A new approach to genomic species delineation could impact policy and lend clarity to legislation for designating a species as endangered or at risk.

The coastal California gnatcatcher is an unassuming little gray songbird that's been at the epicenter of a legal brawl for nearly 28 years, ever since U.S. Fish and Wildlife Service listed it as threatened under the Endangered Species Act.

Found along the Baja California coast, from down south in El Rosario, Mexico to Long Beach, Calif., its natural habitat is the rapidly declining coastal sagebrush that occupies prime, pristine real estate along the West Coast. When this particular gnatcatcher, Polioptila californica, was granted protection, the region's real estate developers went to court to get it delisted.

Central to their argument, which was dismissed in a federal court, was whether it was an independent species or just another population of a more widely found gnatcatcher. This distinction would dictate its threatened status. Evolutionary biologists have developed a new approach to genomic species delineation that improves upon current methods and could impact similar policy in the future.

This approach is based on the fact that in many groups of organisms it can be problematic to decide where one species begins and another ends.

"In the past, when it was challenging to distinguish species based on external characters, scientists relied on approaches that diagnosed signatures in the genome to identify 'breaks' or 'structure' in gene flow indicative of population separation. The problem is this method doesn't distinguish between two populations separated geographically versus two populations being two different species," said Jeet Sukumaran, computational evolutionary biologist at San Diego State University and lead author of a study published May 13, 2021 in PLOS Computational Biology. Sukumaran was a postdoctoral fellow at the University of Michigan’s Department of Ecology and Evolutionary Biology when their research began.

"Our method, DELINEATE, introduces a way to distinguish between these two factors, which is important because most of the natural resources management policy and legislature in our society rests on clearly defined and named species units."

Sukumaran and coauthors L. Lacey Knowles, University of Michigan, Ann Arbor and Mark Holder, the University of Kansas, Lawrence, add a second layer of information to the population phylogeny, to explicitly model the actual speciation process. This allows them to understand how these separate populations sometimes evolve into distinct species, which is the basis for distinguishing between populations and species in the data.

With this framework, scientists can have a better understanding of the status of any species, but especially of species that are members of a species complex – multiple independent species that all look alike.

Many fields of science and medicine depend on the accurate demarcation and identification of species, including ecology, evolution, conservation and wildlife management, agriculture and pest management, epidemiology and vector-borne disease management etc. These fields also intersect government, legislature and policy, with major implications for the day-to-day lives of broader human society.

The DELINEATE model is a first step in a process that will need to be further refined. Funding for this research came from the National Science Foundation.

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