Demographic history of the Malayan tapirs (Tapirus indicus) in Southeast Asia

Malayan tapir is the only extant Asian species in the family Tapiridae, which is endangered and threatened by the risk of inbreeding from population structure. To elucidate the demographic and evolutionary history of the tapirs in Southeast Asia (SEA), this study analyzed whole-genome data from 10 individuals for historical effective population size (Ne) inference using sequentially Markovian coalescent (i.e., PSMC, MSMC, MSMC2), folded site frequency spectrum (i.e., Stairway Plot 2), and their hybrid SMC₊₊. The results revealed that tapir Ne ranged from 6000 to 12,000 in the last glacial period but decreased to <2000 in recent times. Genomic analysis and population split time analysis (PSMC and SMC₊₊) supported a population divergence (Fst > 0.25) between the Sumatran and mainland SEA tapirs 10–6 kya. Subsidence of Sundaland and rainforest reduction were the major drivers for Ne decline. The timing of the population split corresponded well with the inundation of the Straits of Malacca to present-day levels by rapidly rising sea levels ~11 kya. The results of this study, as well as contemporary geographical isolation, support the subspecies status of the Sumatran population. This will have implications for the ex-situ conservation practices that may have produced hybrids of the isolated populations.