Fig. 1

Identification of the Red locus. a Association between RADSeq markers and head colour in Gouldian finches (n_black = 22, n_red = 10). A circle around a dot indicates the only significant signal in GWAS (P < 0.05, 1000 permutations). The region shaded in green on the Z chromosome represents the candidate region (~7.2 cM) based on a previous linkage mapping study²¹, where the Red locus co-segregated perfectly with microsatellite markers. b Genotypes of 161 birds from a wild population (male: n_black = 62, n_red = 27; female: n_black = 64, n_red = 8) based on two contiguous SNPs in the Red locus, where bar colours represent head colour. These SNPs (TG/CA) were identified by RADSeq (M1 at 46,561,597–46,561,598 bp in the zebra finch) and were typed using allele-specific PCR (Supplementary Fig. 2, Supplementary Table 2). c The extent of linkage disequilibrium (LD) associated with the colour trait. In the top panel, the locations of the protein-coding regions on the zebra finch Z chromosome (Mb) are indicated by vertical bars on the horizontal axis and the horizontal arrows below the gene names indicate the direction of transcription. Horizontal blue bars show the overlapping long-range PCR products (totalling ~100 kbp) that were subsequently sequenced, which includes the 72-kbp region with elevated LD defined as the Red locus in this study (see Fig. 2, Supplementary Tables 6, 7). The three vertical red arrows indicate the locations of markers (M1–M3) that were used to genotype the wild birds in association tests (Supplementary Fig. 2, Supplementary Table 2). The middle panel shows −log₁₀P for association tests between phenotype and 282 SNPs from 26 fragments in 16 females (n_black = 8, n_red = 8) typed using Sanger sequencing. The lower panel shows pairwise LD (r²) between SNPs. Finch illustrations by Megan Bishop