New Study Shows That Cape Lions Were Genetically Diverse Prior To Extinction

European naturalists described the Cape lion as having a particularly black mane and as being morphologically distinct. However, alternative depictions and descriptions of Cape lions from Indigenous people reported mixed or light mane coloration. To shed light on this discrepancy, a Field Museum-University of Illinois Urbana-Champaign team compared the genetic diversity and distinctiveness of Cape lions to modern lions across 13 African countries in a new study in the Journal of Heredity. FMNH authors are Thomas Gnoske (Assistant Collections Manager, Birds), Julian Kerbis (Adjunct Curator), Velizar Simeonovski (Research Associate), and from UIUC, Alida de Flamingh (postdoc, and first author), Ripan Malhi (Professor of Anthropology), Alfred Roca (Professor of Animal Sciences), and Julian Catchen (Associate Professor of Integrative Biology).
As Julian told a reporter, “the scientific name of the Cape lion, Panthera leo melanochaitus, literally means black mane, but this description was based on a single specimen. Historically, we see lots of examples of creatures that are large and attractive like lions, where everybody wants to claim that they’d discovered a new one, without taking into account variation in the population, or whether that species is even unique.” Earlier investigations focused on limited segments of the Cape lion genome offered the first indication that these lions might not be as distinct as initially believed. The new study represents the first comprehensive examination of the entire Cape lion genome in comparison to contemporary lion populations across Africa.
The team gathered samples from two Cape lion skulls housed at the Field Museum that were originally components of taxidermy mounts at the South African Institute in Cape Town (1828–1838). “Unlike most other Cape Lion specimens around the world, these specimens had a traceable history and geographic collection location,” noted Tom. “As such, it was a great opportunity and challenge to see what application of the newest genomic methods could tell us about these specimens.” Adds Alida, “working with museums like the Field is an exciting opportunity to apply ancient DNA analyses to better understand human-animal interactions. I think it’s an area that’s going to be studied more and more as genetic technology continues to advance.” The genetic data from the skulls was compared to 118 existing mitogenomes and nuclear genomes of 53 other lions across Africa. Analysis revealed that the genome of the Cape lions was diverse, and demonstrated genomic links with other lions from both the southern and eastern parts of Africa. The researchers also found that the Cape lion genomes exhibited high heterozygosity [the possession of two different forms of a particular gene, one inherited from each parent], and lacked traits commonly associated with small populations and inbreeding, characteristics frequently observed in endangered species facing population decline. The unexpected absence of such traits in the Cape lion genomes is particularly noteworthy, since the skulls were collected as the species was approaching extinction, suggesting that they were hunted so rapidly that their genomes didn’t have time to accumulate the signatures of long-term small population size. The genomic richness also suggests that these lions likely exhibited significant phenotypic variation, including diverse mane coloration, which aligns with alternative descriptions and Indigenous perspectives on the species. As Ripan observed, the genomic data and analysis didn’t match colonial descriptions of Cape lions, thus “identifying type specimens using information from people who are not originally from that area can result in ignoring diversity in a population that is important for understanding evolution.” The study also underscores the importance of trans-country parks and heightened genetic connectivity between populations across Africa in order to maintain genetic diversity and flow. The study was funded by the USAID Wildlife TRAPS Project, USDA, NSF, and the University of Illinois. You can get more information from the UIUC press release.
February 23. 2024