Massive Genetic Diversity Loss Within Asian Elephant Subspecies: New Insights for Determining Conservation Priorities

In this study, we provide a comprehensive genomic analysis of population structure, genetic diversity, and load across the four Asian elephant (Elephas maximus) subspecies using whole-genome sequencing data of 81 wild-born individuals, with most of them currently living under human care. Our results reveal striking contrast in inbreeding: the Bornean subspecies (E.m. borneensis) exhibits the highest level of inbreeding, with ∼65% of its genome in runs of homozygosity (ROH), and the lowest genome-wide heterozygosity (∼46 heterozygous sites per 100 kb). The Sumatran subspecies (E.m. sumatranus) shows intermediate levels of inbreeding (35% ROH) and heterozygosity (∼101 sites per 100 kb), while the mainland and Sri Lankan subspecies (E.m indicus and E.m. maximus) display similarly low inbreeding (∼10% to 11% ROH) and high heterozygosity (∼130 to 134 sites per 100 kb). Notably, when correcting for ROH coverage, heterozygosity levels are comparable across all four subspecies (∼136 to 155 sites per 100 kb), indicating that differences in genetic diversity are primarily driven by loss of heterozygosity within ROHs due to inbreeding. Genetic load remains relatively low in all subspecies, especially in highly conserved genomic regions. The high genetic diversity observed in the island-dwelling E.m. maximus subspecies likely reflects historical gene flow linked to intensive human-mediated elephant trade, raising questions about its taxonomic status. Given its high inbreeding, E.m. borneensis represents the highest conservation priority, with genetic rescue as a potential management strategy. This study highlights the urgent need for focused conservation efforts and further genomic research to safeguard the unique genetic diversity and long-term viability of Asian elephants.