Fig. 1: Identifying inversion polymorphisms.
From: Chromosomal inversion polymorphisms shape the genomic landscape of deer mice
a, Left: photograph of P. maniculatus (Photo credit: E. P. Kingsley, reproduced from ref. 52, Wiley). Right: phylogenetic tree showing the relationships of five focal populations of P. maniculatus (bold branches) and two additional species. Note: P. polionotus subgriseus falls within the maniculatus clade. b–g, Detection of polymorphic inversions. b, Local PCA for example inversions in P. m. bairdii (left) and P. m. gambelii (right), where each dot represents a 100 kb window. Distances between local PCA maps are represented by the MDS1 axis, with outlier windows highlighted in colour (red or blue). c, Clustering of samples by PCA for entire outlier regions found in b, assigned using k-means clustering. Right: P. m. rubidus shown (triangles) for comparison. d, Heterozygosity of samples by cluster assignments from PCA in c. Boxes indicate upper and lower quartiles; centre line represents median; whiskers extend to minimum and maximum values within 1.5× interquartile range; points show outliers beyond whiskers. Sample sizes for clusters 1, 2, 3: (left) n = 7, 9, 1; (right) n = 2, 12, 16. e, LD for chromosomes (chr) harbouring the example inversions, shown as mean r2 values for paired windows across each chromosome. Mean r2 values including all samples from PCA clustering (upper triangle) and for only the more common homozygote genotype as determined by PCA clustering (lower triangle). Coloured bars highlight outlier regions from b. Scales for r2 values are provided. f, Recombination rates (cM Mb−1) shown for laboratory-born inversion heterozygotes. Outlier regions found in b are highlighted. g, FST between homozygous genotypes (clusters 1 and 3 from c). Outlier regions found in b are highlighted.
