Extinct warbler genomes sequenced from museum specimens

The Bachman’s warbler, a songbird last seen in North America nearly 40 years ago, is a distinct species and not a hybrid of its two living sister species, according to a new study in which the complete genomes of seven museum specimens of the bird were sequenced. Comparison of the genome of Bachman’s warbler with that of the golden-winged and blue-winged warblers also helped researchers identify candidate new genes involved in feather pigmentation within the group. A paper describing the study, led by Penn State researchers, highlights the important role museum collections can play in science and appears June 16, 2023 in the journal Current Biology.

“The Bachman’s warbler is the only songbird known to have recently gone extinct in North America,” said David Toews, assistant professor of biology at Penn State Eberly College of Science and leader of the research team. “It is one of three species in the Vermivora genus. Our laboratory studied two living species of this genus, which are known to mate with each other to produce hybrid offspring.”

Golden-winged and blue-winged warblers produce a spectrum of hybrids, but two distinct types of hybrid offspring, each with a unique parent-species color combination, have become the focus of bird watchers and ornithologists. This is because these two hybrids were thought to be distinct species, known as the Brewster’s warbler and Lawrence’s warbler, until careful studies of wild hybrids and, now, modern genetic analysis have confirmed their hybrid origins. The now extinct Bachman’s warbler resembles one of these hybrid breeds in coloration, so there is some question whether the Bachman’s warbler is itself a distinct species or perhaps a hybrid.

The research team collected seven specimens of Bachman’s warbler from museum collections and extracted DNA from the birds’ foot pads. They then performed whole genome sequencing to compare the Bachman’s warbler genome with existing genomes for the two living species in the genus.

“It’s never been easier to obtain DNA for sequencing from museum specimens,” said Andrew Wood, the paper’s first author, who was a research technologist in the Toews lab at the time of the study and is now a postdoctoral researcher at the University of Minnesota. “These birds were collected over a hundred years ago and were not preserved in any special way, but we were able to extract enough DNA to obtain genomic sequences comparable to those from living species.”

The genomes of the golden-winged and blue-winged warblers are very similar to each other, except for a few regions involved in determining the coloration patterns of the plumage. By comparison, the genome of the Bachman’s warbler was very different, indicating to researchers that it is actually a different species.

“We only have a small sample size for the Bachman warbler genome, but one of the interesting findings we saw by comparing the seven specimens was that there is a long ‘homozygosity journey’,” said Toews. “These are regions of the genome where two copies of the genome – one inherited from each parent – are identical to each other and are an indication that the population may be small and there is a lot of inbreeding. We see similar patterns in living species, so understanding if this may have contributed to the extinction of the Bachman’s warbler can help us to better understand the health and conservation of surviving populations.”

The researchers also compared the genomes of the three species to look for genomic regions that might have evolved differently in each lineage. These differences can be indicators that certain genomic regions evolved through natural selection for certain traits or due to other evolutionary processes. Having the genomes of a third species to compare with allowed the researchers to identify regions containing new candidate genes involved in warbler pigmentation.

“We started this research because we were interested in studying the history and biology of Bachman’s warbler,” said Woods. “But our results also highlight how we can use extinct species to study their living relatives. We lose a lot of biological and evolutionary context through the process of extinction and being able to compare Bachman’s warbler to two living species allows us to identify genes we otherwise might not find. Context is very important for understanding biology. Natural history collections allow us to place new observations into contexts that nature may have lost. This fuels discovery, and makes museums a powerful, and underappreciated, tool.

In addition to Toews and Wood, the research team included Zachary A. Szpiech, an assistant professor of biology at Penn State; Irby J. Lovette at the Cornell Lab of Ornithology; and Brian Tilston Smith at the American Museum of Natural History in New York. This research was funded by the US National Science Foundation, the Huck Institutes of the Life Sciences at Penn State, and the Penn State Eberly College of Science. The computations were performed using the Roar supercomputer from the Institute for Computational Data Sciences at Penn State.