A new approach to the genomic delineation of species could impact policies and clarify legislation to designate a species as endangered or at risk.
The California Coastal Flycatcher is a modest, small gray songbird that has been at the epicenter of a legal scuffle for nearly 28 years, since the US Fish and Wildlife Service classified it as threatened under the U.S. Fish and Wildlife Service Act. endangered species.
Found along the coast of Baja California, south to El Rosario, Mexico, to Long Beach, California, its natural habitat is the rapidly declining coastal sagebrush which occupies prime real estate along the Western coast. When this particular gnatcatcher, Polioptila californica, obtained protection, real estate developers in the area took legal action to remove it from the list.
The centerpiece of their argument, which was rejected in federal court, was whether it was an independent species or just another population of a more widespread midge. This distinction would dictate its threatened status. Evolutionary biologists have developed a new approach to delineating genomic species that improves 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 difficult to distinguish species based on external traits, scientists relied on approaches that diagnosed signatures in the genome to identify ‘breaks’ or ‘structure’ of gene flow indicating a gene flow. separation of the population. The problem is, this method doesn’t work. don’t distinguish between two geographically separated populations and two populations being two different species, ”said Jeet Sukumaran, a computational evolutionary biologist at San Diego State University and lead author of a study published May 13 in Computational Biology PlOS.
“Our method, DELINEATE, introduces a way to distinguish these two factors, which is important because most natural resource management policies and legislation in our society are based on clearly defined and named units of species.
Typically, scientists will use a range of different methods to identify the boundaries between different species, including statistical analysis and qualitative data to distinguish between population-level variation and species-level variation. in their samples, in order 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 rather than between two species, they often turn to genomic-based approaches to get the answer. . This is when scientists often use a model that generates a phylogeny of populations, or an evolutionary tree connecting different populations.
Sukumaran and his coauthors, evolutionary biologists L. Lacey Knowles of the University of Michigan, Ann Arbor and Mark Holder of the University of Kansas, Lawrence add a second layer of information to the phylogeny of populations, to explicitly model the actual speciation process. This allows them to understand how these separate populations sometimes evolve into separate species, which is the basis of the distinction between populations and species in the data.
Whether some of the population lines in the sample are attributed to existing species or classified as entirely new species depends on two factors. One is the age of population isolation events such as the division of an ancestral population into multiple daughter populations, which is how species are “born” in a protracted process of speciation. The other is the speciation completion rate, which is the rate at which nascent or nascent species “born” from population-dividing events develop into full-fledged species.
“We now realize that many organisms are cryptic species,” Sukumaran said. “Many of them look similar even though they are in fact separate species separated by tens or hundreds of thousands or even millions of years of evolution.”
This is either due to strong selection pressures to maintain the same morphology, or, more typically, to very recent speciation resulting in insufficient time for external differences to develop.
“When rivers change course, when the terrain changes, previously cohesive populations fragment, and the genetic makeup of the two separate populations, each now a full population, can diverge,” Sukumaran said. “Ultimately, one or both of these populations may evolve into distinct species and may (or may not) have already achieved that status by the time we examine them.
“However, the individuals of these two populations may seem identical to us according to their external appearances, because the differences between them may not have had time to ‘settle’ in one or the other. populations. This is when we turn to genomic data to help us decide whether we are looking at two populations of the same species, or two separate species. “
Currently, scientists are applying a model based on the theory of multispecies coalescence to genomic data to identify the disruption of gene flow between different groups of organisms. This disturbance is fundamental for the formation of species, but it can also occur between two different populations as well as two different species.
While scientists agree that it is essential to distinguish between populations and species boundaries in genomic data, there is not always much agreement on how to do this. “If you ask ten biologists, you’ll get twelve different answers,” Sukumaran said.
By modeling the dynamics of speciation itself in the analysis of species delineation, which previous methods did not do, the researchers’ approach makes it possible to distinguish between the interpopulation limits to gene flow and the interspecific boundaries, depending on the expected rate of speciation events.
With this framework, scientists can gain a better understanding of the status of any species, but especially species that are members of a species complex – several independent species that all look alike.
Many areas of science and medicine depend on the precise delineation and identification of species, including ecology, evolution, conservation and management of wildlife, agriculture and wildlife control. pests, epidemiology and management of vector-borne diseases, etc. These areas also cut across government, legislature and politics, with major implications for the daily life of human society at large.
The DELINEATE model is the first step in a process that will need to be further refined. Funding for this research came from the National Science Foundation.