DOI: 10.5061/dryad.6m905qg42
title: Convergent genomic signatures of local adaptation across a continental-scale environmental gradient

description: Convergent local adaptation offers a glimpse into the role of constraint
 and stochasticity in adaptive evolution, in particular the extent to which
 similar genetic mechanisms drive adaptation to common selective forces.
 Here, we investigated the genomics of local adaptation in two non-sister
 woodpeckers that are co-distributed across an entire continent and exhibit
 remarkably convergent patterns of geographic variation. We sequenced the
 genomes of 140 individuals of Downy (Dryobates pubescens) and Hairy (D.
 villosus) woodpeckers and employed a suite of genomic approaches to
 identify loci under selection. We showed evidence that convergent genes
 have been targeted by selection in response to shared environmental
 pressures, such as temperature and precipitation. Among candidates, we
 found multiple genes putatively linked to key phenotypic adaptations to
 climate, including differences in body size (e.g., IGFPB) and plumage
 (e.g., MREG). These results are consistent with genetic constraints
 limiting the pathways of adaptation to broad climatic gradients, even
 after genetic backgrounds diverge.
description: Whole genome sequencing of 140 samples of Downy
 (<em>Dryobates</em> <em>pubescens</em>) and Hairy
 (<em>D</em>. <em>villosus</em>) Woodpecker from
 seven (n per population = 10) North American populations. 
description: <strong>D.pubescens_T.guttata-pseudochromosomes.cds.gff</strong> - Gene annotation of Downy Woodpecker mapped to the pseudochromosome reference genome. <strong>D.pubescens_candidates_windows_PC1T.csv</strong> - GEA significant windows for PC1 of temperature in <em>D. pubescens</em> <strong>D.pubescens_candidates_windows_PC2T.csv </strong>- GEA significant windows for PC2 of temperature in <em>D. pubescens</em> <strong>D.pubescens_candidates_windows_PC3T.csv</strong> - GEA significant windows for PC3 of temperature in <em>D. pubescens</em> <strong>D.pubescens_candidates_windows_PC1T.csv</strong> - GEA significant windows for PC1 of precipitation in <em>D. pubescens</em> <strong>D.pubescens_candidates_windows_PC2P.csv</strong> - GEA significant windows for PC2 of precipitation in <em>D. pubescens</em> <strong>D.pubescens_candidates_windows_PC3P.csv</strong> - GEA significant windows for PC3 of precipitation in <em>D. pubescens</em> <strong>D.pubescens_PC1T.rol_win</strong> - Per-window median LRT scores for the association with PC1 of temperature in <em>D. pubescens</em> <strong>D.pubescens_PC2T.rol_win</strong> - Per-window median LRT scores for the association with PC2 of temperature in <em>D. pubescens</em> <strong>D.pubescens_PC3T.rol_win</strong> - Per-window median LRT scores for the association with PC3 of temperature in <em>D. pubescens</em> <strong>D.pubescens_PC1T.rol_win</strong> - Per-window median LRT scores for the association with PC1 of precipitation in <em>D. pubescens</em> <strong>D.pubescens_PC2P.rol_win</strong> - Per-window median LRT scores for the association with PC2 of precipitation in <em>D. pubescens</em> <strong>D.pubescens_PC3P.rol_win </strong>- Per-window median LRT scores for the association with PC3 of precipitation in D. pubescens <strong>D.pubescens_PC1T.permutation.rol_win </strong>- Per-window median LRT scores for 200 random permutations of the association with PC1 of temperature in <em>D. pubescens</em> <strong>D.pubescens_PC2T.permutation.rol_win </strong>- Per-window median LRT scores for 200 random permutations of the association with PC2 of temperature in <em>D. pubescens</em> <strong>D.pubescens_PC3T.permutation.rol_win</strong> - Per-window median LRT scores for 200 random permutations of the association with PC3 of temperature in <em>D. pubescens</em> <strong>D.pubescens_PC1T.permutation.rol_win </strong>- Per-window median LRT scores for 200 random permutations of the association with PC1 of precipitation in <em>D. pubescens</em> <strong>D.pubescens_PC2P.permutation.rol_win </strong>- Per-window median LRT scores for 200 random permutations of the association with PC2 of precipitation in <em>D. pubescens</em> <strong>D.pubescens_PC3P.permutation.rol_win </strong>- Per-window median LRT scores for 200 random permutations of the association with PC3 of precipitation in D. pubescens <strong>D.villosus_candidates_windows_PC1T.csv </strong>- GEA significant windows for PC1 of temperature in <em>D. villosus</em> <strong>D.villosus_candidates_windows_PC2T.csv</strong> - GEA significant windows for PC2 of temperature in <em>D. villosus</em> <strong>D.villosus_candidates_windows_PC3T.csv</strong> - GEA significant windows for PC3 of temperature in <em>D. villosus</em> <strong>D.villosus_candidates_windows_PC1T.csv</strong> - GEA significant windows for PC1 of precipitation in <em>D. villosus</em> <strong>D.villosus_candidates_windows_PC2P.csv </strong>- GEA significant windows for PC2 of precipitation in <em>D. villosus</em> <strong>D.villosus_candidates_windows_PC3P.csv </strong>- GEA significant windows for PC3 of precipitation in <em>D. villosus</em> <strong>D.villosus_PC1T.rol_win</strong> - Per-window median LRT scores for the association with PC1 of temperature in <em>D. villosus</em> <strong>D.villosus_PC2T.rol_win</strong> - Per-window median LRT scores for the association with PC2 of temperature in <em>D. villosus</em> <strong>D.villosus_PC3T.rol_win</strong> - Per-window median LRT scores for the association with PC3 of temperature in <em>D. villosus</em> <strong>D.villosus_PC1T.rol_win</strong> - Per-window median LRT scores for the association with PC1 of precipitation in <em>D. villosus</em> <strong>D.villosus_PC2P.rol_win</strong> - Per-window median LRT scores for the association with PC2 of precipitation in <em>D. villosus</em> <strong>D.villosus_PC3P.rol_win</strong> - Per-window median LRT scores for the association with PC3 of precipitation in D. villosus <strong>D.villosus_PC1T.permutation.rol_win</strong> - Per-window median LRT scores for 200 random permutations of the association with PC1 of temperature in <em>D. villosus</em> <strong>D.villosus_PC2T.permutation.rol_win</strong> - Per-window median LRT scores for 200 random permutations of the association with PC2 of temperature in <em>D. villosus</em> <strong>D.villosus_PC3T.permutation.rol_win</strong> - Per-window median LRT scores for 200 random permutations of the association with PC3 of temperature in <em>D. villosus</em> <strong>D.villosus_PC1T.permutation.rol_win</strong> - Per-window median LRT scores for 200 random permutations of the association with PC1 of precipitation in <em>D. villosus</em> <strong>D.villosus_PC2P.permutation.rol_win</strong> - Per-window median LRT scores for 200 random permutations of the association with PC2 of precipitation in <em>D. villosus</em> <strong>D.villosus_PC3P.permutation.rol_win</strong> - Per-window median LRT scores for 200 random permutations of the association with PC3 of precipitation in <em>D. villosus</em> <strong>D.pubescens_FST_comparisons.zip</strong>: <strong>PP-&lt;pop1&gt;-&lt;pop2&gt;.50kb-10kbstep.pdf</strong> - Manhattan plot of Fst values estimated for 50kb windows (10 kb increments) comparing &lt;pop1&gt; and &lt;pop2&gt; in <em>D. pubescens</em> <strong>PP-&lt;pop1&gt;-&lt;pop2&gt;.FST_histogram.pdf</strong> - Histogram of Fst values estimated for 50kb windows (10 kb increments) comparing &lt;pop1&gt; and &lt;pop2&gt; in <em>D. pubescens</em> <strong>PP-&lt;pop1&gt;-&lt;pop2&gt;.fst_slidingwindow</strong> - Fst values estimated for 50kb windows (10 kb increments) comparing &lt;pop1&gt; and &lt;pop2&gt; in <em>D. pubescens</em> <strong>PP-&lt;pop1&gt;-&lt;pop2&gt;.outliers_5sd.csv</strong> - Outlier Fst windows (&gt;5 standard deviations) for the comparison between &lt;pop1&gt; and &lt;pop2&gt; in <em>D. pubescens</em> <strong>PP-&lt;pop1&gt;-&lt;pop2&gt;-candidates.csv </strong>- Candidate genes within outlier Fst windows (&gt;5 standard deviations) for the comparison between &lt;pop1&gt; and &lt;pop2&gt; in <em>D. pubescens</em> <strong>D.villosus_FST_comparisons.zip</strong>: <strong>PV-&lt;pop1&gt;-&lt;pop2&gt;.50kb-10kbstep.pdf</strong> - Manhattan plot of Fst values estimated for 50kb windows (10 kb increments) comparing &lt;pop1&gt; and &lt;pop2&gt; in <em>D. villosus</em> <strong>PV-&lt;pop1&gt;-&lt;pop2&gt;.FST_histogram.pdf</strong> - Histogram of Fst values estimated for 50kb windows (10 kb increments) comparing &lt;pop1&gt; and &lt;pop2&gt; in <em>D. villosus</em> <strong>PV-&lt;pop1&gt;-&lt;pop2&gt;.fst_slidingwindow</strong> - Fst values estimated for 50kb windows (10 kb increments) comparing &lt;pop1&gt; and &lt;pop2&gt; in <em>D. villosus</em> <strong>PV-&lt;pop1&gt;-&lt;pop2&gt;.outliers_5sd.csv</strong> - Outlier Fst windows (&gt;5 standard deviations) for the comparison between &lt;pop1&gt; and &lt;pop2&gt; in <em>D. villosus</em> <strong>PV-&lt;pop1&gt;-&lt;pop2&gt;-candidates.csv</strong> - Candidate genes within outlier Fst windows (&gt;5 standard deviations) for the comparison between &lt;pop1&gt; and &lt;pop2&gt; in <em>D. villosus</em> <strong>D.pubescens_AK_all_chr_Hscan.rol_win </strong>- Median H scores for 50 SNP windows (10 SNP increments) in the Alaska population of <em>D. pubescens</em> <strong>D.pubescens_E_all_chr_Hscan.rol_win</strong> - Median H scores for 50 SNP windows (10 SNP increments) in the East population of <em>D. pubescens</em> <strong>D.pubescens_R_all_chr_Hscan.rol_win</strong> - Median H scores for 50 SNP windows (10 SNP increments) in the Rockies population of <em>D. pubescens</em> <strong>D.pubescens_NW_all_chr_Hscan.rol_win</strong> - Median H scores for 50 SNP windows (10 SNP increments) in the Northwest population of <em>D. pubescens</em> <strong>D.villosus_AK_all_chr_Hscan.rol_win</strong> - Median H scores for 50 SNP windows (10 SNP increments) in the Alaska population of <em>D. villosus</em> <strong>D.villosus_E_all_chr_Hscan.rol_win </strong>- Median H scores for 50 SNP windows (10 SNP increments) in the East population of <em>D. villosus</em> <strong>D.villosus_R_all_chr_Hscan.rol_win</strong> - Median H scores for 50 SNP windows (10 SNP increments) in the Rockies population of <em>D. villosus</em> <strong>D.villosus_NW_all_chr_Hscan.rol_win </strong>- Median H scores for 50 SNP windows (10 SNP increments) in the Northwest population of <em>D. villosus</em> <strong>D.pubescens_PCAdapt.candidates.tsv </strong>- Candidate SNP windows for the PCAdapt analysis in<em> D. pubescens</em> <strong>D.pubescens_PCAdapt.rol_win </strong>- Median p-values of each 50 SNP windows (10 SNP increments) for the PCAdapt analysis in<em> D. pubescens</em> <strong>D.villosus_PCAdapt.candidates.tsv </strong>- Candidate SNP windows for the PCAdapt analysis in <em>D. villosus</em> <strong>D.villosus_PCAdapt.rol_win</strong> - Median p-values of each 50 SNP windows (10 SNP increments) for the PCAdapt analysis in <em>D. villosus</em>