Fig. 2: The genomic architecture of divergence between Baltimore and Bullock’s orioles.
a genome-wide FST estimates between allopatric Baltimore and Bullock’s orioles in 50 kb windows. Dashed line represents the 99th percentile of the mean (FST = 0.75). b Genotype plot for chromosome 5 shows an example of admixture patterns for fixed SNPs across the chromosome. Blue represents homozygotes for the reference allele, orange is homozygotes for the alternate allele, and heterozygotes are in pink. Colors are polarized using a Baltimore Oriole. c Genotype plot for the Z chromosome shows an example of admixture patterns for fixed SNPs. Blue represents homozygotes for the reference allele, orange is homozygotes for the alternate allele, and heterozygotes are in pink. Colors are polarized using a Baltimore Oriole. d PCA of SNPs associated with the larger elevated MDS region (as shown in the dashed black lined box). The 55 individuals sort into three clusters with the ends representing putative homozygotes for the inversion and the middle representing individuals that are putative heterozygotes for the inversion orientation. Individuals are color coded as allopatric/backcrossed for either parental species or hybrid (for this analysis, the hybrid category corresponds only to F1/F2 individuals). Genotypic classes are based on reduced representation sequencing data (see methods). e As predicted, heterozygosity for putative heterozygotes for the inversion is higher than that observed in homozygous individuals. Heterozygosity estimates were calculated for individuals assigned to each of the three clusters based on PCA results from panel c. Color coding for panel e is the same as that in panel d.
