pacific oyster quantitative analysis, we recognize that traditional quantitative trait locus (QTL) mapping strategies use crosses among inbred lines to create segregating populations. Unfortunately, even low levels of inbreeding in the Pacific oyster (Crassostrea gigas) can substantially depress economically important quantitative traits such as yield and survival, potentially complicating subsequent QTL analyses. To circumvent this problem, we constructed an integrated linkage map for Pacific oysters, consisting of 65 microsatellite (18 of which were previously unmapped) and 212 AFLP markers using a full-sib cross between phenotypically differentiated outbred families. We identified 10 linkage groups (LG1-LG10) spanning 710.48 cM, with an average genomic coverage of 91.39% and an average distance between markers of 2.62 cM. Average marker saturation was 27.7 per linkage group, ranging between 19 (LG9) and 36 markers (LG3). Using this map we identified 12 quantitative trait loci (QTLs) and 5 potential QTLs in the F1 outcross population of 236 full-sib Pacific oysters for four growth-related morphometric measures, including individual wet live weight, shell length, shell width and shell depth measured at four post-fertilization time points: plant-out (average age of 140 days), first year interim (average age of 358 days), second year interim (average age of 644 days) and harvest (average age of 950 days). Mapped QTLs and potential QTLs accounted for an average of 11.2% of the total phenotypic variation and ranged between 2.1 and 33.1%. Although QTL or potential QTL were mapped to all Pacific oyster linkage groups with the exception of LG2, LG8 and LG9, three groups (LG4, LG10 and LG5) were associated with three or more QTL or potential QTL. We conclude that alleles accounting for a significant proportion of the total phenotypic variation for morphometric measures that influence harvest yield remain segregating within the broodstock of West Coast Pacific oyster selective breeding programs. Title: Identification of optimal broodstock for Pacific Northwest oysters Author: Stick, David A. The United States Pacific Northwest is well known for its shellfish farming. Historically, commercial harvests were dominated by the native Olympia oyster, Ostrea lurida, but over-exploitation, habitat degradation, and competition and predation by non-native species has drastically depleted their densities and extirpated many local populations. As a result, shellfish aquaculture production has shifted to the introduced Pacific oyster, Crassostrea gigas. An underlying objective of this dissertation is the use of molecular genetics to improve our ability to accurately identifying optimal oyster broodstock for either restoration of Olympia oysters or farming of Pacific oysters. The ecological benefits provided by oysters as well as the Olympia oyster's historical significance, has motivated numerous restoration/supplementation efforts but these efforts are proceeding without a clear understanding of the genetic structure among extant populations, which could be substantial as a consequence of limited dispersal, local adaptation and/or anthropogenic impacts. To facilitate this understanding, we isolated and characterized 19 polymorphic microsatellites and used 8 of these to study the genetic structure of 2,712 individuals collected from 25 remnant Olympia oyster populations between the northern tip of Vancouver Island BC and Elkhorn Slough CA. Gene flow among geographically separated extant Olympia oyster populations is surprisingly limited for a marine invertebrate species whose free-swimming larvae are capable of planktonic dispersal as long as favorable water conditions exist. We found a significant correlation between geographic and genetic distances supporting the premise that coastal populations are isolated by distance. Genetic structure among remnant populations was not limited to broad geographic regions but was also present at sub-regional scales in both Puget Sound WA and San Francisco Bay CA. Until it can be determined whether genetically differentiated O. lurida populations are locally adapted, restoration projects and resource managers should be cautious of random mixing or transplantation of stocks where gene flow is restricted. As we transition from our Olympia oyster population analysis to our Pacific oyster quantitative analysis, we recognize that traditional quantitative trait locus (QTL) mapping strategies use crosses among inbred lines to create segregating populations. Unfortunately, even low levels of inbreeding in the Pacific oyster (Crassostrea gigas) can substantially depress economically important quantitative traits such as yield and survival, potentially complicating subsequent QTL analyses. To circumvent this problem, we constructed an integrated linkage map for Pacific oysters, consisting of 65 microsatellite (18 of which were previously unmapped) and 212 AFLP markers using a full-sib cross between phenotypically differentiated outbred families. We identified 10 linkage groups (LG1-LG10) spanning 710.48 cM, with an average genomic coverage of 91.39% and an average distance between markers of 2.62 cM. Average marker saturation was 27.7 per linkage group, ranging between 19 (LG9) and 36 markers (LG3). Using this map we identified 12 quantitative trait loci (QTLs) and 5 potential QTLs in the F1 outcross population of 236 full-sib Pacific oysters for four growth-related morphometric measures, including individual wet live weight, shell length, shell width and shell depth measured at four post-fertilization time points: plant-out (average age of 140 days), first year interim (average age of 358 days), second year interim (average age of 644 days) and harvest (average age of 950 days). Mapped QTLs and potential QTLs accounted for an average of 11.2% of the total phenotypic variation and ranged between 2.1 and 33.1%. Although QTL or potential QTL were mapped to all Pacific oyster linkage groups with the exception of LG2, LG8 and LG9, three groups (LG4, LG10 and LG5) were associated with three or more QTL or potential QTL. We conclude that alleles accounting for a significant proportion of the total phenotypic variation for morphometric measures that influence harvest yield remain segregating within the broodstock of West Coast Pacific oyster selective breeding programs. Close

• 492. [Article] Modeling abiotic influences on disease dynamics for the complex life cycle of the myxozoan parasite Ceratomyxa shasta

  Most parasites and their hosts live in a balance within their environment; however a disease outbreak can occur when either the parasite, host, or environment, are perturbed. Myxozoan parasites are associated ...

  Citation × Citation Citation Abstract Copy Title: Modeling abiotic influences on disease dynamics for the complex life cycle of the myxozoan parasite Ceratomyxa shasta Author: Ray, Robert Adam Most parasites and their hosts live in a balance within their environment; however a disease outbreak can occur when either the parasite, host, or environment, are perturbed. Myxozoan parasites are associated with a wide variety of cultured and wild fish populations. Most myxozoans are relatively benign to their vertebrate host; however some cause dramatic population level effects on both cultured and wild fish populations. These parasites have a complex life cycle involving a vertebrate host (fish), an invertebrate host (annelid), and two spore stages (actinospore and myxospore). Interactions between these parasites and their hosts can be strongly influenced by environmental factors, most notably by water temperature and water velocity. Given the complex life cycle of myxozoan parasites and the lack of any chemical treatments or preventatives, controlling infections and disease caused by these parasites is challenging, especially for wild populations. The myxozoan Ceratomyxa shasta is endemic to many of the major rivers of the Pacific Northwest and infects all species of Pacific salmon. In the Klamath River, CA, USA, C. shasta infection is associated with decreased returns of adult Chinook salmon (Oncorhynchus tshawytscha). The goals of this dissertation were to 1) quantify the effect that elevated water temperature has on C. shasta-induced disease severity and mortality rate for both Chinook and coho (O. kitsch) salmon, 2) identify transmission patterns and quantify transmission rates of the actinospore stage to the salmon host, 3) develop an epidemiological model of this host-parasite life cycle and assess the sensitivity of specific parameters that may act as suitable management strategies, and 4) utilize a mixture cure model, an alternative survival analysis method, to quantify the effects water temperature and discharge on the total and rate of C. shasta-induced mortality of both Chinook and coho salmon. I found that, similar to disease progression naïve salmon species (i.e. from waters where C. shasta is absent), elevated water temperature increases the rate and overall mortality for salmon species from river systems where the parasite is endemic. Elevated water temperatures also increase the transmission rate of the actinospore stage to the salmon host. The transmission rate of the actinospore stage to the salmon host was inversely related to water velocity, and I identified a potential velocity threshold of ~0.3m/sec, above which transmission was greatly reduced. From the epidemiological model I sensitivity analyses and identified that reduction of the myxospore transmission rate from the adult salmon to the polychaete host during the winter may be the most effective management action to reduce C. shasta-related disease in the Klamath River. This action could potentially be achieved by increasing discharge during the winter to minimize contact between the polychaete host and myxospore stage. Lastly, I applied the mixture cure models to quantify how the daily survival rates of Chinook and coho salmon change over time after the fish become infected with C. shasta. Although varied in approach, the output from both of the models presented in this dissertation can be used to guide management and conservation actions for fish populations affected by myxozoan parasites. Title: Modeling abiotic influences on disease dynamics for the complex life cycle of the myxozoan parasite Ceratomyxa shasta Author: Ray, Robert Adam Most parasites and their hosts live in a balance within their environment; however a disease outbreak can occur when either the parasite, host, or environment, are perturbed. Myxozoan parasites are associated with a wide variety of cultured and wild fish populations. Most myxozoans are relatively benign to their vertebrate host; however some cause dramatic population level effects on both cultured and wild fish populations. These parasites have a complex life cycle involving a vertebrate host (fish), an invertebrate host (annelid), and two spore stages (actinospore and myxospore). Interactions between these parasites and their hosts can be strongly influenced by environmental factors, most notably by water temperature and water velocity. Given the complex life cycle of myxozoan parasites and the lack of any chemical treatments or preventatives, controlling infections and disease caused by these parasites is challenging, especially for wild populations. The myxozoan Ceratomyxa shasta is endemic to many of the major rivers of the Pacific Northwest and infects all species of Pacific salmon. In the Klamath River, CA, USA, C. shasta infection is associated with decreased returns of adult Chinook salmon (Oncorhynchus tshawytscha). The goals of this dissertation were to 1) quantify the effect that elevated water temperature has on C. shasta-induced disease severity and mortality rate for both Chinook and coho (O. kitsch) salmon, 2) identify transmission patterns and quantify transmission rates of the actinospore stage to the salmon host, 3) develop an epidemiological model of this host-parasite life cycle and assess the sensitivity of specific parameters that may act as suitable management strategies, and 4) utilize a mixture cure model, an alternative survival analysis method, to quantify the effects water temperature and discharge on the total and rate of C. shasta-induced mortality of both Chinook and coho salmon. I found that, similar to disease progression naïve salmon species (i.e. from waters where C. shasta is absent), elevated water temperature increases the rate and overall mortality for salmon species from river systems where the parasite is endemic. Elevated water temperatures also increase the transmission rate of the actinospore stage to the salmon host. The transmission rate of the actinospore stage to the salmon host was inversely related to water velocity, and I identified a potential velocity threshold of ~0.3m/sec, above which transmission was greatly reduced. From the epidemiological model I sensitivity analyses and identified that reduction of the myxospore transmission rate from the adult salmon to the polychaete host during the winter may be the most effective management action to reduce C. shasta-related disease in the Klamath River. This action could potentially be achieved by increasing discharge during the winter to minimize contact between the polychaete host and myxospore stage. Lastly, I applied the mixture cure models to quantify how the daily survival rates of Chinook and coho salmon change over time after the fish become infected with C. shasta. Although varied in approach, the output from both of the models presented in this dissertation can be used to guide management and conservation actions for fish populations affected by myxozoan parasites. Close

• 493. [Article] Carbon Dynamics in Response to Land Cover Change in Tropical Peatlands, Kalimantan, Indonesia

  This study focuses in providing the knowledge on carbon (C) stocks, emission and ecosystem productivity related to land use/land cover change in tropical peatlands. The field research activities were ...

  Citation × Citation Citation Abstract Copy Title: Carbon Dynamics in Response to Land Cover Change in Tropical Peatlands, Kalimantan, Indonesia Author: Basuki, Imam This study focuses in providing the knowledge on carbon (C) stocks, emission and ecosystem productivity related to land use/land cover change in tropical peatlands. The field research activities were conducted for about 17 months between August 2013 to December 2015, at Pematang Gadung peat dome (peat depth up to 10.5 m), Ketapang Regency, West Kalimantan, Indonesia. The objectives of this study were: a). to quantify C stocks of tropical coastal peat swamp forest, and the potential impact of forest degradation due to draining and logging activities on the forest’s carbon stocks; b). to examine the change in ecosystem C stocks and the potential C emissions in relation to land conversion from intact peat swamp forest (PSF) to logged peat forest (LPSF), early seral (ES) and oil palm plantation (OP); and c). to estimate net primary production (NPP) and net ecosystem production (NEP) in peat swamp forests, logged peat forest, early seral and smallholder - oil palm plantations. The intact peat forest sites have higher total aboveground C stocks (125 Mg C ha-1) than the logged peat forest sites (77 Mg C ha-1). Mean depths of the LPSF was 725 cm and the PSF was 915 cm (p= 0.06). Mean peat carbon stocks at PSF was 4,243 Mg C ha-1, higher than at LPSF that was 3,675 Mg C ha-1. Logging and draining had reduced the biomass of trees and the peat carbon pools. My study demonstrated that tropical coastal PSF has the largest total carbon stocks among terrestrial ecosystems on earth. The large carbon stocks and high rates of PSF degradation, points to the relevance for inclusion of PSF in nationally appropriate climate change mitigation and adaptation strategies. The mean ecosystem carbon stock for the PSF sites was 4,401 Mg C ha-1. Ecosystem C stocks of LPSF, ES and OP was 3,768, 3,147, and 3,442 Mg C ha-1, respectively. PSF stocks was significantly higher than the degraded land covers. At all sites, soils comprised > 96% of the mean ecosystem carbon stock. Using the estimation based on ecosystem carbon loss to total peat depths, the conversion of PSF to LPSF, ES and OP was estimated to result in a net loss of 1,982, 4,259 and 3,176 Mg C-CO2 ha-1, respectively. My results confirm that land cover change significantly impacted soil properties and reduced ecosystem carbon stocks. The tropical peatlands need urgent and significant efforts in conservation and restoration, to regain its function as a C sink and mitigate climate change. I found that land use/land cover change resulted in large shifts in NPP and NEP. LPSF, ES and OP have significantly lower NPP (11.1 Mg C ha-1 yr-1, 10.8 Mg C ha-1 yr-1 and 3.7 Mg C ha-1 yr-1, respectively) than PSF (13.2 Mg C ha-1 yr-1). ES showed lower heterotrophic respiration (30.7 Mg CO2 ha-1 yr-1) than PSF, LPSF and OP (37.7 Mg CO2 ha-1 yr-1, 40.7 Mg CO2 ha-1 yr-1, 38.7 Mg CO2 ha-1 yr-1, respectively). LPSF and OP were net carbon sources; they have negative mean NEP values (-0.1 Mg CO2-e ha-1 yr-1 and -25.1 Mg CO2-e ha-1 yr-1, respectively). In contrast PSF and ES were net carbon sinks (10.8 Mg CO2-e ha-1 yr-1 and 9.1 CCO2 ha-1 yr-1, respectively). PSF is among the most productive of terrestrial ecosystems, with an NPP exceeding that of many tropical rain forests and similar to the most productive mangrove ecosystems. I found that land use decreases productivity of the LPSF and OP sites. The ES had a similar NEP to the PSF, but frequent fires in this ecosystem likely offset carbon gains during the fire intervals. Land use change and forest degradation have shifted tropical PSFs from net carbon sinks to net carbon sources. My study demonstrated that land conversion in tropical peat swamp forests should be halted and degraded peatlands need to be restored in order to mitigate climate change. Title: Carbon Dynamics in Response to Land Cover Change in Tropical Peatlands, Kalimantan, Indonesia Author: Basuki, Imam This study focuses in providing the knowledge on carbon (C) stocks, emission and ecosystem productivity related to land use/land cover change in tropical peatlands. The field research activities were conducted for about 17 months between August 2013 to December 2015, at Pematang Gadung peat dome (peat depth up to 10.5 m), Ketapang Regency, West Kalimantan, Indonesia. The objectives of this study were: a). to quantify C stocks of tropical coastal peat swamp forest, and the potential impact of forest degradation due to draining and logging activities on the forest’s carbon stocks; b). to examine the change in ecosystem C stocks and the potential C emissions in relation to land conversion from intact peat swamp forest (PSF) to logged peat forest (LPSF), early seral (ES) and oil palm plantation (OP); and c). to estimate net primary production (NPP) and net ecosystem production (NEP) in peat swamp forests, logged peat forest, early seral and smallholder - oil palm plantations. The intact peat forest sites have higher total aboveground C stocks (125 Mg C ha-1) than the logged peat forest sites (77 Mg C ha-1). Mean depths of the LPSF was 725 cm and the PSF was 915 cm (p= 0.06). Mean peat carbon stocks at PSF was 4,243 Mg C ha-1, higher than at LPSF that was 3,675 Mg C ha-1. Logging and draining had reduced the biomass of trees and the peat carbon pools. My study demonstrated that tropical coastal PSF has the largest total carbon stocks among terrestrial ecosystems on earth. The large carbon stocks and high rates of PSF degradation, points to the relevance for inclusion of PSF in nationally appropriate climate change mitigation and adaptation strategies. The mean ecosystem carbon stock for the PSF sites was 4,401 Mg C ha-1. Ecosystem C stocks of LPSF, ES and OP was 3,768, 3,147, and 3,442 Mg C ha-1, respectively. PSF stocks was significantly higher than the degraded land covers. At all sites, soils comprised > 96% of the mean ecosystem carbon stock. Using the estimation based on ecosystem carbon loss to total peat depths, the conversion of PSF to LPSF, ES and OP was estimated to result in a net loss of 1,982, 4,259 and 3,176 Mg C-CO2 ha-1, respectively. My results confirm that land cover change significantly impacted soil properties and reduced ecosystem carbon stocks. The tropical peatlands need urgent and significant efforts in conservation and restoration, to regain its function as a C sink and mitigate climate change. I found that land use/land cover change resulted in large shifts in NPP and NEP. LPSF, ES and OP have significantly lower NPP (11.1 Mg C ha-1 yr-1, 10.8 Mg C ha-1 yr-1 and 3.7 Mg C ha-1 yr-1, respectively) than PSF (13.2 Mg C ha-1 yr-1). ES showed lower heterotrophic respiration (30.7 Mg CO2 ha-1 yr-1) than PSF, LPSF and OP (37.7 Mg CO2 ha-1 yr-1, 40.7 Mg CO2 ha-1 yr-1, 38.7 Mg CO2 ha-1 yr-1, respectively). LPSF and OP were net carbon sources; they have negative mean NEP values (-0.1 Mg CO2-e ha-1 yr-1 and -25.1 Mg CO2-e ha-1 yr-1, respectively). In contrast PSF and ES were net carbon sinks (10.8 Mg CO2-e ha-1 yr-1 and 9.1 CCO2 ha-1 yr-1, respectively). PSF is among the most productive of terrestrial ecosystems, with an NPP exceeding that of many tropical rain forests and similar to the most productive mangrove ecosystems. I found that land use decreases productivity of the LPSF and OP sites. The ES had a similar NEP to the PSF, but frequent fires in this ecosystem likely offset carbon gains during the fire intervals. Land use change and forest degradation have shifted tropical PSFs from net carbon sinks to net carbon sources. My study demonstrated that land conversion in tropical peat swamp forests should be halted and degraded peatlands need to be restored in order to mitigate climate change. Close

• 494. [Article] Converting forest biomass to energy in Oregon : stakeholder perspectives on a growing movement

  Within Oregon there is considerable interest in the possibility of converting woody biomass to energy. This interest stems from three converging factors: the desire to reduce the threat of uncharacteristic ...

  Citation × Citation Citation Abstract Copy Title: Converting forest biomass to energy in Oregon : stakeholder perspectives on a growing movement Author: Stidham, Melanie Within Oregon there is considerable interest in the possibility of converting woody biomass to energy. This interest stems from three converging factors: the desire to reduce the threat of uncharacteristic wildfire by removing excess material from the forests, the possibility to stimulate rural economies that are dependent on forest products, and generation of renewable and/or clean energy from a local source. There have been a number of studies to assess the feasibility of wide-scale conversion of biomass to energy. These efforts have largely focused on technical barriers to the use of biomass for energy rather than social barriers. This study explores the social context of converting forest biomass to energy, through use of semi-structured interviews. Forty interviewees were purposively selected from the following Oregon stakeholder groups: federal and state agencies, elected officials, community organizations, conservation organizations, the forest industry sector, Tribes, energy utilities and non-utility energy experts. Information gained through the interviews was used to meet two research objectives: 1) to understand stakeholders' views on converting forest biomass to energy in Oregon; 2) to identify, from the perspectives of stakeholders, the opportunities for and barriers to converting forest biomass to energy, and potential strategies to overcome the barriers. In addition, there were two secondary objectives: a) to identify areas of common ground and conflict between and within stakeholder groups; and b) to identify policy components that would be necessary in the integration of the forestry and energy industries in Oregon. Among research participants there was wide agreement on what constitutes forest biomass; typically small diameter material that is currently non-merchantable, produced as a by-product of restoration or other forest management activities. There was most agreement that restoration treatments are needed in low-elevation ponderosa pine forests in eastern and southwestern Oregon to reduce the risk of uncharacteristically large and severe wildfire. It is this risk of unusually intense wildfire that many research participants felt was driving this issue in Oregon, rather than potential energy or rural economic development benefits. Many research participants wanted at-risk forests restored to conditions within their historic/natural range of variability, which depended on site specific characteristics, but generally meant fewer trees per acre and inclusion of low-intensity fire. The top three reasons research participants were interested in biomass utilization were the opportunities to generate renewable energy, restore forests, and stimulate economic growth in rural communities. While participants were enthusiastic about these opportunities, they brought up a number of barriers that would have to be addressed before the full suite of opportunities could be realized. The most vital and most challenging barrier was access to supply. Factors making supply more difficult to secure included the expense associated with long transport distances, and that while supply needs to be long-term, continuous, inexpensive, and guaranteed, it is mostly on federal land, where the public is involved in land management decisions and politics plays a role. Another challenge is the long history of contention between parties related to forest products coming from federal land, and these parties would have to all agree that biomass utilization using supply from federal forests is acceptable before supply could be made available. Many research participants suggested that collaboration could allow these projects to be developed in a manner acceptable to all parties. Costs could be federally subsidized to make projects more feasible. Participants encouraged development of pilot projects to move discussion from speculation to actuality. Many research participants expressed more comfort in smaller energy facilities to prevent energy needs from dictating forest management, i.e., to prevent the tail from wagging the dog. The overarching goal of this research is to provide information useful to collaboration groups, policymakers, land managers, communities, and relevant advocacy groups to create a foundation for discussions as forest biomass energy becomes an increasingly prominent issue in Oregon. Title: Converting forest biomass to energy in Oregon : stakeholder perspectives on a growing movement Author: Stidham, Melanie Within Oregon there is considerable interest in the possibility of converting woody biomass to energy. This interest stems from three converging factors: the desire to reduce the threat of uncharacteristic wildfire by removing excess material from the forests, the possibility to stimulate rural economies that are dependent on forest products, and generation of renewable and/or clean energy from a local source. There have been a number of studies to assess the feasibility of wide-scale conversion of biomass to energy. These efforts have largely focused on technical barriers to the use of biomass for energy rather than social barriers. This study explores the social context of converting forest biomass to energy, through use of semi-structured interviews. Forty interviewees were purposively selected from the following Oregon stakeholder groups: federal and state agencies, elected officials, community organizations, conservation organizations, the forest industry sector, Tribes, energy utilities and non-utility energy experts. Information gained through the interviews was used to meet two research objectives: 1) to understand stakeholders' views on converting forest biomass to energy in Oregon; 2) to identify, from the perspectives of stakeholders, the opportunities for and barriers to converting forest biomass to energy, and potential strategies to overcome the barriers. In addition, there were two secondary objectives: a) to identify areas of common ground and conflict between and within stakeholder groups; and b) to identify policy components that would be necessary in the integration of the forestry and energy industries in Oregon. Among research participants there was wide agreement on what constitutes forest biomass; typically small diameter material that is currently non-merchantable, produced as a by-product of restoration or other forest management activities. There was most agreement that restoration treatments are needed in low-elevation ponderosa pine forests in eastern and southwestern Oregon to reduce the risk of uncharacteristically large and severe wildfire. It is this risk of unusually intense wildfire that many research participants felt was driving this issue in Oregon, rather than potential energy or rural economic development benefits. Many research participants wanted at-risk forests restored to conditions within their historic/natural range of variability, which depended on site specific characteristics, but generally meant fewer trees per acre and inclusion of low-intensity fire. The top three reasons research participants were interested in biomass utilization were the opportunities to generate renewable energy, restore forests, and stimulate economic growth in rural communities. While participants were enthusiastic about these opportunities, they brought up a number of barriers that would have to be addressed before the full suite of opportunities could be realized. The most vital and most challenging barrier was access to supply. Factors making supply more difficult to secure included the expense associated with long transport distances, and that while supply needs to be long-term, continuous, inexpensive, and guaranteed, it is mostly on federal land, where the public is involved in land management decisions and politics plays a role. Another challenge is the long history of contention between parties related to forest products coming from federal land, and these parties would have to all agree that biomass utilization using supply from federal forests is acceptable before supply could be made available. Many research participants suggested that collaboration could allow these projects to be developed in a manner acceptable to all parties. Costs could be federally subsidized to make projects more feasible. Participants encouraged development of pilot projects to move discussion from speculation to actuality. Many research participants expressed more comfort in smaller energy facilities to prevent energy needs from dictating forest management, i.e., to prevent the tail from wagging the dog. The overarching goal of this research is to provide information useful to collaboration groups, policymakers, land managers, communities, and relevant advocacy groups to create a foundation for discussions as forest biomass energy becomes an increasingly prominent issue in Oregon. Close

• 495. [Article] Downstream rearing of juvenile Chinook salmon abundance, distribution and growth in the Upper Mainstem of the John Day River

  Abstract -- Juvenile spring Chinook (Oncorhynchus tshawytscha) emerge from the gravel in the late winter or early spring, and most follow a life history pattern known as Natal Reach Rearing (NRR) in which ...

  Citation × Citation Citation Abstract Copy Title: Downstream rearing of juvenile Chinook salmon abundance, distribution and growth in the Upper Mainstem of the John Day River Abstract -- Juvenile spring Chinook (Oncorhynchus tshawytscha) emerge from the gravel in the late winter or early spring, and most follow a life history pattern known as Natal Reach Rearing (NRR) in which juvenile fish remain in the stream reaches where they were spawned until their second spring of life when they start migrating towards the ocean (Healey 1991). However, in Columbia River tributaries, some juveniles have been observed following a Downstream Rearing (DSR) life history, in which they start moving downstream during their first spring towards other nursery habitats or perhaps ocean rearing (Copeland & Venditti 2009; Schroeder et al. 2016). Rearing in different habitats during their first year gives fish with these two life histories access to diverse food resources and, it is hypothesized that, this leads to different survival and growth advantages for these two groups. Differences in growth are of interest in efforts to conserve this threatened species because size is positively correlated to survival for salmon across multiple stages of their life cycle (Groot & Margolis 1991; Healey 1991; Quinn & Peterson 1996; Roni et al. 2012) Chinook salmon in the upper John Day River, Oregon, exhibit both NRR and DSR life history patterns. Fish following the DSR life history pattern are larger than NRR fish late in the spring, possibly due to factors such as higher fish density, lower stream productivity, and colder water temperatures in their natal reach than in the downstream reaches. However, this size advantage may be lost due to adverse summer conditions. Hot summer days combined with the withdrawal of water for agriculture lead to stream water temperatures well above lethal thresholds for salmon in many downstream reaches. DSR fish have been observed in tributaries of the mainstem John Day River, however their growth and survival during summer is unknown. Title: Downstream rearing of juvenile Chinook salmon abundance, distribution and growth in the Upper Mainstem of the John Day River Abstract -- Juvenile spring Chinook (Oncorhynchus tshawytscha) emerge from the gravel in the late winter or early spring, and most follow a life history pattern known as Natal Reach Rearing (NRR) in which juvenile fish remain in the stream reaches where they were spawned until their second spring of life when they start migrating towards the ocean (Healey 1991). However, in Columbia River tributaries, some juveniles have been observed following a Downstream Rearing (DSR) life history, in which they start moving downstream during their first spring towards other nursery habitats or perhaps ocean rearing (Copeland & Venditti 2009; Schroeder et al. 2016). Rearing in different habitats during their first year gives fish with these two life histories access to diverse food resources and, it is hypothesized that, this leads to different survival and growth advantages for these two groups. Differences in growth are of interest in efforts to conserve this threatened species because size is positively correlated to survival for salmon across multiple stages of their life cycle (Groot & Margolis 1991; Healey 1991; Quinn & Peterson 1996; Roni et al. 2012) Chinook salmon in the upper John Day River, Oregon, exhibit both NRR and DSR life history patterns. Fish following the DSR life history pattern are larger than NRR fish late in the spring, possibly due to factors such as higher fish density, lower stream productivity, and colder water temperatures in their natal reach than in the downstream reaches. However, this size advantage may be lost due to adverse summer conditions. Hot summer days combined with the withdrawal of water for agriculture lead to stream water temperatures well above lethal thresholds for salmon in many downstream reaches. DSR fish have been observed in tributaries of the mainstem John Day River, however their growth and survival during summer is unknown. Close

• 496. [Image] Oregon aquatic habitat restoration and enhancement guide

  	"May 1999"
  	Citation × Citation Citation Abstract Copy Title: Oregon aquatic habitat restoration and enhancement guide Author: Oregon Plan for Salmon and Watersheds Year: 1999, 2005, 2004 "May 1999" Title: Oregon aquatic habitat restoration and enhancement guide Author: Oregon Plan for Salmon and Watersheds Year: 1999, 2005, 2004 "May 1999" Close

• 497. [Image] The Water Report - Critical habitat, bull trout and politics

  	Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. Includes bibliographical references. See the full report at http://www.thewaterreport.com/
  	Citation × Citation Citation Abstract Copy Title: The Water Report - Critical habitat, bull trout and politics Author: Envirotech Publications Year: 2005, 2008, 2006 Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. Includes bibliographical references. See the full report at http://www.thewaterreport.com/ Title: The Water Report - Critical habitat, bull trout and politics Author: Envirotech Publications Year: 2005, 2008, 2006 Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. Includes bibliographical references. See the full report at http://www.thewaterreport.com/ Close

• 498. [Image] Review of the hatchery measures in the Oregon plan for salmon and watersheds. Part I, Consistency of the Oregon plan with recommendations from recent scientific review panels

  	"December 10, 1998."
  	Citation × Citation Citation Abstract Copy Title: Review of the hatchery measures in the Oregon plan for salmon and watersheds. Part I, Consistency of the Oregon plan with recommendations from recent scientific review panels Author: Independent Multidisciplinary Science Team (Or.) Year: 1998, 2005 "December 10, 1998." Title: Review of the hatchery measures in the Oregon plan for salmon and watersheds. Part I, Consistency of the Oregon plan with recommendations from recent scientific review panels Author: Independent Multidisciplinary Science Team (Or.) Year: 1998, 2005 "December 10, 1998." Close

• 499. [Image] Klamath Basin summary of recent federal government activities, March 2003

  	The Department of the Interior, Klamath River Basin Work Plans and Reports
  	Citation × Citation Citation Abstract Copy Title: Klamath Basin summary of recent federal government activities, March 2003 Author: United States. Dept. of the Interior Year: 2003, 2005 The Department of the Interior, Klamath River Basin Work Plans and Reports Title: Klamath Basin summary of recent federal government activities, March 2003 Author: United States. Dept. of the Interior Year: 2003, 2005 The Department of the Interior, Klamath River Basin Work Plans and Reports Close

• 500. [Image] Endangered Species Act : successes and challenges in agency collaboration and the use of scientific information in the decision making process : testimony before the Subcommittee on Fisheries, Wildlife and Water, Committee on Environment and Public Works, United States Senate / statement of Robin M. Nazzaro

  	Summary In summary, we found that federal agencies have taken steps to improve collaboration as a way to reduce conflicts that often occur between species protections and other resource uses, but that ...
  	Citation × Citation Citation Abstract Copy Title: Endangered Species Act : successes and challenges in agency collaboration and the use of scientific information in the decision making process : testimony before the Subcommittee on Fisheries, Wildlife and Water, Committee on Environment and Public Works, United States Senate / statement of Robin M. Nazzaro Author: Nazzaro, Robin M Year: 2005, 2007 Summary In summary, we found that federal agencies have taken steps to improve collaboration as a way to reduce conflicts that often occur between species protections and other resource uses, but that more could be done to promote routine use of collaboration and clarify agencies' responsibilities under the Endangered Species Act. In September 2003, we reported on efforts taken by the Department of Defense (DOD) to coordinate with other federal land managers in order to reduce the impact of species protections on military activities. We found several cases where such efforts were successful. For example, at the Barry M. Goldwater range in Arizona, Air Force officials worked with officials at FWS and the National Park Service to enhance food sources for the endangered Sonoran pronghorn in locations away from military training areas. As a result, the Air Force was able to minimize the impact of restrictions on training missions due to the presence of the pronghorn. However, such cases were few and far between because, among other things, there were no procedures or centralized information sources for facilitating such collaboration. In March 2004, we reported on collaboration that takes place pursuant to section 7(a)(2) of the act?referred to as the consultation process?in the Pacific Northwest. In this area, large numbers of protected species and vast amounts of federal land conspire to make balancing species protection and resource use a contentious endeavor. We found that steps the Services and other federal agencies had taken made the consultation process run smoother and contributed to improved interagency relationships. However, some problems have persisted. For example, some agencies disagree with the Services about when consultation is necessary and how much analysis is required to determine potential impacts on protected species. In each of these reports, we made recommendations intended to further improve collaboration among federal agencies with regard to balancing species protections and other resource uses, and?in the March 2004 report?to resolve disagreements about the consultations process. DOD and FWS have begun discussing an implementation strategy to improve collaboration regarding species protection on military and other federal lands and development of a training program. With regard to the consultation process, while FWS and NMFS have continued to take steps to expand their collaboration processes, the agencies did not believe that disagreements about the consultation process require additional steps. They believe that current training and guidance is sufficient to address questions about the process. With regard to the use of science, we have found that FWS generally used the best available information in key Endangered Species Act decisions, although the agency was not always integrating new research into ongoing species management decisions. In addition, we identified concerns with the adequacy of the information available to make critical habitat decisions. In December 2002, we reported on many aspects of the decision making for species protections regarding the Mojave Desert tortoise. We found that the decision to list the tortoise as threatened, its critical habitat designation, and the recommended steps in the species' recovery plan, were based on the best available information. However, despite over $100 million in expenditures on recovery actions and research over the past 25 years, it is still unclear what the status of the tortoise is and what effect, if any, recovery actions are having on the species because research has not been coordinated in a way to provide essential management information. Such information is critically important as some of the protective actions, such as restrictions on grazing and off road vehicle use, are vigorously opposed by interest groups who question whether they are necessary for the tortoise's recovery. Accordingly, we recommended that FWS better link land management decisions with research results to ensure that conservation actions and land use restrictions actually benefit the tortoise. In response, FWS recently established a new office with a tortoise recovery coordinator and plans to create an advisory committee to ensure that monitoring and recovery actions are fed back into management decisions. In August 2003, we found that, similar to the decision making regarding the tortoise, FWS decisions about listing species for protection under the act were generally based on the best available information. However, while most critical habitat designations also appeared to be based on the best available information, there were concerns about the adequacy of the information available at the time these decisions are made. Specifically, critical habitat decisions require detailed information of a species' life history and habitat needs and the economic impacts of such decisions?information that is often not available and that FWS is unable to gather before it is obligated under the act to make the decision. As a result, we recommended that the Secretary of the Interior clarify how and when critical habitat should be designated and identify if any policy, regulatory, or legislative changes are required to enable the department to make better informed designations. FWS has not responded to our recommendation. Title: Endangered Species Act : successes and challenges in agency collaboration and the use of scientific information in the decision making process : testimony before the Subcommittee on Fisheries, Wildlife and Water, Committee on Environment and Public Works, United States Senate / statement of Robin M. Nazzaro Author: Nazzaro, Robin M Year: 2005, 2007 Summary In summary, we found that federal agencies have taken steps to improve collaboration as a way to reduce conflicts that often occur between species protections and other resource uses, but that more could be done to promote routine use of collaboration and clarify agencies' responsibilities under the Endangered Species Act. In September 2003, we reported on efforts taken by the Department of Defense (DOD) to coordinate with other federal land managers in order to reduce the impact of species protections on military activities. We found several cases where such efforts were successful. For example, at the Barry M. Goldwater range in Arizona, Air Force officials worked with officials at FWS and the National Park Service to enhance food sources for the endangered Sonoran pronghorn in locations away from military training areas. As a result, the Air Force was able to minimize the impact of restrictions on training missions due to the presence of the pronghorn. However, such cases were few and far between because, among other things, there were no procedures or centralized information sources for facilitating such collaboration. In March 2004, we reported on collaboration that takes place pursuant to section 7(a)(2) of the act?referred to as the consultation process?in the Pacific Northwest. In this area, large numbers of protected species and vast amounts of federal land conspire to make balancing species protection and resource use a contentious endeavor. We found that steps the Services and other federal agencies had taken made the consultation process run smoother and contributed to improved interagency relationships. However, some problems have persisted. For example, some agencies disagree with the Services about when consultation is necessary and how much analysis is required to determine potential impacts on protected species. In each of these reports, we made recommendations intended to further improve collaboration among federal agencies with regard to balancing species protections and other resource uses, and?in the March 2004 report?to resolve disagreements about the consultations process. DOD and FWS have begun discussing an implementation strategy to improve collaboration regarding species protection on military and other federal lands and development of a training program. With regard to the consultation process, while FWS and NMFS have continued to take steps to expand their collaboration processes, the agencies did not believe that disagreements about the consultation process require additional steps. They believe that current training and guidance is sufficient to address questions about the process. With regard to the use of science, we have found that FWS generally used the best available information in key Endangered Species Act decisions, although the agency was not always integrating new research into ongoing species management decisions. In addition, we identified concerns with the adequacy of the information available to make critical habitat decisions. In December 2002, we reported on many aspects of the decision making for species protections regarding the Mojave Desert tortoise. We found that the decision to list the tortoise as threatened, its critical habitat designation, and the recommended steps in the species' recovery plan, were based on the best available information. However, despite over $100 million in expenditures on recovery actions and research over the past 25 years, it is still unclear what the status of the tortoise is and what effect, if any, recovery actions are having on the species because research has not been coordinated in a way to provide essential management information. Such information is critically important as some of the protective actions, such as restrictions on grazing and off road vehicle use, are vigorously opposed by interest groups who question whether they are necessary for the tortoise's recovery. Accordingly, we recommended that FWS better link land management decisions with research results to ensure that conservation actions and land use restrictions actually benefit the tortoise. In response, FWS recently established a new office with a tortoise recovery coordinator and plans to create an advisory committee to ensure that monitoring and recovery actions are fed back into management decisions. In August 2003, we found that, similar to the decision making regarding the tortoise, FWS decisions about listing species for protection under the act were generally based on the best available information. However, while most critical habitat designations also appeared to be based on the best available information, there were concerns about the adequacy of the information available at the time these decisions are made. Specifically, critical habitat decisions require detailed information of a species' life history and habitat needs and the economic impacts of such decisions?information that is often not available and that FWS is unable to gather before it is obligated under the act to make the decision. As a result, we recommended that the Secretary of the Interior clarify how and when critical habitat should be designated and identify if any policy, regulatory, or legislative changes are required to enable the department to make better informed designations. FWS has not responded to our recommendation. Close