Phylogeography of the Asian elephant (Elephas maximus) based on mitochondrial DNA

Populations of the Asian elephant (Elephas maximus) have been reduced in si ze and become highly fragmented during the past 3000 to 4000 years. Histori cal records reveal elephant dispersal by humans via trade and war. How have these anthropogenic impacts affected genetic variation and structure of As ian elephant populations? We sequenced mitochondrial DNA (mtDNA) to assay g enetic variation and phylogeography across much of the Asian elephant's ran ge. Initially we compare cytochrome b sequences (cyt b) between nine Asian and five African elephants and use the fossil-based age of their separation (similar to5 million years ago) to obtain a rate of about 0.013 (95% CI = 0.011-0.018) corrected sequence divergence per million years. We also asses s variation in part of the mtDNA control region (CR) and adjacent tRNA gene s in 57 Asian elephants from seven countries (Sri Lanka, India, Nepal, Myan mar, Thailand, Malaysia, and Indonesia). Asian elephants have typical level s of mtDNA variation, and coalescence analyses suggest their populations we re growing in the late Pleistocene. Reconstructed phylogenies reveal two ma jor clades (A and B) differing on average by HKY85/Gamma -corrected distanc es of 0.020 for cyt b and 0.050 for the CR segment (corresponding to a coal escence time based on our cyt b rate of similar to1.2 million years). Indiv iduals of both major clades exist in all locations but Indonesia and Malays ia. Most elephants from Malaysia and all from Indonesia are in well-support ed, basal clades within clade A, thus supporting their status as evolutiona rily significant units (ESUs). The proportion of clade A individuals decrea ses to the north, which could result from retention and subsequent loss of ancient lineages in long-term stable populations or, perhaps more likely, v ia recent mixing of two expanding populations that were isolated in the mid -Pleistocene. The distribution of clade A individuals appears to have been impacted by human trade in elephants among Myanmar. Sri Lanka, and India, a nd the subspecies and ESU statuses of Sri Lankan elephants are not supporte d by molecular data.