Genomes of the extinct Bachman’s Warbler shows high divergence and no evidence of admixture with other extant Vermivora Warblers

Bachman’s Warbler (Vermivora bachmanii) – last sighted in 1988 – is one of the few North American passerines that have gone extinct. Given the extensive ongoing hybridization of its two extant congeners – the Blue-Winged Warbler (V. cyanoptera) and Golden-Winged Warbler (V. chrysoptera) – and shared patterns of plumage variation between Bachman’s Warbler and hybrids between those extant species, it has been suggested that Bachman’s Warbler might have also had a component of hybrid ancestry. Here, we use historic DNA (hDNA) and whole genome sequencing of Bachman’s Warblers collected at the turn of the 20th century to address this possibility. We combine these data with genomes of the two extant Vermivora species to examine patterns of population differentiation, inbreeding, and gene flow. In contrast to the admixture hypothesis, the genomic evidence is consistent with V. bachmanii being a highly divergent, reproductively isolated species, with no evidence of introgression. We show that both V. bachmanii and V. chrysoptera have elevated runs of homozygosity compared to V. cyanoptera, consistent with the effects of a small effective population size or population bottlenecks in the former two species. We also found—using population branch statistic estimates of all three species—previously undocumented evidence of lineage-specific evolution in V. chrysoptera near a novel pigmentation gene candidate for warblers, CORIN, which is a known modifier of ASIP, which is in turn involved in melanic throat and mask coloration in this family of birds. Together, these genomic results also highlight how natural history collections are such invaluable repositories of information about extant and extinct species. Significance Few common North American passerines have gone extinct. Bachman’s Warbler is, unfortunately, one that has—the last sighting was in 1988. Here we use whole genome historical DNA from museum specimens of Bachman’s warblers collected at the turn of the 20th century to learn about the evolution of this species and test whether there was evidence for hybridization and gene flow between it and two extant members of the same genus which, today, hybridize extensively. We find Bachman’s warbler was highly divergent with no evidence of gene flow. We also find evidence of elevated “runs of homozygosity” in both Bachman’s warbler and one of the two extant Vermivora species, suggesting the effects of a small population size or population bottlenecks.