Genomes of the extinct Bachman's warbler show high divergence and no evidence of admixture with other extant Vermivora warblers

Bachman's warbler1 (Vermivora bachmanii)-last sighted in 1988-is one of the only North American passerines to recently go extinct.2-4 Given extensive ongoing hybridization of its two extant congeners-the blue winged warbler (V. cyanoptera) and golden-winged warbler (V. chrysoptera)5-8-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 genomes of Bachman's warblers collected at the turn of the 20th century to address this. We combine these data with 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 having been a highly divergent, reproductively isolated species, with no evidence of introgression. We show that these three species have similar levels of runs of homozygosity (ROH), consistent with effects of a small long-term effective population size or population bottlenecks, with one V. bachmanii outlier showing numerous long ROH and a FROH greater than 5%. We also found-using population branch statistic estimates-previously undocumented evidence of lineage-specific evolution in V. chrysoptera near a pigmentation gene candidate, 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.

Automated summary

Bachman's warbler, last spotted in 1988, is one of the few North American passerines that have recently become extinct. The extensive hybridization between its two extant congeners and similarities in plumage variation suggest a possible hybrid ancestry for Bachman's warbler. However, analysis of historic DNA and whole genomes of Bachman's warblers collected in the early 20th century provides genomic evidence that contradicts the admixture hypothesis, indicating that Bachman's warbler was a highly divergent and reproductively isolated species.