Integration of Random Forest with population-based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)

2015 ◽  
Vol 24 (11) ◽  
pp. 2729-2746 ◽  
Author(s):  
Marine S. O. Brieuc ◽  
Kotaro Ono ◽  
Daniel P. Drinan ◽  
Kerry A. Naish
Keyword(s):  
Random Forest ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Population Based ◽  
Genomic Basis ◽  
Run Timing

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.

Systematic hexamitid (Protozoa: Diplomonadida) Infection in seawater pen-reared Chinook salmon Oncorhynchus tshawytscha

1992 ◽  
Vol 14 ◽  
pp. 81-89 ◽  
Author(s):  
ML Kent ◽  
J Ellis ◽  
JW Fournie ◽  
SC Dawe ◽  
JW Bagshaw ◽  
...  
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha

scholarly journals Managed Wetlands Can Benefit Juvenile Chinook Salmon in a Tidal Marsh

2021 ◽  
Author(s):  
Nicole M. Aha ◽  
Peter B. Moyle ◽  
Nann A. Fangue ◽  
Andrew L. Rypel ◽  
John R. Durand
Keyword(s):  
San Francisco ◽  
Growth Rates ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Nursery Habitat ◽  
San Francisco Estuary ◽  
Rice Fields ◽  
Fish Growth ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook

AbstractLoss of estuarine and coastal habitats worldwide has reduced nursery habitat and function for diverse fishes, including juvenile Chinook salmon (Oncorhynchus tshawytscha). Underutilized off-channel habitats such as flooded rice fields and managed ponds present opportunities for improving rearing conditions and increasing habitat diversity along migratory corridors. While experiments in rice fields have shown enhanced growth rates of juvenile fishes, managed ponds are less studied. To evaluate the potential of these ponds as a nursery habitat, juvenile Chinook salmon (~ 2.8 g, 63 mm FL) were reared in cages in four contrasting locations within Suisun Marsh, a large wetland in the San Francisco Estuary. The locations included a natural tidal slough, a leveed tidal slough, and the inlet and outlet of a tidally muted managed pond established for waterfowl hunting. Fish growth rates differed significantly among locations, with the fastest growth occurring near the outlet in the managed pond. High zooplankton biomass at the managed pond outlet was the best correlate of salmon growth. Water temperatures in the managed pond were also cooler and less variable compared to sloughs, reducing thermal stress. The stress of low dissolved oxygen concentrations within the managed pond was likely mediated by high concentrations of zooplankton and favorable temperatures. Our findings suggest that muted tidal habitats in the San Francisco Estuary and elsewhere could be managed to promote growth and survival of juvenile salmon and other native fishes.

Analysis of straying variation in Alaskan hatchery chinook salmon (Oncorhynchus tshawytscha) following transplantation

1999 ◽  
Vol 56 (4) ◽  
pp. 578-589 ◽  
Author(s):  
Jeffrey J Hard ◽  
William R Heard
Keyword(s):  
British Columbia ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Release Site ◽  
Substantial Variation

In 1976 chinook salmon (Oncorhynchus tshawytscha) gametes from the Chickamin and Unuk rivers in southeastern Alaska were transplanted 250 km to establish hatchery runs at Little Port Walter (LPW), Baranof Island. From 1977 to 1989, 1 862 058 marked smolts from 12 broods were released from LPW. Homing and straying were estimated from adult recoveries at 25 locations in Alaska and British Columbia between 1981 and 1989. Of 22 198 LPW fish recovered over this period, 21 934 (98.8%) were collected at LPW. Of 264 fish recovered elsewhere, 38.3% were within 7 km of LPW; 64.4% were within 25 km of LPW. No LPW fish were recovered from the ancestral rivers, but nine fish were recovered from rivers supporting wild chinook salmon. Straying declined with distance from the release site but varied between hatcheries and streams. Straying declined with increasing age and run size. Straying was similar between the populations but varied among broods, and analysis of straying in experimental groups provided evidence for a heritable component. Males strayed more often than females. Population, gender, run size, and recovery age interacted to produce substantial variation in straying, indicating that run composition can produce complex straying responses.

Route selection in a large river during the homing migration of Chinook salmon (Oncorhynchus tshawytscha)

2006 ◽  
Vol 63 (8) ◽  
pp. 1752-1762 ◽  
Author(s):  
Matthew L Keefer ◽  
Christopher C Caudill ◽  
Christopher A Peery ◽  
Theodore C Bjornn
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Columbia River ◽  
Large River ◽  
Migration Route ◽  
Route Selection ◽  
Behavioral Differences ◽  
Long Distance ◽  
Selection Decisions ◽  
Efficient Route

Upstream-migrating adult salmon must make a series of correct navigation and route-selection decisions to successfully locate natal streams. In this field study, we examined factors influencing migration route selections early in the migration of 4361 radio-tagged adult Chinook salmon (Oncorhynchus tshawytscha) as they moved upstream past dams in the large (~1 km wide) Columbia River. Substantial behavioral differences were observed among 11 conspecific populations, despite largely concurrent migrations. At dams, Chinook salmon generally preferred ladder passage routes adjacent to the shoreline where their natal tributaries entered, and the degree of preference increased as salmon proximity to natal tributaries increased. Columbia River discharge also influenced route choices, explaining some route selection variability. We suggest that salmon detect lateral gradients in orientation cues across the Columbia River channel that are entrained within tributary plumes and that these gradients in cues can persist downstream for tens to hundreds of kilometres. Detection of tributary plumes in large river systems, using olfactory or other navigation cues, may facilitate efficient route selection and optimize energy conservation by long-distance migrants.

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