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Convergent local adaptation to climate in distantly related conifers

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Science  23 Sep 2016:
Vol. 353, Issue 6306, pp. 1431-1433
DOI: 10.1126/science.aaf7812
  • Fig. 1 Signatures of convergent adaptation at the phenotypic and genomic level.

    Spearman correlations were calculated between each SNP and the 22 environmental and 17 phenotypic variables. (A) Top-candidate genes for each of the 39 tests were identified as those with an extreme number of outlier SNPs relative to a binomial expectation, shown in blue (mean annual temperature in pine). (B) Cold injury response phenotypes were strongly correlated to temperature variables in both lodgepole pine and interior spruce, with the most strongly correlated cases shown in purple (“main variables”). (C and D) The seven main variables with strong phenotype-environment correlations also had the largest number of top-candidate genes for phenotypes (C) and environments (D); labels are omitted for data points near the axes for clarity. EMT, extreme minimum temperature; MCMT, mean coldest-month temperature; DD_0, degree-days below 0°C; LAT, latitude; TD, temperature difference; MAT, mean annual temperature; PAS, precipitation as snow; MAP, mean annual precipitation; AHM, annual heat-moisture index; LONG, longitude (see tables S1 and S2).

  • Fig. 2 Signatures of genetic association to environment and phenotype in lodgepole pine and interior spruce.

    (A to C) Genes with the deepest shades of blue have the greatest average strength of association for each gene, for one-to-one orthology (A); one ortholog to multiple genes, at least one of which is a top candidate (B); and multiple orthologs to one top candidate (C). In all cases, one gene is shown per row, genes that are duplicates (paralogs) in one species are grouped between thick horizontal black lines, and the ordering of genes is maintained so that orthologs are adjacent within each contrast. Boxes outlining the panels of the ortholog columns correspond to the color scheme in Fig. 3.

  • Fig. 3 Proportion of top-candidate orthologs with significant signatures of convergent local adaptation.

    All orthologs from Fig. 2 were tested with the null-W test with α = 0.05; colors correspond to the outlines in the respective panels. The horizontal gray line at 0.05 indicates the expected number of significant results under the null hypothesis of pure drift. Hatching indicates the upper 95% confidence limit for this null hypothesis (based on a binomial test with P = 0.05).

  • Table 1 Number of genes with signatures of convergence.

    Columns report the number of cases where a gene from one species that was orthologous to a top candidate in the other species was significantly associated to at least one of the seven main variables by the null-W test after adjusting for false discovery rate.

    False discovery
    rate
    One-to-one
    orthologs
    One-to-many:
    Both duplicates
    convergent
    One-to-many:
    One duplicate
    convergent
    Total number
    of genes with strong
    signatures of convergence
    0.016006
    0.05400747
    0.10712883
  • Convergent local adaptation to climate in distantly related conifers

    Sam Yeaman, Kathryn A. Hodgins, Katie E. Lotterhos, Haktan Suren, Simon Nadeau, Jon C. Degner, Kristin A. Nurkowski, Pia Smets, Tongli Wang, Laura K. Gray, Katharina J. Liepe, Andreas Hamann, Jason A. Holliday, Michael C. Whitlock, Loren H. Rieseberg, Sally N. Aitken

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Supplementary Text
    • Figs. S1 to S24
    • Tables S1 to S10
    • References

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