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

• Published in: Current biology 2023-07, Vol.33 (13), p.2823-2829.e4
• Main Authors: Wood, Andrew W., Szpiech, Zachary A., Lovette, Irby J., Smith, Brian Tilston, Toews, David P.L.
• Format: Article
• Language: English
• Subjects: conservation; extinction; genomics; historical DNA; hybridization; museum; runs of homozygosity; speciation; Vermivora
• ISSN: 0960-9822; 1879-0445
• DOI: 10.1016/j.cub.2023.05.058

Bachman’s warbler1 (Vermivora bachmanii)—last sighted in 1988—is one of the only North American passerines to recently go extinct.2,3,4 Given extensive ongoing hybridization of its two extant congeners—the blue-winged warbler (V. cyanoptera) and golden-winged warbler (V. chrysoptera)5,6,7,8—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. [Display omitted] •Genomes show Bachman’s warbler was a highly divergent, reproductively isolated taxon•There is no evidence of admixture between V. bachmanii and extant Vermivora•Vermivora have similar levels of ROH, implying small effective population sizes•PBS in V. chrysoptera highlights CORIN as a novel color gene candidate in warblers Wood et al. sequenceed the genomes of extinct Bachman’s warblers and find that it was likely a highly divergent, reproductively isolated species, with no evidence of admixture between V. bachmanii and other extant Vermivora warblers.