Fig. 2: Chromosome 1 supergene.
From: A supergene underlies linked variation in color and morphology in a Holarctic songbird
a Chromosome 1 SNPs significantly associated with phenotype (black dots) using mixed model analysis in GEMMA with an alpha of 1 × 10−5 to correct for multiple comparisons. Numbers indicate the two most significant SNP associations outside (1,2) and inside (3,4) the inversion region and correspond to genotypes in (b) for those specific SNPs. Lightest yellow cells indicate individuals homozygous for the reference allele, darkest indicate homozygous for the alternative allele, intermediate indicate heterozygotes, and white are missing data. c Pi (black and gray lines for AA and AB individuals, respectively) and dXY (green line) in 50-kb windows for the first 80 Mb of chromosome 1. d LD calculated as r2 comparing chromosome 1 (black line) to 4 of the other largest chromosomes (shades of gray) and LD within the supergene (black) to the rest of chromosome 1 (gray). e PCA of chromosome 1 with a 40% minor allele frequency cutoff showing three main clusters along PC1. Taxa colors correspond to Fig. 1. All sequences were aligned to a brown-capped rosy-finch (Leucosticte australis) reference genome. Source data are provided as Source data file.
