Genetic Composition of the Warm Springs River Chinook Salmon Population Maintained following Eight Generations of Hatchery Production

AbstractGenomic diversity is the fundamental building block of biodiversity and the necessary ingredient for adaptation. Our rapidly increasing ability to quantify functional, compositional, and structural genomic diversity of populations forces the question of how to balance conservation goals – should the focus be on important functional diversity and key life history traits or on maximizing genomic diversity as a whole? Specifically, the intra-specific diversity (biocomplexity) comprised of phenotypic and genetic variation can determine the ability of a population to respond to changing environmental conditions. Here, we explore the biocomplexity of California’s Central Valley Chinook salmon population complex at a genomic level. Notably, despite apparent gene flow among individuals of different migration (life history) phenotypes inhabiting the same tributaries, each group is characterized by a component of unique genomic diversity. Our results emphasize the importance of formulating conservation goals focused on maintaining biocomplexity at both the phenotypic and genotypic level. Doing so will maintain the adaptive potential to increase the probability of persistence of the population complex despite changing environmental pressures.

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Population viability of the Snake River chinook salmon (Oncorhynchus tshawytscha)

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f95-139 ◽

1995 ◽

Vol 52 (7) ◽

pp. 1442-1448 ◽

Cited By ~ 20

Author(s):

John M. Emlen

Keyword(s):

Chinook Salmon ◽

Oncorhynchus Tshawytscha ◽

Population Viability ◽

Snake River ◽

Management Actions ◽

Population Dynamics Model ◽

The Status ◽

Salmon Population ◽

Mortality Improvement ◽

Best Fit

In the presence of historical data, population viability models of intermediate complexity can be parameterized and utilized to project the consequences of various management actions for endangered species. A general stochastic population dynamics model with density feedback, age structure, and autocorrelated environmental fluctuations was constructed and parameterized for best fit over 36 years of spring chinook salmon (Oncorhynchus tshawytscha) redd count data in five Idaho index streams. Simulations indicate that persistence of the Snake River spring chinook salmon population depends primarily on density-independent mortality. Improvement of rearing habitat, predator control, reduced fishing pressure, and improved dam passage all would alleviate density-independent mortality. The current value of the Ricker α should provide for a continuation of the status quo. A recovery of the population to 1957–1961 levels within 100 years would require an approximately 75% increase in survival and (or) fecundity. Manipulations of the Ricker β are likely to have little or no effect on persistence versus extinction, but considerable influence on population size.

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Translating restoration scenarios into habitat conditions: an initial step in evaluating recovery strategies for Chinook salmon (Oncorhynchus tshawytscha)

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f06-055 ◽

2006 ◽

Vol 63 (7) ◽

pp. 1578-1595 ◽

Cited By ~ 26

Author(s):

Krista K Bartz ◽

Kerry M Lagueux ◽

Mark D Scheuerell ◽

Tim Beechie ◽

Andrew D Haas ◽

...

Keyword(s):

Land Use ◽

Chinook Salmon ◽

Oncorhynchus Tshawytscha ◽

Initial Step ◽

Decision Makers ◽

Habitat Conditions ◽

Recovery Strategies ◽

Salmon Population ◽

Alternative Scenarios ◽

Imperiled Species

One of the challenges associated with recovering imperiled species, such as Chinook salmon (Oncorhynchus tshawytscha), is identifying a set of actions that will ensure species' persistence. Here we evaluate the effects of alternative land use scenarios on habitat conditions potentially important to Chinook salmon. We first summarize the alternative scenarios as target levels for certain land use characteristics. We then use the target levels to estimate changes in current habitat conditions. The scenarios we explore indicate considerable potential to improve both the quality and quantity of salmon habitat through protection and restoration. Results from this analysis constitute the habitat inputs to a population model linking changes in habitat to salmon population status. By transparently documenting the approach we use to translate land use actions into changes in salmon habitat conditions, we provide decision makers with a clear basis for choosing strategies to recover salmon.

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Chinook salmon exhibit long-term rearing and early marine growth in the Fraser River, B.C., a large urban estuary

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2020-0247 ◽

2020 ◽

Author(s):

Lia Chalifour ◽

David C Scott ◽

Misty MacDuffee ◽

Steven Stark ◽

John F Dower ◽

...

Keyword(s):

Chinook Salmon ◽

Oncorhynchus Tshawytscha ◽

Pacific Salmon ◽

Genetic Stock ◽

Daily Growth ◽

Estuarine Habitat ◽

Salmon River ◽

Salmon Population ◽

Brackish Marshes ◽

Saline Habitats

Estuaries represent a transition zone for salmon migrating from freshwater to marine waters, yet their contribution to juvenile growth is poorly quantified. Here, we use genetic stock identification and otolith analyses to quantify estuarine habitat use by Chinook salmon (<i>Oncorhynchus tshawytscha</i>) – the Pacific salmon species considered most reliant on this habitat – in Canada’s most productive salmon river, the Fraser. Two years of sampling revealed subyearling migrant (“ocean-type”) Chinook from the Harrison River to be the estuary’s dominant salmon population throughout the emigration period. These Chinook salmon were caught predominantly in the estuary’s brackish marshes but shifted to more saline habitats as they grew. Otolith analyses indicated that these Chinook salmon have wide-ranging entry timing (from February to May), and longer estuarine residency (weeks to months, mean 41.8 days) than estimated by prior studies, but similar daily growth rates (mean 0.57 mm +/- 0.13 SD) across entry dates and residency periods, implying sufficient foraging opportunities throughout the emigration period and habitats. Together, these results suggest that estuarine habitat is more important for early marine growth of subyearling migrant Chinook salmon than previously recognized.

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Weakening portfolio effect strength in a hatchery-supplemented Chinook salmon population complex

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2015-0169 ◽

2015 ◽

Vol 72 (12) ◽

pp. 1860-1875 ◽

Cited By ~ 27

Author(s):

William H. Satterthwaite ◽

Stephanie M. Carlson

Keyword(s):

Chinook Salmon ◽

North Pacific ◽

Oncorhynchus Tshawytscha ◽

Environmental Variability ◽

Central Valley ◽

Simultaneous Increase ◽

Environmental Forcing ◽

Salmon Population ◽

Portfolio Effect ◽

Considerable Degradation

Biocomplexity contributes to asynchronous population dynamics, buffering stock complexes in temporally variable environments, a phenomenon referred to as a “portfolio effect”. We previously revealed a weakened but persistent portfolio effect in California’s Central Valley fall-run Chinook salmon (Oncorhynchus tshawytscha), despite considerable degradation and loss of habitat. Here, we further explore the timing of changes in variability and synchrony and relate these changes to factors hypothesized to influence variability in adult abundance, including hatchery release practices and environmental variables. We found evidence for increasing synchrony among fall-run populations that coincided temporally with increased off-site hatchery releases into the estuary but not with increased North Pacific environmental variability (measured by North Pacific Gyre Oscillation), nor were common trends well explained by a suite of environmental covariates. Moreover, we did not observe a simultaneous increase in synchrony in the nearby Klamath–Trinity system, where nearly all hatchery releases are on-site. Wavelet analysis revealed that variability in production was higher and at a longer time period later in the time series, consistent with increased environmental forcing and a shift away from dynamics driven by natural spawners.

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Can the Atlantic Salmon Restoration Program Safely Re-Integrate Atlantic Salmon to Lake Ontario?

Inquiry@Queen's Undergraduate Research Conference Proceedings ◽

10.24908/iqurcp.9261 ◽

2018 ◽

Author(s):

Laura Gibson ◽

Leia De Guzman ◽

Michelle Lavery ◽

Christine Ly ◽

Kira MacDougall

Keyword(s):

Atlantic Salmon ◽

Salmo Salar ◽

Chinook Salmon ◽

Agonistic Behavior ◽

Lake Ontario ◽

Early Mortality ◽

Eastern Canada ◽

Early Mortality Syndrome ◽

Salmon Population ◽

The 19Th Century

Atlantic salmon (Salmo salar) are an economically valuable species and have inhabited the lakes and rivers of Eastern Canada since the last post-glacial period. However, since the end of the 19th century, Atlantic salmon populations have collapsed in Lake Ontario due to land clearance and dam and mill construction. In 2006, the Atlantic Salmon Reintroduction Program (ASRP) was established in Lake Ontario in an effort to recreate a self-sustaining salmon population. The ASRP aims to rebuild the Lake Ontario Atlantic salmon population by stocking fish from genetically diverse broodstock, restoring Atlantic salmon habitat and monitoring water quality. The ASRP also includes a public education component to emphasize the importance of maintaining the Atlantic salmon population. However, re- introduction programs like the ASRP can be challenged by interspecific competition. Chinook salmon are known to induce male agonistic behavior in Atlantic salmon. In addition, Atlantic salmon juveniles are out-competed by Rainbow trout. Furthermore, the prospective diet of Atlantic salmon in Lake Ontario is thiamin-deficient, which may lead to neurological, developmental and reproductive problems as well as Early Mortality Syndrome (EMS). We will conduct research in partnership with Bring Back the Salmon Lake Ontario, Atlantic Salmon Conservation Fund and the Atlantic Salmon Federation to investigate the potential threats to both Atlantic salmon and existing species that may result from the ASRP for Lake Ontario. Findings will be presented as well as recommendations for alterations to the program to ensure that the ASRP is a safe and successful endeavor.

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Introgressive hybridization among major Columbia River Chinook salmon (Oncorhynchus tshawytscha) lineages within the Klickitat River due to hatchery practices

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f2011-107 ◽

2011 ◽

Vol 68 (11) ◽

pp. 1876-1891 ◽

Cited By ~ 6

Author(s):

Jon E. Hess ◽

Andrew P. Matala ◽

Joseph S. Zendt ◽

Chris R. Frederiksen ◽

Bill Sharp ◽

...

Keyword(s):

Chinook Salmon ◽

Oncorhynchus Tshawytscha ◽

Isolation By Distance ◽

Introgressive Hybridization ◽

Columbia River ◽

Genetic Composition ◽

Negative Effects ◽

Temporal Shift ◽

Natural Processes ◽

Relationship Of

Major lineages of anadromous salmonids show resilience to natural introgressive hybridization; however, Klickitat River spring-run Chinook salmon (KRSC, Oncorhynchus tshawytscha ) have an enigmatic origin because of their intermediate genetic and geographic relationship among Columbia River Chinook salmon lineages. We used computer simulations to evaluate four anthropogenic and natural processes as likely causes of the apparent introgressed genetic composition of KRSC: recent admixture (∼5 generations), historical admixture (>200 generations), isolation-by-distance gene flow, and natural selection. We also genotyped 2413 fish (32 collections) across 96 single nucleotide polymorphism loci to clarify the relationship of KRSC among the three major Columbia River lineages (Lower Columbia and interior ocean- and stream-types) and to quantify introgression among collections. Between 1980 and 2000, we observed a decline of pure interior stream-type individuals in the KRSC collections. This temporal shift in genetic composition was coincident with relevant changes in hatchery practices. Based on results from the simulations and time-series samples, a recent and anthropogenically caused admixture was most likely responsible for introgression of KRSC. Potential long-term negative effects of introgression may require some form of mitigation.

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