The complete mitochondrial genome of the brown brocket deer Mazama gouazoubira and a set of polymorphic microsatellite markers were identified by 454-pyrosequencing. De novo genome assembly recovered 98% of the mitochondrial genome with a mean coverage of 9-fold. The mitogenome consisted of 16,356 base pairs that included 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and the control region, as found in other deer. The genetic divergence between the mitogenome described here and a previously published report was ∼0.5%, with the control region and ND5 gene showing the highest intraspecific variation. Seven polymorphic loci were characterized using 15 unrelated individuals; there was moderate genetic variation across most loci (mean of 5.6 alleles/locus, mean expected heterozygosity = 0.70), with only one locus deviating significantly from Hardy-Weinberg equilibrium, probably because of null alleles. Marker independence was confirmed with tests for linkage disequilibrium. The genetic variation of the mitogenome and characterization of microsatellite markers will provide useful tools for assessing the phylogeography and population genetic patterns in M. gouazoubira, particularly in the context of habitat fragmentation in South America.

The Neotropical deer genus Mazama is characterized by homoplastic morphological characters, a high karyotypic diversity, and a polyphyletic condition. The species of the genus have been recovered into two multigeneric lineages, the subtribes Odocoileina and Blastocerina, of the tribe Odocoileini (New World deer) in the family Cervidae. Within the Blastocerina, gray brockets include two non-sister species, Subulo gouazoubira, occurring south of the Amazon region, and Passalites nemorivagus, occurring in the Guianas and in the Amazon region. We clarify the taxonomic status and phylogenetic position of Mazama americana citus Osgood, 1912 (referred to as either S. gouazoubira or P. nemorivagus by other authors). We collected a topotype of M. a. citus from the eastern shore of Lake Maracaibo, Venezuela, characterize it morphologically and cytogenetically (conventional banding and fluorescence in situ hybridization), and carry out a phylogenetic analysis of its whole mitogenome and Cytb alongside two additional specimens of M. a. citus from northwestern Venezuela. Our analyses reveal the topotype to be a large gray brocket with a cinnamon band above the eyes and 2n = 61 and FN = 70 karyotype. Using cattle whole chromosome painting and bacterial artificial chromosome X probes, we determined its karyotype to differ in at least 10 rearrangements from that of S. gouazoubira. Bayesian inference recovers M. a. citus within the Blastocerina subtribe, separated phylogenetically from other gray brockets (100% branch value), revealing the Osgood’s gray brocket to be a valid species that should be assigned to a new genus. We propose the generic name Bisbalus, with Bisbalus citus (Osgood, 1912) as the type species.

Coalescent theory provides powerful models for population genetic inference and is now increasingly important in estimates of divergence times and speciation research. We use molecular data and methods based on coalescent theory to investigate whether genetic evidence supports the hypothesis of A. pretrei and A. tucumana as separate species and whether genetic data allow us to assess which allopatric model seems to better explain the diversification process in these taxa. We sampled 13 A. tucumana from two provinces in northern Argentina and 28 A. pretrei from nine localities of Rio Grande do Sul, Brazil. A 491 bp segment of the mitochondrial gene cytochrome c oxidase I was evaluated using the haplotype network and phylogenetic methods. The divergence time and other demographic quantities were estimated using the isolation and migration model based on coalescent theory. The network and phylogenetic reconstructions showed similar results, supporting reciprocal monophyly for these two taxa. The divergence time of lineage separation was estimated to be approximately 1.3 million years ago, which corresponds to the lower Pleistocene. Our results enforce the current taxonomic status for these two Amazon species. They also support that A. pretrei and A. tucumana diverged with little or no gene flow approximately 1.3 million years ago, most likely after the establishment of a small population in the Southern Yungas forest by dispersion of a few founders from the A. pretrei ancestral population. This process may have been favored by habitat corridors formed in hot and humid periods of the Quaternary. Considering that these two species are considered threatened, the results were evaluated for their implications for the conservation of these two species.