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• 1. [Article] Can Salmonids (Oncorhynchus spp.) Be Identified to Species Using Vertebral Morphometrics?

  Remains of anadromous Pacific salmon and trout (genus Oncorhynchus) are common in archaeological sites from California to Alaska; however, morphological similarity generally precludes species identification, ...

  Citation × Citation Citation Abstract Copy Title: Can Salmonids (Oncorhynchus spp.) Be Identified to Species Using Vertebral Morphometrics? Author: Huber, Harriet R., Jorgensen, Jeffery C., Butler, Virginia L., Baker, Greg, Stevens, Rebecca Year: 2011 Remains of anadromous Pacific salmon and trout (genus Oncorhynchus) are common in archaeological sites from California to Alaska; however, morphological similarity generally precludes species identification, limiting the range of questions that salmonid remains can address in relation to past human use and ongoing efforts in conservation biology. We developed a relatively simple, rapid, and non-destructive way to classify salmon and trout vertebrae from archaeological contexts to species using length, height and the ratio of length to height. Modern reference material was obtained from all seven anadromous Oncorhynchus species native to the west coast of North America. A minimum of ten adult Chinook (Oncorhynchus tshawytscha), chum (O. keta), coho (O. kisutch), pink (O.gorbuscha), and sockeye salmon (O. nerka) and cutthroat (O. clarki clarki) and steelhead trout (O. mykiss) were skeletonized and vertebra length and height were measured. Morphometric analyses compared species classification success based on Linear Discriminant Analysis (LDA), Classification and Regression Trees (CART), and randomForest, with CART performing the best. Classification analyses used all seven species individually, but because of considerable overlap among several species we also conducted analyses on four species groupings. We assigned Chinook salmon and cutthroat to their own groups based on their dissimilarities from each other and the other species. The remaining species were divided into two group complexes (a) chum, coho, and steelhead; and (b) pink and sockeye. When we grouped species according to similar morphology, CART overall success rates increased, ranging from 92 to 100%. Individual species with the highest successful classification rates using CART were Chinook salmon and cutthroat, from 92 to 100%, respectively. We applied our classification to an assemblage of ancient (1000 to 3000 year old) salmonid vertebrae from the Swiftwater Rockshelters excavations on the upper Wenatchee River in Washington State, U.S.A. Title: Can Salmonids (Oncorhynchus spp.) Be Identified to Species Using Vertebral Morphometrics? Author: Huber, Harriet R., Jorgensen, Jeffery C., Butler, Virginia L., Baker, Greg, Stevens, Rebecca Year: 2011 Remains of anadromous Pacific salmon and trout (genus Oncorhynchus) are common in archaeological sites from California to Alaska; however, morphological similarity generally precludes species identification, limiting the range of questions that salmonid remains can address in relation to past human use and ongoing efforts in conservation biology. We developed a relatively simple, rapid, and non-destructive way to classify salmon and trout vertebrae from archaeological contexts to species using length, height and the ratio of length to height. Modern reference material was obtained from all seven anadromous Oncorhynchus species native to the west coast of North America. A minimum of ten adult Chinook (Oncorhynchus tshawytscha), chum (O. keta), coho (O. kisutch), pink (O.gorbuscha), and sockeye salmon (O. nerka) and cutthroat (O. clarki clarki) and steelhead trout (O. mykiss) were skeletonized and vertebra length and height were measured. Morphometric analyses compared species classification success based on Linear Discriminant Analysis (LDA), Classification and Regression Trees (CART), and randomForest, with CART performing the best. Classification analyses used all seven species individually, but because of considerable overlap among several species we also conducted analyses on four species groupings. We assigned Chinook salmon and cutthroat to their own groups based on their dissimilarities from each other and the other species. The remaining species were divided into two group complexes (a) chum, coho, and steelhead; and (b) pink and sockeye. When we grouped species according to similar morphology, CART overall success rates increased, ranging from 92 to 100%. Individual species with the highest successful classification rates using CART were Chinook salmon and cutthroat, from 92 to 100%, respectively. We applied our classification to an assemblage of ancient (1000 to 3000 year old) salmonid vertebrae from the Swiftwater Rockshelters excavations on the upper Wenatchee River in Washington State, U.S.A. Close

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

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

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

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

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

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

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

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

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

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

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

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