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. 2020 Jan 14;11:253. doi: 10.1038/s41467-019-14213-y

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a Reading guide for panels b and c. The leftmost panel shows the distribution of F_ST values for all SNPs. The SNPs shaded in gray are not differentiated between the two subpopulations compared, i.e. their genotype cannot be explained by population structure. The converse is true for the SNPs shaded in red; their genotypes can be fully explained by population structure. The second panel from the left shows distributions of F_ST values for the 200 SNPs with highest -log(p) GWA scores for the trait indicated. The third panel from the left shows experimental cumulative distribution graphs for the F_ST values for all SNPs (blue) and the SNPs shown in the panel to the left (orange). If the orange curve lies below the blue curve, it indicates a shift to higher F_ST values for the SNPs with high GWA scores. Each of the semi-transparent black lines indicate F_ST distributions for the top 200 SNPs from a GWA analysis of permuted phenotype data. The green line indicates the distribution for all 1000 sets of permuted data. The false discovery rate shown in the lower right hand corner indicates the frequency (%) of permuted distributions shifted to higher F_ST values than the observed data. The rightmost panel shows F_ST values plotted versus GWA -log(p) scores. The false discovery rate shown in the upper right hand corner indicates the frequency (%) of F_ST versus GWA -log(p) Spearman correlation coefficients with larger values than the correlation coefficient of the observed data. a, b F_ST values were calculated based on a pop3 vs. non-pop3 comparison. c F_ST values were calculated based on a pop1 vs. pop2 comparison. Traits likely associated with local adaptation are highlighted (orange). All analyses were carried out using top 200 GWA SNPs, except for the lower panel in c where the top 400 SNPs were used. Source data are provided as a Source Data file.