New Insights into the Molecular Evolution of Tapirus pinchaque (Tapiridae, Perissodactyla) and the Rise and Fall of Tapirus kabomani as a Full Species

Large wild mammals are extremely important in their respective ecological communities and are frequently considered to be emblematic. This is the case of the different tapir species, the largest terrestrial mammals from the Neotropics. Despite their large size and being objects of interest for many naturalists, the field still lacks critical genetics and systematics information about tapir species. In the current work, we analyzed four molecular datasets (mitogenomes, and three nuclear genes, <i>RAG 1-2</i>, <i>IRBP</i>, and <i>BRCA1</i>) of two South American tapirs: the Andean tapir (<i>Tapirus pinchaque</i>) and the alleged new species of tapir, <i>Tapirus kabomani</i>. We derived four main findings. (1) Our molecular phylogenetic analyses showed <i>T. pinchaque</i> as the youngest tapir branch in Neotropics and a sister species of <i>Tapirus terrestris</i>. This contradicts the traditional morphological observations of renowned zoologists and paleontologists, who considered <i>T. pinchaque</i> as the oldest Neotropical tapir. (2) Our data does not support that the alleged <i>T. kabomani</i> is a full species. Rather, it is a specific group within <i>T. terrestris</i>. (3) <i>T. pinchaque</i> is the Neotropical tapir species which yielded the lowest levels of genetic diversity (both for mitochondrial and nuclear data). (4) The spatial genetic structure for <i>T. pinchaque</i> shows differences depending on the type of molecular marker used. With mitogenomes, the spatial structure is relatively weak, whereas with two nuclear genes (<i>RAG 1-2</i> and <i>IRBP</i>), the spatial structure is highly significant. Curiously, for the other nuclear gene (<i>BRCA1</i>), the spatial structure is practically nonexistent. In any case, the northernmost population of <i>T. pinchaque</i> we studied (Los Nevados National Park in Colombia) was in a peripatric situation and was the most genetically differentiated. This is important for the adequate conservation of this population. (5) <i>T. pinchaque</i> showed clear evidence of population expansion during the last part of the Pleistocene, a period during which the dryness and glacial cold extinguished many large mammals in the Americas. However, <i>T. pinchaque</i> survived and spread throughout the Northern Andes.