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• 1. [Article] Development of a Standardized DNA Database for Chinook Salmon

  An international multi-laboratory project was conducted to develop a standardized DNA database for Chinook salmon (Oncorhynchus tshawytscha). This project was in response to the needs of the Chinook Technical ...

  Citation × Citation Citation Abstract Copy Title: Development of a Standardized DNA Database for Chinook Salmon Author: Beacham, T.D., Banks, Michael A., Stephenson, J.J., Guthrie III, C.M., Antonovich, A., Templin, W.D., Seeb, L.W., Decovich, N.A., Lundrigan, T.A., Bellinger, M.R., Campbell, M.R., Blankenship, S.M., Wenburg, J.K., Garza, J.C., Supernault, K.J., Narum, S.R., Moran, P., Smith, C.T., Teel, D.J., Young, S.F. An international multi-laboratory project was conducted to develop a standardized DNA database for Chinook salmon (Oncorhynchus tshawytscha). This project was in response to the needs of the Chinook Technical Committee of the Pacific Salmon Commission to identify stock composition of Chinook salmon caught in fisheries during their oceanic migrations. Nine genetics laboratories identified 13 microsatellite loci that could be reproducibly assayed in each of the laboratories. To test that the loci were reproducible among laboratories, blind tests were conducted to verify scoring consistency for the nearly 500 total alleles. Once standardized, a dataset of over 16,000 Chinook salmon representing 110 putative populations was constructed ranging throughout the area of interest of the Pacific Salmon Commission from Southeast Alaska to the Sacramento River in California. The dataset differentiates the major known genetic lineages of Chinook salmon and provides a tool for genetic stock identification of samples collected from mixed fisheries. A diverse group of scientists representing the disciplines of fishery management, genetics, fishery administration, population dynamics, and sampling theory are now developing recommendations for the integration of these genetic data into ocean salmon management.Original Abstract: Se realizo un proyecto internacional con la participation de diversos laboratorios con la finalidad de desarrollar una base de datos estandarizada de DNA para el salmon rey (Oncorhynchus tshawytscha). Dicho proyecto surgi6 como respuesta a las necesidades del Comite Tecnico Chinook de la Comision del Salmon del Pacifico para identificar la composition poblacional del salmon rey que es capturado por la pesqueria durante su migration. Un total de nueve laboratorios de analisis geneticos identificaron y reprodujeron cada uno 13 loci microsatelites. Con el objeto de probar que dichos loci fueran reproducibles entre laboratorios, se condujeron pruebas anonimas para verificar la consistencia de casi 500 alelos. Una vez estandarizada, se construyo una base de datos construida con information proveniente de mas de 16,000 salmones que representan 110 poblaciones putativas distribuidas a lo largo del area de interes de la Comision del Salm6n del Pacifico, del sureste de Alaska hasta el Rio Sacramento, California. La base de datos sirve tanto para identificar gene'ticamente los distintos stocks de salmon rey a partir de muestras combinadas provenientes de la pesqueria como para diferenciar el linaje genetico conocido mas importante de esta especie. En la actualidad, un importante grupo de cientificos especializados en disciplinas como el manejo y administracion de pesquerias, genetica, dinamica poblacional y teoria del muestreo estan desarrollando recomendaciones para que esta base de datos geneticos se incorpore en el manejo del salmon. Title: Development of a Standardized DNA Database for Chinook Salmon Author: Beacham, T.D., Banks, Michael A., Stephenson, J.J., Guthrie III, C.M., Antonovich, A., Templin, W.D., Seeb, L.W., Decovich, N.A., Lundrigan, T.A., Bellinger, M.R., Campbell, M.R., Blankenship, S.M., Wenburg, J.K., Garza, J.C., Supernault, K.J., Narum, S.R., Moran, P., Smith, C.T., Teel, D.J., Young, S.F. An international multi-laboratory project was conducted to develop a standardized DNA database for Chinook salmon (Oncorhynchus tshawytscha). This project was in response to the needs of the Chinook Technical Committee of the Pacific Salmon Commission to identify stock composition of Chinook salmon caught in fisheries during their oceanic migrations. Nine genetics laboratories identified 13 microsatellite loci that could be reproducibly assayed in each of the laboratories. To test that the loci were reproducible among laboratories, blind tests were conducted to verify scoring consistency for the nearly 500 total alleles. Once standardized, a dataset of over 16,000 Chinook salmon representing 110 putative populations was constructed ranging throughout the area of interest of the Pacific Salmon Commission from Southeast Alaska to the Sacramento River in California. The dataset differentiates the major known genetic lineages of Chinook salmon and provides a tool for genetic stock identification of samples collected from mixed fisheries. A diverse group of scientists representing the disciplines of fishery management, genetics, fishery administration, population dynamics, and sampling theory are now developing recommendations for the integration of these genetic data into ocean salmon management.Original Abstract: Se realizo un proyecto internacional con la participation de diversos laboratorios con la finalidad de desarrollar una base de datos estandarizada de DNA para el salmon rey (Oncorhynchus tshawytscha). Dicho proyecto surgi6 como respuesta a las necesidades del Comite Tecnico Chinook de la Comision del Salmon del Pacifico para identificar la composition poblacional del salmon rey que es capturado por la pesqueria durante su migration. Un total de nueve laboratorios de analisis geneticos identificaron y reprodujeron cada uno 13 loci microsatelites. Con el objeto de probar que dichos loci fueran reproducibles entre laboratorios, se condujeron pruebas anonimas para verificar la consistencia de casi 500 alelos. Una vez estandarizada, se construyo una base de datos construida con information proveniente de mas de 16,000 salmones que representan 110 poblaciones putativas distribuidas a lo largo del area de interes de la Comision del Salm6n del Pacifico, del sureste de Alaska hasta el Rio Sacramento, California. La base de datos sirve tanto para identificar gene'ticamente los distintos stocks de salmon rey a partir de muestras combinadas provenientes de la pesqueria como para diferenciar el linaje genetico conocido mas importante de esta especie. En la actualidad, un importante grupo de cientificos especializados en disciplinas como el manejo y administracion de pesquerias, genetica, dinamica poblacional y teoria del muestreo estan desarrollando recomendaciones para que esta base de datos geneticos se incorpore en el manejo del salmon. Close

• 2. [Article] Differential gene expression between fall- and spring-run Chinook salmon assessed by long serial analysis of gene expression

  Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been ...

  Citation × Citation Citation Abstract Copy Title: Differential gene expression between fall- and spring-run Chinook salmon assessed by long serial analysis of gene expression Author: Banks, Michael A., McArthur, Andrew G., Birkeland, Shanda R., Bernier, Jeremiah C., Cipriano, Michael J. Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been well described. Current methods, such as long serial analysis of gene expression (LongSAGE) and microarrays, allow gene expression to be analyzed for thousands of genes simultaneously. To investigate whether differential gene expression is observed between fall- and spring-run Chinook salmon from California's Central Valley, LongSAGE libraries were constructed. Three libraries containing between 25,512 and 29,372 sequenced tags (21 base pairs/tag) were generated using messenger RNA from the brains of adult Chinook salmon returning in fall and spring and from one ocean-caught Chinook salmon. Tags were annotated to genes using complementary DNA libraries from Atlantic salmon Salmo salar and rainbow trout O. mykiss. Differentially expressed genes, as estimated by differences in the number of sequence tags, were found in all pairwise comparisons of libraries (freshwater versus saltwater = 40 genes; fall versus spring = 11 genes; and spawning versus nonspawning = 51 genes). The gene for ependymin, an extracellular glycoprotein involved in behavioral plasticity in fish, exhibited the most differential expression among the three groupings. Reverse transcription polymerase chain reaction analysis verified the differential expression of ependymin between the fall- and spring-run samples. These LongSAGE libraries, the first reported for Chinook salmon, provide a window of the transcriptional changes during Chinook salmon return migration to freshwater and spawning and increase the amount of expressed sequence data. Title: Differential gene expression between fall- and spring-run Chinook salmon assessed by long serial analysis of gene expression Author: Banks, Michael A., McArthur, Andrew G., Birkeland, Shanda R., Bernier, Jeremiah C., Cipriano, Michael J. Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been well described. Current methods, such as long serial analysis of gene expression (LongSAGE) and microarrays, allow gene expression to be analyzed for thousands of genes simultaneously. To investigate whether differential gene expression is observed between fall- and spring-run Chinook salmon from California's Central Valley, LongSAGE libraries were constructed. Three libraries containing between 25,512 and 29,372 sequenced tags (21 base pairs/tag) were generated using messenger RNA from the brains of adult Chinook salmon returning in fall and spring and from one ocean-caught Chinook salmon. Tags were annotated to genes using complementary DNA libraries from Atlantic salmon Salmo salar and rainbow trout O. mykiss. Differentially expressed genes, as estimated by differences in the number of sequence tags, were found in all pairwise comparisons of libraries (freshwater versus saltwater = 40 genes; fall versus spring = 11 genes; and spawning versus nonspawning = 51 genes). The gene for ependymin, an extracellular glycoprotein involved in behavioral plasticity in fish, exhibited the most differential expression among the three groupings. Reverse transcription polymerase chain reaction analysis verified the differential expression of ependymin between the fall- and spring-run samples. These LongSAGE libraries, the first reported for Chinook salmon, provide a window of the transcriptional changes during Chinook salmon return migration to freshwater and spawning and increase the amount of expressed sequence data. Close

• 3. [Article] Microsatellites Reveal Population Identity of Individual Pink Salmon to Allow Supportive Breeding of a Population at Risk of Extinction

  Efforts to restore depressed populations of Pacific salmon Oncorhynchus spp. are often hampered by the inability to assign population identity to individuals in an admixture. This knowledge is of particular ...

  Citation × Citation Citation Abstract Copy Title: Microsatellites Reveal Population Identity of Individual Pink Salmon to Allow Supportive Breeding of a Population at Risk of Extinction Author: Shaklee, James B., Bentzen, Paul, Olsen, Jeffrey B., Young, Sewall, Banks, Michael A. Efforts to restore depressed populations of Pacific salmon Oncorhynchus spp. are often hampered by the inability to assign population identity to individuals in an admixture. This knowledge is of particular concern in supportive breeding programs, in which misidentification of individuals to population may result in progeny of mixed heritage, which, in turn, results in the erosion of the genetic population structure and of the existing genetic diversity and local adaptations of the target population. We evaluated two classes of genetic markers, allozymes and microsatellites, for estimating population identity of pink salmon Oncorhynchus gorbuscha in a supportive breeding program on the Dungeness River in Washington State. Fall-run pink salmon of the Dungeness River are the target of restoration, but they presumably overlap, in terms of timing, with an earlier summer run. Both marker types revealed similarly low estimates of relative genetic differentiation ( <(theta)over cap> = 0.02), which suggests that there is little variation in allele frequency among populations. However, microsatellites provided a more accurate estimate of population identity. When applying a log-likelihood ratio criterion of greater than 1.3, 74.8% of individuals were correctly assigned to population using microsatellites (versus 3.1% of individuals using allozymes). The difference in assignment accuracy was best predicted by the statistic <(delta)over cap>, which estimates cumulative allele frequency differences among populations. Our results suggest that genetic markers with many alleles are preferred when populations exhibit little genetic differentiation (as is the case in pink salmon), because <(delta)over cap> is more likely to be large, presumably as a result of genetic drift at each allele. The use of microsatellites to select fall-run pink salmon for supportive breeding confirmed the run-timing overlap and prevented unintentional crosses between the two populations. Title: Microsatellites Reveal Population Identity of Individual Pink Salmon to Allow Supportive Breeding of a Population at Risk of Extinction Author: Shaklee, James B., Bentzen, Paul, Olsen, Jeffrey B., Young, Sewall, Banks, Michael A. Efforts to restore depressed populations of Pacific salmon Oncorhynchus spp. are often hampered by the inability to assign population identity to individuals in an admixture. This knowledge is of particular concern in supportive breeding programs, in which misidentification of individuals to population may result in progeny of mixed heritage, which, in turn, results in the erosion of the genetic population structure and of the existing genetic diversity and local adaptations of the target population. We evaluated two classes of genetic markers, allozymes and microsatellites, for estimating population identity of pink salmon Oncorhynchus gorbuscha in a supportive breeding program on the Dungeness River in Washington State. Fall-run pink salmon of the Dungeness River are the target of restoration, but they presumably overlap, in terms of timing, with an earlier summer run. Both marker types revealed similarly low estimates of relative genetic differentiation ( <(theta)over cap> = 0.02), which suggests that there is little variation in allele frequency among populations. However, microsatellites provided a more accurate estimate of population identity. When applying a log-likelihood ratio criterion of greater than 1.3, 74.8% of individuals were correctly assigned to population using microsatellites (versus 3.1% of individuals using allozymes). The difference in assignment accuracy was best predicted by the statistic <(delta)over cap>, which estimates cumulative allele frequency differences among populations. Our results suggest that genetic markers with many alleles are preferred when populations exhibit little genetic differentiation (as is the case in pink salmon), because <(delta)over cap> is more likely to be large, presumably as a result of genetic drift at each allele. The use of microsatellites to select fall-run pink salmon for supportive breeding confirmed the run-timing overlap and prevented unintentional crosses between the two populations. Close

• 4. [Article] Umpqua Coho Salmon Genetic Pedigree

  Suggested citation: "Blouin, Michael S.; Banks, Michael A.; Moyer, Gregory R.; Theriault, Veronique; Whitcomb, Amelia; Loomis, David; Jackson, Laura S. (2013): Umpqua Coho Salmon Genetic Pedigree. Oregon ...

  Citation × Citation Citation Abstract Copy Title: Umpqua Coho Salmon Genetic Pedigree Author: Blouin, Michael S., Jackson, Laura S., Loomis, David, Theriault, Veronique, Moyer, Gregory R., Whitcomb, Amelia, Banks, Michael A. Suggested citation: "Blouin, Michael S.; Banks, Michael A.; Moyer, Gregory R.; Theriault, Veronique; Whitcomb, Amelia; Loomis, David; Jackson, Laura S. (2013): Umpqua Coho Salmon Genetic Pedigree. Oregon State University Libraries. Dataset. doi:10.7267/N9H41PB9." Title: Umpqua Coho Salmon Genetic Pedigree Author: Blouin, Michael S., Jackson, Laura S., Loomis, David, Theriault, Veronique, Moyer, Gregory R., Whitcomb, Amelia, Banks, Michael A. Suggested citation: "Blouin, Michael S.; Banks, Michael A.; Moyer, Gregory R.; Theriault, Veronique; Whitcomb, Amelia; Loomis, David; Jackson, Laura S. (2013): Umpqua Coho Salmon Genetic Pedigree. Oregon State University Libraries. Dataset. doi:10.7267/N9H41PB9." Close

• 5. [Article] Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s central valley

  Suggested citation: "Banks, Michael A. (2013): Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s Central Valley. Oregon State University Libraries. ...

  Citation × Citation Citation Abstract Copy Title: Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s central valley Author: Brandes, Pat, Rashbrook, Vanessa K., Bernier-Latmani, Jeremiah, Banks, Michael A., Jacobson, David P., Greene, Sheila, O’Malley, Kathleen G., Greig, Carolyn A., Van Sickle, John, Meusnier, Isabelle, Ardren, William R., Smith, Christian T. Year: 2000 Suggested citation: "Banks, Michael A. (2013): Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s Central Valley. Oregon State University Libraries. Dataset. doi:10.7267/N9KW5CXX" Title: Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s central valley Author: Brandes, Pat, Rashbrook, Vanessa K., Bernier-Latmani, Jeremiah, Banks, Michael A., Jacobson, David P., Greene, Sheila, O’Malley, Kathleen G., Greig, Carolyn A., Van Sickle, John, Meusnier, Isabelle, Ardren, William R., Smith, Christian T. Year: 2000 Suggested citation: "Banks, Michael A. (2013): Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s Central Valley. Oregon State University Libraries. Dataset. doi:10.7267/N9KW5CXX" Close

• 6. [Article] Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the author(s) ...

  Citation × Citation Citation Abstract Copy Title: Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test Author: Banks, Michael A., Ardren, William R., Bernier-Latmani, Jeremiah, Meusnier, Isabelle, Van Sickle, John, Rashbrook, Vanessa K., Jacobson, David P., Smith, Christian T., O'Malley, Kathleen G., Greig, Carolyn A. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd. The published article can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2052. Title: Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test Author: Banks, Michael A., Ardren, William R., Bernier-Latmani, Jeremiah, Meusnier, Isabelle, Van Sickle, John, Rashbrook, Vanessa K., Jacobson, David P., Smith, Christian T., O'Malley, Kathleen G., Greig, Carolyn A. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd. The published article can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2052. Close

• 7. [Article] DescriptionBanksDataset.pdf

  Citation × Citation Citation Abstract Copy Title: DescriptionBanksDataset.pdf Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Title: DescriptionBanksDataset.pdf Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Close

• 8. [Article] Banks_etal_2013_Dataset.zip

  Citation × Citation Citation Abstract Copy Title: Banks_etal_2013_Dataset.zip Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Title: Banks_etal_2013_Dataset.zip Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Close

• 9. [Article] FieldNames_Metadata.pdf

  Citation × Citation Citation Abstract Copy Title: FieldNames_Metadata.pdf Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Title: FieldNames_Metadata.pdf Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Close

• 10. [Article] CompletionReport_Banks.pdf

  Citation × Citation Citation Abstract Copy Title: CompletionReport_Banks.pdf Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Title: CompletionReport_Banks.pdf Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Close