Genetic Diversity and Population Structure of the Black-Footed Cat: Insights into Felis's Deadliest Predator

Background Black-footed cats (Felis nigripes) are one of Africa's least studied felines. The population dynamics and demographic history of this solitary species have not been well-described. Reports of ongoing decline of present-day populations resulted in the IUCN Red List categorizing the species as vulnerable to extinction. As populations decline and become isolated from each other, they become susceptible to strong genetic drift and inbreeding, which can lead to the accumulation of deleterious alleles and increased extinction risk. However, the IUCN cited data deficiencies across the species range as a limitation in this categorization for black-footed cats. In cases where ecological surveys are lacking, range-wide population genomic surveys can improve our understanding of population dynamics. Results In the first genomic study of free-roaming individuals, we sequenced whole genomes of black-footed cats (N=44) from across their distribution. To do so, we incorporated whole genome sequences generated from both modern biological samples and century-old museum specimens. We assembled a highly contiguous reference genome using a combination of PacBio HiFi data and publicly available Hi-C data and investigated the demographic history, population structure, and genetic diversity of wild black-footed cats. We found evidence of historical effective population sizes of ~11,500 individuals, which is lower than estimates reported in other felid species. Consistent with modest historical population sizes, we found that present-day genome-wide diversity was low ({pi}{approx}0.0004). However, despite low genetic diversity, we find that black-footed cat genomes do not harbor long runs of homozygosity. Simulation results indicate that low present-day genetic diversity may simply result from modest historical population size. However, other analyses point to evidence of a population contraction in the last 50 generations, which could contribute to future genomic erosion. We also compared genomic variation in populations across the range to evaluate patterns of population structure, finding evidence of higher genetic similarity between individuals in closer geographic proximity. Conclusion Overall, these results provide range-wide information about the demographic history and present-day genetic diversity of an understudied species. Together with analyses of population structure, we speculate that there may be greater connectivity between populations of black-footed cats than previously assumed. Our study underscores the utility of genomic data in providing insights into population dynamics for better conservation management.