Data from: Parallel plumage color evolution and introgressive hybridization in wheatears

Genetic and phenotypic mosaics, in which various phenotypes and different
genomic regions show discordant patterns of species or population
divergence, offer unique opportunities to study the role of ancestral and
introgressed genetic variation in phenotypic evolution. Here, we
investigated the evolution of discordant phenotypic and genetic divergence
in a monophyletic clade of four songbird taxa – pied wheatear (O.
pleschanka), Cyprus wheatear (O. cypriaca), and western and eastern
subspecies of black-eared wheatear (O. h. hispanica and O. h.
melanoleuca). Phenotypically, black back and neck-sides distinguish pied
and Cyprus wheatears from the white-backed/necked black-eared wheatears.
Meanwhile, mitochondrial variation only distinguishes western black-eared
wheatear. In the absence of nuclear genetic data, and given frequent
hybridization among eastern black-eared and pied wheatear, it remains
unclear whether introgression is responsible for discordance between
mitochondrial divergence patterns and phenotypic similarities, or whether
plumage coloration evolved in parallel. Multispecies coalescent analyses
of about 20’000 SNPs obtained from RAD data mapped to a draft genome
assembly resolve the species tree, provide evidence for the parallel
evolution of color phenotypes, and establish western and eastern
black-eared wheatears as independent taxa that should be recognized as
full species. The presence of the entire admixture spectrum in the Iranian
hybrid zone and the detection of footprints of introgression from pied
into eastern black-eared wheatear beyond the hybrid zone despite strong
geographic structure of ancestry proportions furthermore suggest a
potential role for introgression in parallel plumage color evolution. Our
results support the importance of standing heterospecific and/or ancestral
variation in phenotypic evolution.