Patterns of genetic diversity, gene flow and genetic structure of three Peninsular Indian elephant populations indicate population connectivity

The Peninsular Indian population of the endangered Asian elephant occurs in the Western and Eastern Ghats, and further north-east in the Eastern Central Indian (ECI) range. Using DNA obtained from fresh elephant dung, this study assessed the genetic variation, population structure, and gene flow in the two southern populations, SI1 and SI2, separated by the Palghat Gap in the Western Ghats, and the third population in the ECI range. As these populations have been shown to be genetically associated in previous studies, the hypotheses that their combined genetic diversity would be high and gene flow via migration would be evident, were tested. A total of 379 elephants were genotyped at 10 microsatellite markers, and a 630 bp mitochondrial DNA (mtDNA) fragment from the D-loop region was sequenced from 33 individuals. Four previously documented mtDNA haplotypes were identified: SI1 and ECI each had a single haplotype (BN and BL, respectively), while SI2 had two haplotypes (BA and BF). The mtDNA markers indicated substantial genetic differentiation among the populations, while differentiation using microsatellite data was moderate. The populations were assigned to three genetic groups: SI1, SI2, and the ECI. However, 39% of these individuals showed mixed ancestry, indicating ongoing gene flow despite natural and human-made barriers. Several first-generation male migrants were identified providing further evidence of contemporary gene flow. The sex ratio was female-biased, which is consistent with the existing census data. These three populations should be managed as a single conservation unit to ensure their long term viability.