Fig. 2: Whole-genome differentiation between alba and personata subspecies and the results of admixture mapping.
From: Asymmetric introgression reveals the genetic architecture of a plumage trait
a, b Show relative genomic differentiation (FST) between remote allopatric populations and sympatric alba and personata head plumage phenotypes, respectively, estimated in 25 kb windows with 10 kb steps. Note that among multiple regions differentiated between allopatric populations, only two peaks on chromosomes 1A and 20 (highlighted in blue) remain distinct in sympatry. c, d Expand the highlighted regions on chromosomes 1A and 20. Gray circles are by-locus Weir-and-Cockerham FST, light gray and black lines are window-based estimates of the relative (FST) and absolute (dXY) differentiation, respectively. Red and blue lines are window-based estimates of nucleotide diversity in alba and personata, respectively. Orange dots are window-based ABBA–BABA (fd) indicating a fraction of shared ancestry between sympatric and allopatric personata (50 kb windows with 10 kb steps, see the “Methods” section for details). Below each plot are gene models with arrows indicating the direction of reading frame where it is known. Note that the divergent peak on chromosome 1A is mostly located in a non-coding region but includes the coiled-coil domain-containing protein 91 (CCDC91) gene. The peak on chromosome 20 overlaps three genes: adenosylhomocysteinase (AHCY), eukaryotic translation initiation factor 2 subunit beta (EIF2S2), and is centered around agouti signaling protein (ASIP). e Results of admixture mapping for head plumage. Each dot is a −log10-transformed P-value for rejecting a model assuming no association between variation in a trait and a genetic locus. Dashed lines on a and b are 0.995 quantiles.
