Fig. 4: Structural variants under viability selection.

Series of analyses testing for evidence of structural variants on chromosomes 1 (left) and 5 (right), including a estimates of recombination rates, b linkage disequilibrium in all individuals (bottom) or individuals homozygous (top) for putative variants (purple shading reflects the strength of r2 [linkage disequilibrium]), c local PCA analyses (100 kb windows with outlier population structure shown in gray), d PCA on outlier windows and levels of heterozygosity in the PCA clusters (boxplots show minimum, maximum, median, first and third quartiles; colors reflect birds genotyped as pure [purple or green] or hybrid at these loci; n = 296 birds, including those from our largest hybrid populations and pure, allopatric populations), and e Hi–C link pattern between inland and coastal genomes (red indicates elevated long-distance interactions; blue decreased long-distance interactions).