African Leopard - Population Genomics

Large carnivores are generally sensitive to ecosystem changes because their specialized diet and position on top of the trophic pyramid is associated with small population sizes. Accordingly, low genetic diversity has been confirmed at the whole-genome level for all big cat species, including the widely distributed leopard. However, all previous whole-genome analyses of leopards are based on the Far Eastern Amur leopards that live at the extremity of the species' distribution, and therefore, are not necessarily representative of the whole species. We sequenced 53 whole genomes of African leopards. Strikingly, we found that the genomic diversity in the African leopard is two-to-five-fold higher than in other big cats, including the Amur leopard. This can be explained by an exceptionally high effective population size maintained by the African leopard throughout the Pleistocene. Furthermore, we detected ongoing gene flow and very low population differentiation within African leopards compared to other big cats. We corroborated this by showing a complete absence of an otherwise ubiquitous equatorial forest barrier to gene flow. This sets the leopard apart from most other widely distributed large African mammals, including lions. These results revise our understanding of trophic sensitivity and highlight the remarkable resilience of the African leopard, likely due to its extraordinary habitat versatility and broad dietary niche.