Genetic characterisation of fragmented Asian elephant populations with one recent extinction in its eastern-central Indian range

Habitat fragmentation results in loss of genetic variation in populations and increases inbreeding processes that are measurable by genetic markers. The fragmented forests of Eastern Ghats-Central India support around 3000 Asian elephants (Elephas maximus L.), of which 2000 are in Odisha state. We obtained samples of fresh elephant dung from four protected areas (PAs) in Odisha: Similipal, Satkosia, Kuldiha and the recently extinct Chandaka population, and assessed levels of genetic variation, gene flow, recent genetic bottleneck, inbreeding and relatedness using 10 polymorphic microsatellite markers. We tested whether the PAs would be similar in levels of genetic variation and inbreeding due to recent fragmentation, using standard methodology for DNA amplification, genotyping, and sex identification. Among the 154 samples collected, 108 individuals were identified, of which 78 were female, 20 male and 10 unclassified. Levels of genetic variation were moderately high overall, and higher within than between the three extant populations. There was no isolation by distance, two long-distance first-generation migrants were detected in Chandaka, and inbreeding and recent bottlenecks were not evident. Bayesian individual-based clustering approaches and multivariate methods identified three populations and Kuldiha was strongly differentiated from the other three. This could partly be explained by missing data and high proportion of full siblings. The sex ratio was female-biased, which could be attributed to higher mortality of males. Our results suggest that elephant populations in Odisha are already undergoing genetic drift and that restoration of habitats and connectivity are urgently needed to avert further population extinctions.