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

Andrew W Wood; Zachary A Szpiech; Irby J Lovette; Brian Tilston Smith; David P L Toews

doi:10.1016/j.cub.2023.05.058

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

Curr Biol. 2023 Jul 10;33(13):2823-2829.e4. doi: 10.1016/j.cub.2023.05.058. Epub 2023 Jun 16.

Authors

Andrew W Wood¹, Zachary A Szpiech², Irby J Lovette³, Brian Tilston Smith⁴, David P L Toews⁵

Affiliations

¹ Department of Biology, Pennsylvania State University, 619 Mueller Laboratory, University Park, State College, PA 16802, USA.
² Department of Biology, Pennsylvania State University, 619 Mueller Laboratory, University Park, State College, PA 16802, USA; Institute for Computational and Data Sciences, Pennsylvania State University, University Park, State College, PA 16802, USA.
³ Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA.
⁴ Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.
⁵ Department of Biology, Pennsylvania State University, 619 Mueller Laboratory, University Park, State College, PA 16802, USA. Electronic address: toews@psu.edu.

PMID: 37329885
DOI: 10.1016/j.cub.2023.05.058

Abstract

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 20^th 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 F_ROH 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.

Keywords: Vermivora; conservation; extinction; genomics; historical DNA; hybridization; museum; runs of homozygosity; speciation.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Genome
Hybridization, Genetic
Inbreeding
Passeriformes* / genetics
Songbirds* / genetics