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. 2019 May 28;11(7):2023–2034. doi: 10.1093/gbe/evz112

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Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2019. This work is written by US Government employees and is in the public domain in the US.

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Fig. 4. — —Identification and characterization of potential genomic targets of selection. (A) Manhattan plot of SNP outlier tests from whole-genome resequencing of six sage-grouse populations. Elevated X^TX values are indicative of loci with extreme population differentiation, while controlling for underlying neutral population structure. Dashed red line represents the 1% probability threshold as estimated from analysis of pseudo-observed data sets. Contrasting gray points correspond to different chromosomes based on syntenic alignment to the chicken genome. Highlighted are SNPs that occur in regions (gene ± 10-kb flanking region) containing candidate genes for metabolic adaptation (green = cytochrome P450 genes, yellow = other important pharmacogenes). (B) Proportion of SNP effects in different genomic regions across each quintile of the observed X^TX distribution. Asterisks indicate significant overrepresentation of SNP effects in a given genomic region. (C) PCA of 1% X^TX outlier SNPs (8,592 sites). Axes represent first (PC1) and second (PC2) principal components, with percentage of total genetic variance explained by each component shown in parentheses.