Historical Biogeography and Genetic Status of the Enigmatic Pig‐Nosed Turtle ( <i>Carettochelys insculpta</i> ) Within the Australo‐Papuan Region

ABSTRACT Aim We examine the phylogeographic genetic structure of the endangered pig‐nosed turtle Carettochelys insculpta , the last remaining member of a once globally widespread family, now restricted to northern Australia and southern New Guinea, a region with a complex geological and eustatic history. We examine their historical biogeography, demographic history and genetic status of threatened populations. Location Northern Australia, Southern New Guinea. Methods We reconstruct phylogenetic relationships and patterns of genetic diversity using a genome‐wide dataset of 15,081 single nucleotide polymorphisms and two mitochondrial loci from samples spanning the full species' range. Results The Australian, Papua New Guinea and Indonesian Papua turtles are recovered as three distinct lineages; the Australian lineage diverged from the New Guinea lineages ca 660 Kya, while the Papua New Guinea and Indonesian Papua Province lineages diverged ca 564 Kya. Although the fossil record shows that C. insculpta has been a long‐standing representative of the Australia and New Guinea fauna (since at least the Miocene), extant lineages diverged later in the Middle Pleistocene. Both the Australian and Papua New Guinea lineages were likely shaped by bottlenecks, isolation and genetic drift, which in the Australian lineage greatly reduced effective population sizes to 48–88. Main Conclusions The contemporary genetic structure of C. insculpta is most consistent with a vicariance model whereby a large interchanging population occupying northern Australia and New Guinea came to be fragmented and diverged into Australian, Papua New Guinea and Indonesian Papua lineages. Subsequent dispersal via paleodrainages of the submerged continental shelf under the influence of Pleistocene sea‐level change is thought to have been impeded by the isolation of the Akimeugah and Arafura Basins. All populations of the Australian lineage show low genetic diversity without contemporary gene flow, suggesting they are vulnerable to inbreeding and reduced fitness, requiring the consideration of genetic rescue.