scholarly journals Genomic region associated with run‐timing has similar haplotypes and phenotypic effects across three lineages of Chinook salmon

2021 ◽  
Author(s):  
Stuart C. Willis ◽  
Jon E. Hess ◽  
Jeff K. Fryer ◽  
John M. Whiteaker ◽  
Shawn R. Narum
Keyword(s):  
Chinook Salmon ◽  
Genomic Region ◽  
Run Timing

Run Timing, Spawn Timing, and Spawning Distribution of Hatchery- and Natural-Origin Spring Chinook Salmon in the Imnaha River, Oregon

2008 ◽  
Vol 28 (1) ◽  
pp. 148-164 ◽  
Author(s):  
Timothy L. Hoffnagle ◽  
Richard W. Carmichael ◽  
Kathryn A. Frenyea ◽  
Patrick J. Keniry
Keyword(s):  
Chinook Salmon ◽  
Natural Origin ◽  
Run Timing

A complex phenotype in salmon controlled by a simple change in migratory timing

Science ◽  
2020 ◽  
Vol 370 (6516) ◽  
pp. 609-613 ◽  
Author(s):  
Neil F. Thompson ◽  
Eric C. Anderson ◽  
Anthony J. Clemento ◽  
Matthew A. Campbell ◽  
Devon E. Pearse ◽  
...  
Keyword(s):  
Chinook Salmon ◽  
Sexual Maturity ◽  
Single Gene ◽  
Genomic Region ◽  
Seasonal Patterns ◽  
Diverse Population ◽  
Complex Phenotype ◽  
Migration Timing ◽  
Simple Change ◽  
Migratory Phenotype

Differentiation between ecotypes is usually presumed to be complex and polygenic. Seasonal patterns of life history in salmon are used to categorize them into ecotypes, which are often considered “distinct” animals. Using whole-genome sequencing and tribal fishery sampling of Chinook salmon, we show that a single, small genomic region is nearly perfectly associated with spawning migration timing but not with adiposity or sexual maturity, traits long perceived as central to salmon ecotypes. Distinct migration timing does not prevent interbreeding between ecotypes, which are the result of a simple, ancient polymorphism segregating within a diverse population. Our finding that a complex migratory phenotype results from a single gene region will facilitate conservation and restoration of this iconic fish.

Bayesian information updating procedures for Pacific salmon run size indicators: evaluation in the presence and absence of auxiliary migration timing information

2019 ◽  
Vol 76 (10) ◽  
pp. 1719-1727
Author(s):  
Benjamin A. Staton ◽  
Matthew J. Catalano
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Pacific Salmon ◽  
Forecast Model ◽  
Migration Timing ◽  
Timing Information ◽  
Information Updating ◽  
Harvest Decisions ◽  
Size Estimates ◽  
Run Timing

Preseason forecasts of Pacific salmon run size are notoriously uncertain and are thus often updated using various abundance indices collected during the run. However, interpretation of these in-season indices is confounded by uncertainty in migration timing. We assessed the performance of two Bayesian information-updating procedures for Kuskokwim River Chinook salmon (Oncorhynchus tshawytscha), one that uses auxiliary run timing information and one that does not, and compared the performance with methods that did not involve updating. We found that in-season Bayesian updating provided more accurate run size estimates during the time when harvest decisions needed to be made, but that the incorporation of run timing forecasts had little utility in terms of providing more accurate run size estimates. The latter finding is conditional on the performance of the run timing forecast model we used; a more accurate timing forecast model might yield a different conclusion. The Bayesian approach we developed provided a probabilistic expression of run size beliefs, which could be useful in a transparent risk-assessment framework for setting and altering harvest targets during the season.

scholarly journals Population Trends for Chinook and Summer Chum Salmon in Two Yukon River Tributaries in Alaska

2020 ◽  
Author(s):  
Randy J. Brown ◽  
Catherine Bradley ◽  
Jeffery L. Melegari
Keyword(s):  
Chinook Salmon ◽  
Chum Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Demographic Data ◽  
Main Stem ◽  
Strongly Correlated ◽  
Yukon River ◽  
Over Time ◽  
Run Timing

Abstract An essential management objective of the Yukon Delta and Koyukuk National Wildlife Refuges in Alaska is to conserve fish and wildlife populations and habitats in their natural diversity. In keeping with this objective, the U.S. Fish and Wildlife Service installed weirs in two tributaries of the Yukon River, the East Fork Andreafsky and Gisasa rivers, in 1994 to collect information on salmon populations that used them. The weirs have been in operation for >23 y. Chinook Oncorhynchus tshawytscha and summer Chum Salmon O. keta were counted and sampled for various demographic data each year as they migrated through the weirs to upstream spawning areas. Here we examine this record of population data to describe and compare long-term variation in run abundance, run timing, length and age structure, sex composition, and production for these salmon populations. Fishery managers often look to multiple monitoring projects in-season seeking corroboration of observed run qualities; therefore, we also considered whether Yukon River main-stem indicators of abundance were correlated with these tributary escapements. Our analyses suggest long-term stability of these populations despite large annual variations in most metrics we examined. Annual escapements have varied by factors of 3–5 for Chinook Salmon and >23 for summer Chum Salmon, yet only the Chinook Salmon population in the Gisasa River appears to be declining. Main-stem abundance indicators were not correlated with Chinook Salmon escapements but were strongly correlated with summer Chum Salmon escapements. Run timing has varied annually by as much as a week earlier or later than average for all four populations with no trend over time. Mean age of the Chinook Salmon populations declined over time but remained stable for the summer Chum Salmon populations. Chinook Salmon populations in the East Fork Andreafsky and Gisasa rivers averaged 35% and 28% female, respectively. Both summer Chum Salmon populations averaged close to 50% female. Length at age has been stable or slightly declining for all four populations. Production over time was strongly correlated within species for populations in the two rivers, and averaged >1 recruit/spawner for all populations except Chinook Salmon from the Gisasa River. We discuss these findings in the context of major changes in the fishery and the environments these populations experience.

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