Mitochondrial DNA variation, phylogeography and population structure of the Asian elephant

We report the first genetic analysis of free-ranging Asian elephants (Eleph as maximus). We sampled 118 elephants from Sri Lanka, Bhutan/North India, a nd Laos/Vietnam by extracting DNA from dung, PCR amplifying and sequencing 630 nucleotides of mitochondrial DNA, including part of the variable left d omain of the control region. Comparison with African elephant (Loxodonta af ricana) sequences indicated a relatively slow molecular clock in the Probos cidea with a sequence divergence of approximate to 1%/Myr. Genetic diversit y within Asian elephants was low, suggesting a small long-term effective po pulation size. Seventeen haplotypes were identified within Asian elephants, which clustered into two well-differentiated assemblages with an estimated Pliocene divergence of 2.5-3.5 million years ago. The two assemblages show ed incomplete geographical partitioning, suggesting allopatric divergence a nd secondary admixture. On the mainland, little genetic differentiation was observed between elephant populations of Bhutan and India or Laos and Viet nam. A significant difference in haplotype frequencies but relatively weak subdivision was observed between the regions Bhutan-India and Laos-Vietnam. Significant genetic differentiation was observed between the mainland and Sri Lanka, and between northern, mid-latitude and southern regions in Sri L anka.