Elephants inhabiting two forested sites in western Uganda exhibit contrasting patterns of species identity, density, and history of hybridization

Elephant populations across much of Africa face severe rates of decline due to poaching and habitat loss. The recent decision by the International Union for the Conservation of Nature (IUCN) to separately list African forest (Loxodonta cyclotis) and savanna (L. africana) elephants on the IUCN Red List both highlights the different threats of extinction faced by these two species and emphasizes the need for genetic data to classify taxonomically undefined populations across the continent. This includes western Uganda - a region that harbors the largest known modern hybrid zone between the two species. We combined a new high-throughput amplicon sequencing (HTAS) approach with fecal DNA-based Capture Mark Recapture (CMR) analysis to infer the population sizes and species compositions of elephants living in two forests. We demonstrate that Kibale National Park hosts a relatively large elephant population (573 individuals, 95% CI: 410 to 916; 0.72 elephants/km2) composed primarily of hybrids (81.5%) and savanna elephants (17.7%), while Bwindi Impenetrable National Park hosts a smaller population (96 individuals, 95% CI: 64 to 145; 0.29 elephants/km2) composed of forest elephants (86.8%) and hybrids (13.2%). We then sequenced maternally inherited (mtDNA) and paternally inherited (AMELY) genetic markers and found that the two parks populations exhibit different patterns of sex-linked genetic variation. The contrasting patterns of species identity and genetic variation between these parks demonstrate different histories of hybridization and highlight the importance of site-specific monitoring where elephants are taxonomically undefined.