Examining Genetic Lineages of Chinook Salmon in the Columbia River Basin

Narum, Shawn R.; Hess, Jon E.; Matala, Andrew P.

doi:10.1577/t09-150.1

Cited by 47 publications

(94 citation statements)

References 37 publications

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“…Note that from among our panel, the locus Omy_stat3‐273 was previously identified among desert and montane resident O. mykiss populations as being associated with temperature (Narum et al. ). We demonstrated in our evaluation that this locus was correlated with precipitation but not with temperature, yet in actuality it is likely associated with overall climate and thus affected by myriad aspects of habitat variability.…”

Section: Discussionmentioning

confidence: 62%

Relative contributions of neutral and non‐neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

Matala

Ackerman

Campbell

et al. 2014

Evolutionary Applications

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Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non-neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad-scale population structure consistent with previous studies, but fine-scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non-neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non-neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long-term conservation of this species.

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Section: Discussionmentioning

confidence: 62%

Relative contributions of neutral and non‐neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

Matala

Ackerman

Campbell

et al. 2014

Evolutionary Applications

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“…There are many species of salmon in the Pacific (Groot and Margolis 1991), and there is still controversy about their taxonomy and genetic lineages (Narum et al 2010). Chinook or king salmon have a major fall run in many rivers of northwest North America (and are often called fall Chinook).…”

Section: Chinook Salmonmentioning

confidence: 99%

Complexity of bioindicator selection for ecological, human, and cultural health: Chinook salmon and red knot as case studies

Burger

Gochfeld

Niles³

et al. 2015

Environ Monit Assess

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There is considerable interest in developing bioindicators of ecological health that are also useful indicators for human health. Yet, human health assessment usually encompasses physical/chemical exposures and not cultural well-being. In this paper, we propose that bioindicators can be selected for all three purposes. We use Chinook or king salmon (Oncorhynchus tshawytscha) and red knot (Calidris canutus rufa, a sandpiper) as examples of indicators that can be used to assess human, ecological, and cultural health. Even so, selecting endpoints or metrics for each indicator species is complex and is explored in this paper. We suggest that there are several endpoint types to examine for a given species, including physical environment, environmental stressors, habitat, life history, demography, population counts, and cultural/societal aspects. Usually cultural endpoints are economic indicators (e.g., number of days fished, number of hunting licenses), rather than the importance of a fishing culture. Development of cultural/societal endpoints must include the perceptions of local communities, cultural groups, and tribal nations, as well as governmental and regulatory communities (although not usually so defined, the latter have cultures as well). Endpoint selection in this category is difficult because the underlying issues need to be identified and used to develop endpoints that tribes and stakeholders themselves see as reasonable surrogates of the qualities they value. We describe several endpoints for salmon and knots that can be used for ecological, human, and cultural/societal health.

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“…Narum et al 2010). Although this is an oversimplification, these lineages are commonly differentiated by a suite of traits including spawning location, adult upstream run timing and marine distribution.…”

Section: Species Run and Rearing Typementioning

confidence: 99%

Testing for delayed mortality effects in the early marine life history of Columbia River Basin yearling Chinook salmon

Rechisky¹,

Welch²,

Porter³

et al. 2014

Mar. Ecol. Prog. Ser.

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Juvenile Snake River Chinook salmon Oncorhynchus tshawytscha pass through 8 major hydroelectric dams during their > 700 km migration to the sea, or are transported downriver to avoid these dams. Both of these anthropogenic processes may decrease fitness and lead to delayed mortality in the estuary and coastal ocean, and thus reduce the rate at which adults return to spawn. Using a large-scale telemetry array, we tested whether there was support for (1) hydrosysteminduced delayed mortality (hydro-DM) of yearlings migrating from the Snake River relative to yearlings migrating from the mid-Columbia River, and (2) transportation-induced delayed mortality (transport-DM) for transported Snake River yearlings relative to yearlings which migrated in-river. We also tested for differential early marine survival between yearlings migrating from the Snake and upper Columbia Rivers. In 2010, seaward migrating yearling Chinook were captured at dam bypasses and origin was based on capture location; in 2011, dam-caught fish were identified using genetic stock identification. Survival of all groups during the initial 750 km, >1 mo long migration through the estuary and coastal ocean to northwestern Vancouver Island ranged between 14 and 19% in 2010 and was lower in 2011 (1.5−8%). We found no support for hydro-DM, as survival of inriver migrating Snake and mid-Columbia River yearlings was indistinguishable. We found mixed results for our transportation study, with no support for transport-DM in 2010, and weak support in 2011. Our study provides further evidence that freshwater management strategies may not increase the rate of Chinook salmon returning to the Snake River if prior freshwater experience has no substantial influence on subsequent survival in the ocean.

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Examining Genetic Lineages of Chinook Salmon in the Columbia River Basin

Cited by 47 publications

References 37 publications

Relative contributions of neutral and non‐neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

Relative contributions of neutral and non‐neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

Complexity of bioindicator selection for ecological, human, and cultural health: Chinook salmon and red knot as case studies

Testing for delayed mortality effects in the early marine life history of Columbia River Basin yearling Chinook salmon

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