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Thursday, March 23, 2023

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Evolutionary biologists have developed a new computational approach to genomic species delineation that improves upon current methods and could impact policy in the future. Evolutionary biologists have developed a new computational approach to genomic species delineation that improves upon current methods and could impact policy in the future.

New Approach to Identify Genetic Boundaries of Species Could Impact Policy

Evolutionary biologists model the process of speciation, which follows population formation, improving on current species delineation methods.
By Padma Nagappan

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 the U.S. Fish and Wildlife Service listed it as threatened under the Endangered Species Act.

Found along the Baja California coast, from 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 Polioptila californica was granted protection, the region’s real estate developers sued to delist it. 

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 computational 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 in PloS Computational Biology. 

“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.”

Typically, scientists will use a range of different methods to identify boundaries between different species, including statistical analysis and  qualitative data to distinguish between population-level variation and species-level variation in their samples, to complete the classification of an organism. In cases where it is difficult to sort the variation between individuals into differences due to variation within a species, they often turn to genomic data based approaches for the answer. This is when scientists often use a model that generates an evolutionary tree relating different populations. 

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

"Our method allows researchers to make statements about how confident they are that two populations are members of the same species,” Holder said. “That is an advance over just making a best estimate of species assignments."

Whether some of the population lineages in the sample are assigned to existing species or classified as entirely new species depends on two factors. One is the age of the population isolation events such as the splitting of an ancestral population into multiple daughter populations, which is how species are “born” in an extended process of speciation. The other is the rate of speciation completion, which is the rate at which the nascent or incipient species “born” from population splitting events develop into true full species.

Organisms can look alike, Sukumaran said, “even though they are actually distinct species separated by many tens or hundreds of thousands or even millions of years of evolution.” 

“When rivers change course, when terrain changes, previously cohesive populations get fragmented, and the genetic makeup of the two separate populations, now each a population in their own right, can diverge,” Sukumaran said. “Eventually, one or both these populations may evolve into separate species, and may (or may not) already have reached this status by the time we look at them. 

“Yet individuals of these two populations may look identical to us based on their external appearances, as differences in these may not have had time to ‘fix’ in either population. This is when we turn to genomic data to help guide us toward deciding whether we are looking at two populations of the same species, or two separate species.” 

While scientists agree that it is critical to distinguish between populations and species boundaries in genomic data, there is not always a lot of agreement on how to go about doing it. 

“If you ask ten biologists, you will get twelve different answers,” Sukumaran said. 

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

The work has implications far beyond real estate battles. 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.