Figure 2. Two regions of genomic differentiation and H3K27ac enrichment distinguish scale- and feather-footed pigeons.

(A) Whole-genome pFst comparisons between genomes of feather-footed and scale-footed pigeons. Scaffolds are ordered by genetic position in a linkage map from an F₂ cross (see Figure 1). Dashed line, genome-wide significance threshold. (B) pFst and extended haplotype homozygosity (EHH) plots for region of high differentiation on scaffold 79. Feather-footed birds (n=10, red in EHH plot) homozygous for a 44-kb deletion are differentiated from scale-footed birds (n=28, black) and show extended haplotype homozygosity in this region. Smoothed lines follow a generalized additive model (Wickham, 2009). (C) H3K27ac ChIP-seq enrichment differed significantly between embryonic wing and leg buds of the scale-footed racing homer (RH) in several regions (blue shading), including within a 44-kb interval that is deleted in the muffed Indian fantail (IF; blue arrowheads). This deleted region is orthologous to a known human limb enhancer (hs1473). (D) Selection scans show similar patterns of differentiation on scaffold 70 between muffed (n=11, red in EHH plot) and scale-footed birds (n=28, black). (E) H3K27ac ChIP-seq enrichment differed significantly between leg buds of racing homer and Indian fantail embryos in regions immediately 5’ of Tbx5 (blue shading). Foot and wing drawings modified after Levi (1986).

DOI: http://dx.doi.org/10.7554/eLife.12115.007

Figure 2—figure supplement 1. Synteny and genomic differentiation of pigeon LG20.

(A) Lastz alignment of pigeon scaffolds corresponding to linkage group 20 with chicken chromosome 15. (B) pFst scan of scaffolds from linkage group 20, ordered based on genetic linkage and synteny with chicken chromosome 15. green = scaffold 70, aqua = scaffold 95, blue = scaffold 737, black = scaffold 143, red = scaffold 20. Red line = whole genome significance threshold (2.11 x 10^–9).

DOI: http://dx.doi.org/10.7554/eLife.12115.008

Figure 2—figure supplement 2. Genomic association scans.

(A) pFst scans on scaffold 79 showing all feather-footed birds vs. all scale-footed birds, feather-footed birds homozygous for deletion vs. scale-footed birds, feather-footed birds lacking the deletion (alt) vs. scale-footed birds, and feather-footed birds lacking the deletion (alt) vs. feather-footed birds homozygous for the deletion. (B) Histogram of genotypes for scaffold 79 deletion, scale-footed vs. feather-footed phenotype. (C) pFst scans on scaffold 70 showing all feather-footed birds vs. scale-footed birds, muff birds vs. scale-footed birds, muff vs. grouse birds, and grouse vs. scale-footed birds. Range of –log₁₀(pFst) values on left side of each plot.

DOI: http://dx.doi.org/10.7554/eLife.12115.009

Figure 2—figure supplement 3. Haplotype diagram of scaffold 70 candidate interval.

Haplotypes clustered based on binary distance from muff (red), grouse (blue), and scale-footed (black) birds.

DOI: http://dx.doi.org/10.7554/eLife.12115.010