Research ArticleEVOLUTIONARY GENETICS

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

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Science Advances  16 Aug 2017:
Vol. 3, no. 8, e1603198
DOI: 10.1126/sciadv.1603198
  • Fig. 1 Genetic structure of premature and mature migrating steelhead populations.

    (A) Map of steelhead sample locations and migration phenotypes; color indicates location, and shape indicates migration phenotype. (B) Bimonthly proportion of annual adult steelhead return over Winchester Dam on the North Umpqua River (2003 to 2013); horizontal bars depict migration and spawn timing of premature and mature migrating populations. (C and D) Principal component analysis (PCA) and (E) pairwise FST estimates using genome-wide single-nucleotide polymorphism (SNP) data.

  • Fig. 2 Genetic and evolutionary basis of premature migration in steelhead.

    Association mapping of migration category in (A) North Umpqua River and (B) Eel River steelhead. (C) Gene annotation of region with strong association; red numbers indicate genomic positions of two restriction sites flanked by strongest associated SNPs, and blue asterisks indicate positions of amplicon sequencing. (D) Phylogenetic tree depicting maximum parsimony of phased amplicon sequences from all individuals; branch lengths, with the exception of terminal tips, reflect nucleotide differences between haplotypes; numbers identify individuals with one haplotype in each migration category clade. (E) Genome-wide and GREB1L region diversity estimates in North Umpqua for each migration category with 95% confidence intervals from coalescent simulations.

  • Fig. 3 Genetic and evolutionary basis of premature migration in Chinook.

    (A) Map of Chinook sample locations and migration phenotypes; color indicates location, and shape indicates migration category. (B) PCA and (C) pairwise FST estimates using genome-wide SNP data. (D) Association mapping of migration category in Chinook; red numbers indicate significant SNPs. (E) Allele frequency shift at significant SNPs between premature and mature migrating populations. Black numbers indicate SNP position on scaffold79929e.

  • Fig. 4 Inheritance pattern of GREB1L locus.

    (A) Association mapping of migration date in Klickitat River steelhead. (B) Mean migration date and 95% confidence interval of the mean in Klickitat River steelhead categorized as homozygous for the premature migration allele, heterozygous, and homozygous mature. *P = 0.00574; **P = 2.95 × 10−5.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/3/8/e1603198/DC1

    fig. S1. Observed versus expected statistics for association mapping of migration phenotype.

    fig. S2. Migration date distribution of Klickitat River steelhead at Lyle Falls with weekly binning.

    table S1. Steelhead samples.

    table S2. Steelhead RAD sequence.

    table S3. Steelhead migration associated SNPs.

    table S4. Steelhead amplicon primers.

    table S5. Steelhead amplicon sequence.

    table S6. Chinook samples.

    table S7. Chinook RAD sequence.

    table S8. Chinook migration associated SNPs.

    table S9. Scaffold links.

    table S10. Scaffold79929e assembly.

  • Supplementary Materials

    This PDF file includes:

    • fig. S1. Observed versus expected statistics for association mapping of migration phenotype.
    • fig. S2. Migration date distribution of Klickitat River steelhead at Lyle Falls with weekly binning.

    Download PDF

    Other Supplementary Material for this manuscript includes the following:

    • table S1 (Microsoft Excel format). Steelhead samples.
    • table S2 (Microsoft Excel format). Steelhead RAD sequence.
    • table S3 (Microsoft Excel format). Steelhead migration associated SNPs.
    • table S4 (Microsoft Excel format). Steelhead amplicon primers.
    • table S5 (Microsoft Excel format). Steelhead amplicon sequence.
    • table S6 (Microsoft Excel format). Chinook samples.
    • table S7 (Microsoft Excel format). Chinook RAD sequence.
    • table S8 (Microsoft Excel format). Chinook migration association SNPs.
    • table S9 (Microsoft Excel format). Scaffold links.
    • table S10 (Microsoft Excel format). Scaffold79929e assembly.

    Download Tables S1 to S10

    Files in this Data Supplement:

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