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Researchers Use SNP Data to Trace Zebra Phylogeographic, Demographic History

NEW YORK (GenomeWeb) – An international team led by the University of Copenhagen has performed genome-wide testing on subspecies of zebras in Africa in order to determine within-species evolutionary processes.

In the study, published today in Nature Ecology and Evolution, the researchers applied genome-wide single nucleotide polymorphism (SNP) data from restriction-site-associated (RAD) DNA sequencing to identify the genetic structure of the plains zebra and unravel its phylogeographic and demographic history.

Coauthor Hans Sigismund of the University of Copenhagen and his colleagues extracted data from more than 167,000 loci for 59 plains zebras across the species range, covering all recognized subspecies across Africa, in addition to three mountain zebras (Equus zebra) and three Grevy's zebras (Equus grevyi). One of the most widely distributed ungulates in Africa, the plains zebra is extremely mobile and able to feed on relatively low-quality forage. The team tested whether the genetic structure in the plains zebra coincides with currently recognized subspecies.

According to the study, the plains zebra "has high effective population sizes and high genetic diversity, with notable exceptions, such as the populations in northeastern Uganda, southwestern Uganda, and southeastern Tanzania."

To the researchers' surprise, the populations' genetic structure did not mirror the morphology-based subspecies descriptions, indicating the potential danger of classifying exclusively on morphological variation. They identified up to nine extant populations with distinct evolutionary properties and demonstrated that the genetic structure was discrete rather than clinal.

While the trend of isolation by distance has been reported before, the researchers wrote that past studies do not "distinguish between true clinal variation and a stepping stone pattern with discrete demes." The SNP biomarkers allowed the team to identify fine-scale structures in the plains zebra that past studies could not detect with mitochondrial DNA and microsatellite markers.

In addition to detecting fine-scale structures, the team used demographic modelling to provide insights into the past phylogeography of the species. From the modeling, Sigismund and his colleagues identified a region encompassing northern Botswana and Zambia as the most likely source area from which living zebra populations expanded around 370,000 years ago. The region's two crucial features include the Zambezi and the Okavango, wide wetland areas that have been climatically stable over a long time scale.  

The study also highlighted genetic evidence that the extinct quagga (Equus quagga quagga) was a southernmost variant of plains zebra, rather than a distinct zebra. Using a method based on the number of derived mutations between the quagga and the Namibia subspecies, the team estimated that the two populations had a coalescence time of 650,000 to 718,000 years ago. They also estimated that the coalescence time of the quagga and plains zebras is the same as that between plains individuals from different populations.

The team acknowledged limitations of the study, including the small sample size of different zebra populations. An increased and comprehensive sampling of zebra subspecies could reveal further substructure and additional clusters not represented in the study. For example, the East African Rift Valley, is a known driver of biodiversity and within-species structuring, most likely by its complicated topography and climatic history. 

According to the study, phylogeographic inference further confirms the valley's role as a migration corridor for the plains zebra. The researchers estimated that "effective migration surface and directionality analyses indicate a bipartition in the northwards expansion overlapping strikingly with the two main branches of the Great Rift Valley system."

Although conservation agencies have used the morphological subspecies classification to examine populations, Siegismund and his colleagues suggest that agencies should supplement assessments with genetic analyses to identify population structure of relevance for understanding phylogeography, in addition to prioritizing conservation of genetic resources.

While the Rift Valley acts as a barrier to gene flow in some species, the team believes the region can also play an important phylogeographic role by promoting long-term gene flow in zebra populations. In addition, they argue that conservation strategies must keep the zebra habitats connected for the species survival.  

"Gene flow — and consequently habitat connectivity — is the main prerequisite for maintaining genetically diverse plain zebra populations," the authors concluded.