Parallel evolution of the summer steelhead ecotype in multiple populations from Oregon and Northern California

Arciniega, Martha; Clemento, Anthony J.; Miller, Michael R.; Peterson, Matt; Garza, John Carlos; Pearse, Devon E.

doi:10.1007/s10592-015-0769-2

Cited by 20 publications

(20 citation statements)

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“…Genetic analysis of native, sympatric summer and winter runs indicate that these two migratory forms are more similar within drainages than either type is to other populations of the same migratory type [13,14]. However, the degree of gene flow among the two migratory types can vary depending on location.…”

Section: Introductionmentioning

confidence: 99%

Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

et al. 2016

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Migration traits are presumed to be complex and to involve interaction among multiple genes. We used both univariate analyses and a multivariate random forest (RF) machine learning algorithm to conduct association mapping of 15 239 single nucleotide polymorphisms (SNPs) for adult migration-timing phenotype in steelhead (Oncorhynchus mykiss). Our study focused on a model natural population of steelhead that exhibits two distinct migration-timing life histories with high levels of admixture in nature. Neutral divergence was limited between fish exhibiting summer-and winter-run migration owing to high levels of interbreeding, but a univariate mixed linear model found three SNPs from a major effect gene to be significantly associated with migration timing ( p , 0.000005) that explained 46% of trait variation. Alignment to the annotated Salmo salar genome provided evidence that all three SNPs localize within a 46 kb region overlapping GREB1-like (an oestrogen target gene) on chromosome Ssa03. Additionally, multivariate analyses with RF identified that these three SNPs plus 15 additional SNPs explained up to 60% of trait variation. These candidate SNPs may provide the ability to predict adult migration timing of steelhead to facilitate conservation management of this species, and this study demonstrates the benefit of multivariate analyses for association studies.

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Section: Introductionmentioning

confidence: 99%

Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

et al. 2016

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Section: Introductionmentioning

confidence: 99%

“…Migration is an important determinant of steelhead population structure, and numerous studies have examined the genetic structure of O. mykiss populations in California coastal and Central Valley watersheds (Arciniega et al, 2016;Clemento et al, 2009;Garza et al, 2014;Nielsen, Carpanzano, Fountain, & Gan, 1997;Nielsen, Pavey, Wiacek, & Williams, 2005;Pearse, Donohoe, & Garza, 2007;Pearse & Garza, 2015). Garza et al (2014) highlighted the correlation between genetic variation and geographic distance, a relationship known as isolation by distance, which is influenced by major geographic features but has also changed over time (Pearse, Martinez, & Garza, 2011).…”

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confidence: 99%

“…Expression of life-history variation, such as the timing of migration and maturation, may differ in relation to the phylogeographic structure of populations (Arciniega et al, 2016;Vähä et al, 2011). This phenotypic variation may be influenced by a combination of plasticity and heritable variation in salmonid fishes, including O. mykiss (Abadía-Cardoso, Anderson, Pearse, & Garza, 2013;Liedvogel, Åkesson, & Bensch, 2011;Phillis et al, 2016;Quinn, Kinnison, & Unwin, 2001).…”

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Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (Oncorhynchus mykiss) in the San Francisco bay area: application of adaptive genomic variation to conservation in a highly impacted landscape

Leitwein

Garza

Pearse

2016

Evolutionary Applications

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The streams draining of into San Francisco Bay, California, have been impacted by habitat alteration for over 150 years, and roads, dams, water diversions, and other impediments now block the paths of many aquatic migratory species. These changes can affect the genetic structure of fish populations, as well as driving adaptive evolution to novel environmental conditions. Here, we determine the evolutionary relationships of San Francisco Bay Area steelhead/rainbow trout (Oncorhynchus mykiss) populations and show that (i) they are more closely related to native coastal steelhead than to the California Central Valley lineage, with no evidence of introgression by domesticated hatchery rainbow trout, (ii) populations above and below barriers within watersheds are each other's closest relatives, and (iii) adaptive genomic variation associated with migratory life‐history traits in O. mykiss shows substantial evolutionary differences between fish above and below dams. These findings support continued habitat restoration and protection of San Francisco Bay Area O. mykiss populations and demonstrate that ecological conditions in novel habitats above barriers to anadromy influence life‐history evolution. We highlight the importance of considering the adaptive landscape in conservation and restoration programs for species living in highly modified habitats, particularly with respect to key life‐history traits.

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“…From a conservation perspective, premature migrating salmonids are especially vulnerable to anthropogenic interventions even when mature migrating populations exist within the same river system, because they utilize the freshwater habitat for longer as adults and require access to upstream river reaches that are often blocked by dams (Arciniega et al , ; Quinn et al , ). Thus, these results show the significance of a specific AGV in shaping phenotypic traits with important cultural, commercial and conservation consequences.…”

Section: Examples Of Agv In Salmonid Life Historiesmentioning

confidence: 99%

Saving the spandrels? Adaptive genomic variation in conservation and fisheries management

Pearse

2016

Journal of Fish Biology

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As highlighted by many of the papers in this issue, research on the genomic basis of adaptive phenotypic variation in natural populations has made spectacular progress in the past few years, largely due to the advances in sequencing technology and analysis. Without question, the resulting genomic data will improve the understanding of regions of the genome under selection and extend knowledge of the genetic basis of adaptive evolution. What is far less clear, but has been the focus of active discussion, is how such information can or should transfer into conservation practice to complement more typical conservation applications of genetic data. Before such applications can be realized, the evolutionary importance of specific targets of selection relative to the genome-wide diversity of the species as a whole must be evaluated. The key issues for the incorporation of adaptive genomic variation in conservation and management are discussed here, using published examples of adaptive genomic variation associated with specific phenotypes in salmonids and other taxa to highlight practical considerations for incorporating such information into conservation programmes. Scenarios are described in which adaptive genomic data could be used in conservation or restoration, constraints on its utility and the importance of validating inferences drawn from new genomic data before applying them in conservation practice. Finally, it is argued that an excessive focus on preserving the adaptive variation that can be measured, while ignoring the vast unknown majority that cannot, is a modern twist on the adaptationist programme that Gould and Lewontin critiqued almost 40 years ago.

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Parallel evolution of the summer steelhead ecotype in multiple populations from Oregon and Northern California

Abstract: viiDedication ix Acknowledgments x

Cited by 20 publications

References 83 publications

Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (Oncorhynchus mykiss) in the San Francisco bay area: application of adaptive genomic variation to conservation in a highly impacted landscape

Saving the spandrels? Adaptive genomic variation in conservation and fisheries management

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