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The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation

Daniel J Prince, Sean M O'Rourke, Tasha Q Thompson, Omar A Ali, Martha Arciniega, Hannah S Lyman, Ismail K Saglam, Anthony J Clemento, Thomas J Hotaling, Andrew P Kinziger, Adrian P Spidle, John Carlos Garza, Devon E Pearse, Michael R Miller
doi: https://doi.org/10.1101/056853
Daniel J Prince
Department of Animal Science, University of California, Davis, CA, USA;
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Sean M O'Rourke
Department of Animal Science, University of California, Davis, CA, USA;
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Tasha Q Thompson
Department of Animal Science, University of California, Davis, CA, USA;
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Omar A Ali
Department of Animal Science, University of California, Davis, CA, USA;
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Martha Arciniega
Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA;
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Hannah S Lyman
Department of Animal Science, University of California, Davis, CA, USA;
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Ismail K Saglam
Department of Animal Science, University of California, Davis, CA, USA;
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Anthony J Clemento
Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA;
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Thomas J Hotaling
Salmon River Restoration Council, Sawyers Bar, CA, USA;
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Andrew P Kinziger
Department of Fisheries Biology, Humboldt State University, Arcata, CA, USA;
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Adrian P Spidle
Northwest Indian Fisheries Commission, Olympia, WA, USA
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John Carlos Garza
Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA;
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Devon E Pearse
Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA;
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Michael R Miller
Department of Animal Science, University of California, Davis, CA, USA;
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  • For correspondence: micmiller@ucdavis.edu
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Abstract

The delineation of conservation units (CUs) is a challenging issue that has profound implications for minimizing the loss of biodiversity and ecosystem services. CU delineation typically seeks to prioritize evolutionary significance and genetic methods play a pivotal role in the delineation process by quantifying overall differentiation between populations. While CUs that primarily reflect overall genetic differentiation do protect adaptive differences between distant populations, they do not necessarily protect adaptive variation within highly connected populations. Advances in genomic methodology facilitate the characterization of adaptive genetic variation, but the potential utility of this information for CU delineation is unclear. Here we use genomic methods to investigate the evolutionary basis of premature migration in Pacific salmon, a complex behavioral and physiological adaptation that exists within highly-connected populations and has experienced severe declines. Strikingly, we find that premature migration is associated with the same single locus across multiple populations in each of two different species. Patterns of variation at this locus suggest that the premature migration alleles arose from a single evolutionary event within each species and were subsequently spread to distant populations through straying and positive selection. Our results reveal that complex adaptive variation can depend on rare mutational events at a single locus, demonstrate that CUs reflecting overall genetic differentiation can fail to protect evolutionarily significant variation that has substantial ecological and societal benefits, and suggest that a supplemental framework for protecting specific adaptive variation will sometimes be necessary to prevent the loss of significant biodiversity and ecosystem services.

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  • Posted June 3, 2016.

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The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation
Daniel J Prince, Sean M O'Rourke, Tasha Q Thompson, Omar A Ali, Martha Arciniega, Hannah S Lyman, Ismail K Saglam, Anthony J Clemento, Thomas J Hotaling, Andrew P Kinziger, Adrian P Spidle, John Carlos Garza, Devon E Pearse, Michael R Miller
bioRxiv 056853; doi: https://doi.org/10.1101/056853
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The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation
Daniel J Prince, Sean M O'Rourke, Tasha Q Thompson, Omar A Ali, Martha Arciniega, Hannah S Lyman, Ismail K Saglam, Anthony J Clemento, Thomas J Hotaling, Andrew P Kinziger, Adrian P Spidle, John Carlos Garza, Devon E Pearse, Michael R Miller
bioRxiv 056853; doi: https://doi.org/10.1101/056853

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