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• 1. [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

• 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] Marine distributions of chinook salmon from the West Coast of North America determined by coded wire tag recoveries

  The coded wire tag (CWT) database contains detailed information on millions of Pacific salmon Oncorhynchus spp. released from hatcheries or smolt traps and recovered in the north Pacific Ocean and its ...

  Citation × Citation Citation Abstract Copy Title: Marine distributions of chinook salmon from the West Coast of North America determined by coded wire tag recoveries Author: Weitkamp, Laurie A. The coded wire tag (CWT) database contains detailed information on millions of Pacific salmon Oncorhynchus spp. released from hatcheries or smolt traps and recovered in the north Pacific Ocean and its tributaries. I used this data set to examine the spatial and temporal variation in the marine distributions of 77 hatchery and 16 wild populations of Chinook salmon O. tshawytscha based on recoveries of an estimated 632,000 tagged salmon in coastal waters from southern California to the Bering Sea during 1979–1994 (and 1995–2004 for select hatcheries). Chinook salmon showed 12 distinct region-specific recovery patterns. Chinook salmon originating in a common freshwater region had similar marine distributions, which were distinct from those of adjacent regions. Different run types (e.g., spring, summer, and fall runs) originating in the same region exhibited variation in their marine distributions consistent with recovery at different stages of their ocean residence period. Recovery patterns were surprisingly stable across years, despite high interannual variation in ocean conditions. By contrast, ocean age influenced recovery patterns, as older fish were recovered further from their natal stream than younger fish. Although most of the CWT data used in the analysis came from hatchery fish, recoveries of tagged wild populations indicate patterns similar to those of fish from nearby hatcheries. The consistency in these findings across broad geographic areas suggests that they apply to Chinook salmon across the entire Pacific Rim. Similar findings for tagged coho salmon O. kisutch indicate that the observed patterns may apply to Pacific salmon as a whole and provide a model for other highly migratory fishes that have not benefited from such intensive tagging programs. The results also have implications for the genetic control of migration and salmon’s ability to respond to climate change. Title: Marine distributions of chinook salmon from the West Coast of North America determined by coded wire tag recoveries Author: Weitkamp, Laurie A. The coded wire tag (CWT) database contains detailed information on millions of Pacific salmon Oncorhynchus spp. released from hatcheries or smolt traps and recovered in the north Pacific Ocean and its tributaries. I used this data set to examine the spatial and temporal variation in the marine distributions of 77 hatchery and 16 wild populations of Chinook salmon O. tshawytscha based on recoveries of an estimated 632,000 tagged salmon in coastal waters from southern California to the Bering Sea during 1979–1994 (and 1995–2004 for select hatcheries). Chinook salmon showed 12 distinct region-specific recovery patterns. Chinook salmon originating in a common freshwater region had similar marine distributions, which were distinct from those of adjacent regions. Different run types (e.g., spring, summer, and fall runs) originating in the same region exhibited variation in their marine distributions consistent with recovery at different stages of their ocean residence period. Recovery patterns were surprisingly stable across years, despite high interannual variation in ocean conditions. By contrast, ocean age influenced recovery patterns, as older fish were recovered further from their natal stream than younger fish. Although most of the CWT data used in the analysis came from hatchery fish, recoveries of tagged wild populations indicate patterns similar to those of fish from nearby hatcheries. The consistency in these findings across broad geographic areas suggests that they apply to Chinook salmon across the entire Pacific Rim. Similar findings for tagged coho salmon O. kisutch indicate that the observed patterns may apply to Pacific salmon as a whole and provide a model for other highly migratory fishes that have not benefited from such intensive tagging programs. The results also have implications for the genetic control of migration and salmon’s ability to respond to climate change. Close