Genomic approaches can provide critical insights into the genetic health of endangered species and the impacts of long-term management on semi-captive populations. Asian elephants (Elephas maximus), listed as Endangered, include a large semi-captive population in Myanmar that may represent an important reservoir of genetic diversity. However, their genetic structure, levels of inbreeding, and relatedness remain poorly characterized.

We assembled the largest genomic dataset to date for semi-captive Asian elephants, comprising reduced representation data (RADseq, N = 261) and whole-genome data (WGS, N = 64). Heterozygosity values showed no significant differences between wild-born and captive-born individuals. Both RADseq and WGS data revealed low to medium levels of inbreeding and no evidence of an increase among younger generations. Population structure analyses confirmed a homogeneous population with no geographic-based genetic structure, likely reflecting management practices and natural mating with wild bulls. Demographic inference indicated a sharp decline in effective population size (Ne) between 60 and 30 generations ago, consistent with a long-term population contraction, and current Ne was estimated as being very low. Relatedness analyses identified 657 first-cousin or closer relationships, including 124 first-degree pairs. We also uncovered 35 previously undocumented father-offspring pairs with some males having disproportionately high reproductive success. To facilitate future monitoring, we developed three reduced relatedness-informative marker (RIM) panels. The smallest panel (274 SNPs) provided sufficient resolution for reliable parentage assignment at reduced cost.

Our findings demonstrate how genomic tools uncovered the genetic consequences of management of the largest semi-captive elephant population of Myanmar, highlighting the need for continuous monitoring to safeguard its genetic diversity. More broadly, this study illustrates how integrating WGS and RADseq can inform conservation planning for semi-managed populations and offers transferable approaches applicable to other endangered species.