Mitochondrial genome and ultraconserved elements reveal a species complex within the Central American brocket deer Mazama temama (Artiodactyla: Cervidae)

Mazama temama (Kerr, 1792) is a neotropical deer with a wide distribution across the humid forests from Mexico through Colombia. While three subspecies are currently recognized based on morphological and pelage coloration, the presence of a phylogeographic structure is unknown, and recent debates suggest the possibility of it being a species complex. Here, we conduct phylogenetic analyses, explore demographic history, and perform species delimitation analyses using genome-wide ultraconserved elements (UCE) and the whole mitochondrial genome sequenced from museum specimens. Our results reveal three well-supported lineages within M. temama. Based on the mitochondrial dataset, these lineages diverged from the sister clade formed by other Mazama species 2.3 million years ago. The northernmost lineage diverged from southern Central America around 1.2 and 1.4 million years ago, as the UCE and mitochondrial datasets indicated, respectively. The ancestral small population size and Late Pleistocene dispersal patterns contributed to an isolation-by-distance scenario. We propose that M. temama represents a species complex divided by ecological barriers. Consequently, we recommend recognizing three separate species: M. temama (Kerr, 1792) for populations from Mexico to Honduras, M. reperticia Goldman, 1913 for populations from Nicaragua to Panama, and M. zetta Thomas, 1913 for populations in Colombia and Ecuador, limited by the northern Andean Cordillera.