In this study, we provide a comprehensive genomic analysis of population structure, genetic diversity and genetic load across the four recognized Asian elephant (Elephas maximus) subspecies using whole-genome sequencing data of 81 wild-born individuals. 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 correspondingly, 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 (~10-11% ROH) and high heterozygosity (~130-134 sites per 100 kb). Notably, when ROH regions are excluded, heterozygosity levels are comparable across all four subspecies (~136-155 sites per 100 kb), indicating that differences in genetic diversity are primarily driven by loss of heterozygosity within ROHs due to inbreeding rather than accumulation of unique variation after divergence. Genetic load remains relatively low in all subspecies, even in the highly inbred borneensis subspecies, especially in highly conserved genomic regions, suggesting effective purging of deleterious alleles. The unexpected 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 and low genetic diversity, E.m. borneensis represents the highest conservation priority, with genetic rescue as a viable management strategy, due to minimal risk of outbreeding depression among subspecies due to the lack of unique genetic variation. This study highlights the urgent need for focused conservation efforts and further genomic research, particularly for the Bornean elephant population, to safeguard the unique genetic diversity and long-term viability of Asian elephants.

The Asian elephant (Elephas maximus), a keystone species, faces significant threats from habitat loss, poaching, and population fragmentation. Understanding the evolutionary history of its subspecies is essential for developing targeted conservation strategies and mitigating risks to their survival.This study introduces, for the first time, whole-genome sequencing (WGS) data from predominantly wild-origin Asian elephants housed in European zoos, covering the distribution range of Asian elephants. Our data aims to validate the Asian elephant subspecies designation and address ambiguities about their origin, particularly concerning Bornean and Sri Lankan elephants. Analysis reveals a clear population structure with relatively recent splits, delineating three distinct genetic clusters: Borneo, Sumatra, and Mainland, with Sri Lanka forming an additional group. Hypotheses on the origin of Bornean elephants—native dispersal or human introduction—are explored. Our data reflects the current Asian elephant subspecies designation. This study is estimating the divergence time between Bornean and Sumatra elephants, around 170,000 years ago. Their genome also exhibited severe bottlenecks as recently as 8 and 38 generations ago, further supporting hypotheses of introduction. The divergence of Sri Lankan elephant from the Mainland is estimated at 48,000 years ago, with Sri Lankan elephants predominantly clustering with those from Myanmar, possibly due to historical trade networks. Additionally, the Sumatra elephant is confirmed as a distinct subspecies. Furthermore, the study discusses genetic management strategies for ex-situ populations, emphasizing the importance of implementing cluster-specific conservation measures. Despite data constraints, recognizing Bornean elephants as a distinct subspecies, informs conservation strategies, and suggests avenues for further research.