Pan-India population genetics signifies the importance of habitat connectivity for wild Asian elephant conservation

Asian elephants are endangered while they have faced ~70% population decline in India in the last 60 years. Climate change projections indicate exacerbation of ongoing habitat loss (>40%) by 2070, potentially impacting genetic structure of wild elephants across India. Therefore, we provide consolidated baseline data on genetic diversity and structure of elephants across four eco-regions of India, i.e., north-western (NW), north-eastern (NE), east-central (ECI), and southern India (SI), to identify populations at greater risk of further divergence. We genotyped 169 faecal samples across 14 microsatellites with 90.0% overall success rate. The genetic diversity levels were moderate and varied between the eco-regions (HE =0.57–0.74). Allelic richness was higher in NE (3.73–3.78) and SI (3.62–3.71). We observed a high inbreeding coefficient in NE (FIS=0.55–0.58) compared to the other elephant populations, probably due to the presence of related individuals in our samples. Genetic differentiation between populations using FST statistics (FST=0.06–0.18) was significant. Bayesian and multivariate analyses identified three major genetic clusters in India – NW, NE, and combined ECI-SI, mostly consistent with their geographic distribution. We also observed an unexpected pattern of high genetic distance between adjacent populations. This fine-scale genetic structure suggests the presence of barriers (natural and anthropogenic) and complex social organisation. Additionally, incipient sub-structuring within NE and SI indicates potential genetic discontinuity. These results highlight the importance of maintaining genetic diversity, particularly of NE and ECI populations, by retaining habitat connectivity and ensuring gene flow for effective elephant conservation in India.