Mitogenomics of the mountain tapir (Tapirus pinchaque, Tapiridae, Perissodactyla, Mammalia) in Colombia and Ecuador: Phylogeography and insights into the origin and systematics of the South American tapirs

We sampled 45 Andean mountain tapirs (Tapirus pinchaque) from Colombia and Ecuador and sequenced 15 mitochondrial genes (two rRNA and 13 protein codifying genes)-making up 13,939 base pairs, approximately 83.1% of the total mitochondrial DNA's length. The overall sample had low to medium levels of nucleotide diversity with diversity slightly higher for the Colombian population. Both populations experienced high historical gene flow and our genetic heterogeneity analyses revealed a low genetic differentiation between them. Therefore, we did not detect any molecular subspecies, or significantly different evolutionary units for T. pinchaque. This species experienced a population expansion in the last 100,000 years but this expansion was more pronounced in the Ecuadorian population especially in the last 10,000 years, whereas the Colombian population underwent a strong bottleneck in the last 5,000 years. There was no significant spatial trend in genetic structure for the mountain tapir in Colombia and Ecuador. Phylogenetic analyses did not detect any important geographic clade within this species. Temporal split between T. pinchaque and T. terrestris might have occurred around 7-1.5 million years ago (MYA). T. pinchaque and T. terrestris + T. kabomani are two monophyletic clades, suggesting that T. kabomani is not a full species.