Two competing hypotheses have been proposed: one suggests that elephants are non-native to Borneo and were historically introduced and the other that they are indigenous to the island.
The origin of elephants on Borneo has been controversial and the subject of intense debate. It is classified as endangered according to the IUCN (International Union for Conservation of Nature) Red list of threatened species. The Bornean elephant ( Elephas maximus borneensis) is one of four recognized subspecies of Asian elephant and is morphologically and behaviourally distinct from the elephants of mainland Asia 1. Our results are important not only in understanding the unique history of the colonization of Borneo by elephants, but also for their long-term conservation. Altogether the data support a natural colonization of Bornean elephants at a time when large terrestrial mammals could colonise from the Sunda shelf when sea levels were much lower. We find that genetic data favour a scenario in which Bornean elephants experienced a bottleneck during the last glacial period, possibly as a consequence of the colonization of Borneo, and from which it has slowly recovered since. Our results are at odds with both the recent and ancient colonization hypotheses, and favour a third intermediate scenario. We investigated the demographic history of Bornean elephants using full-likelihood and approximate Bayesian computation analyses. Lack of elephant fossils has been interpreted as evidence for a very recent introduction, whereas mtDNA divergence from other Asian elephants has been argued to favor an ancient colonization. Research has suggested two alternative hypotheses: the Bornean elephant stems either from a recent introduction in the 17th century or from an ancient colonization several hundreds of thousands years ago. The origin of the elephant on the island of Borneo remains elusive.