Range-wide phylogeographic structure of the endangered Irrawaddy dolphin (Orcaella brevirostris) using expanded sampling from contemporary and historical specimens

The Irrawaddy dolphin (Orcaella brevirostris) is an endangered cetacean that ranges throughout much of Southeast Asia and lives in coastal, estuarine, and riverine habitats including three river systems: Ayeyarwady, Mekong, and Mahakam. Many populations face risks from human interference, but overall rangewide diversity and connectivity is not well-understood. Here we sequenced 77 complete mitogenomes from across the range of the Irrawaddy dolphin including all obligate riverine populations; eighteen of these were sequenced from historical museum specimens. Phylogenetic analysis showed haplotypes from each riverine population formed separate clades nested within the wider species implying each river system was separately invaded only once. All Irrawaddy dolphin mitogenomes were dated to a last common ancestor ~764 kya. Most lineages appeared after inundation cycles of the Sunda Shelf were initiated ~400 kya. Despite the lack of monophyly among many haplotypes from the same population, no population shared any haplotypes. Rangewide nucleotide diversity was average compared to other odontocetes, but riverine populations were especially low. Differentiation was significant among all populations analyzed with the most divergence occurring between isolated riverine populations. These analyses add more evidence for the necessity of conservation efforts directed towards riverine and other isolated populations of the Irrawaddy dolphin.