First description of the mitochondrial genomes of the Central American brocket deer Mazama temama (Kerr, 1792) and the Yucatán Peninsula brocket deer Odocoileus pandora Merriam, 1901.

BACKGROUND: The Central American (Mazama temama) and the Yucatán Peninsula brocket deer (Odocoileus pandora) are deer species with cryptic habits, and little is known about their biology. Odocoileus pandora is listed as Vulnerable on the 2015 IUCN Red List of Threatened Species, while M. temama is considered Data Deficient; however, it currently faces a decreasing population trend. METHODS AND RESULTS: We assembled the complete mitochondrial genome for two M. temama specimens and one complete and one partial for O. pandora from Illumina 150 bp paired-end reads. The mitogenomes of M. temama and O. pandora have a length of 16,479-16,480 and 16,419 bp, respectively, AT-biased; they consist of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region, most of them follow a transcription direction in the heavy strand of the molecule. The mitochondrial genome of O. pandora shows some particularities compared to other deer species, like a shorter control region of 987-990 bp and a cytochrome b gene with a length of 1,143 bp. Our phylogenetic analyses confirm the close affinity of M. temama to South American M. americana and the nested position of the genus Odocoileus, including O. pandora, into the genus Mazama. CONCLUSIONS: Here, we described for the first time the complete mitochondrial genome for these two species. While our study provides additional information about the taxonomic status of the northern neotropical brocket deer, further research is needed to solve the complicated taxonomy of neotropical deer.

A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling.

The taxonomy of American deer has been established almost entirely on the basis of morphological data and without the use of explicit phylogenetic methods; hence, phylogenetic analyses including data for all of the currently recognized species, even if based on a single gene, might improve current understanding of their taxonomy. We tested the monophyly of the morphology-defined genera and species of New World deer (Odocoileini) with phylogenetic analyses of mitochondrial DNA sequences. This is the first such test conducted using extensive geographic and taxonomic sampling. Our results do not support the monophyly of Mazama, Odocoileus, Pudu, M. americana, M. nemorivaga, Od. hemionus, and Od. virginianus. Mazama contains species that belong to other genera. We found a novel sister-taxon relationship between "Mazama" pandora and a clade formed by Od. hemionus columbianus and Od. h. sitkensis, and transfer pandora to Odocoileus. The clade formed by Od. h. columbianus and Od. h. sitkensis may represent a valid species, whereas the remaining subspecies of Od. hemionus appear closer to Od. virginianus. Pudu (Pudu) puda was not found sister to Pudu (Pudella) mephistophiles. If confirmed, this result will prompt the recognition of the monotypic Pudella as a distinct genus. We provide evidence for the existence of an undescribed species now confused with Mazama americana, and identify other instances of cryptic, taxonomically unrecognized species-level diversity among populations here regarded as Mazama temama, "Mazama" nemorivaga, and Hippocamelus antisensis. Noteworthy records that substantially extend the known distributions of M. temama and "M." gouazoubira are provided, and we unveil a surprising ambiguity regarding the distribution of "M." nemorivaga, as it is described in the literature. The study of deer of the tribe Odocoileini has been hampered by the paucity of information regarding voucher specimens and the provenance of sequences deposited in GenBank. We pinpoint priorities for future systematic research on the tribe Odocoileini.