Fecal DNA Identifies a Disjunct Population of an Endemic Deer (Mazama jucunda) From the Atlantic Forest, Brazil

Limited knowledge of brocket deer distribution persists due to their elusive behavior and the morphological similarities among species. A population of red brocket deer (genus Mazama) was recently discovered in the Rio Doce State Park (PERD), a protected area within the Brazilian Atlantic Forest; however, species-level identification was lacking. Given that two endemic and threatened red brocket species inhabit this biome, we aimed to identify the species present in PERD using fecal DNA analyses. We sequenced six mitochondrial DNA regions (1450 bp) from fecal samples collected in PERD and other Atlantic Forest sites, analyzing them against reference specimens. We conducted phylogenetic analyses and employed coalescent-based molecular species delimitation methods (GMYC and bPTP) to define molecular operational taxonomic units (MOTUs). Additionally, we constructed a haplotype network and a genetic distance matrix. Our analyses linked the PERD samples to Mazama jucunda (small red brocket) but revealed a reciprocally monophyletic topology, identifying two distinct MOTUs. PERD harbors unique haplotypes, and its genetic distance to M. jucunda is comparable to that between M. jucunda and M. nana (Brazilian dwarf brocket). We propose that PERD hosts an evolutionarily significant unit (ESU) of M. jucunda, located 700 km from its known range. The observed genetic structure and PERD's isolation support the hypothesis of a potentially new red brocket species, warranting further cytogenetic investigation. This study represents a significant advancement in understanding the distribution and genetic structure of a threatened Neotropical forest deer and has immediate conservation implications in one of the world's most degraded biodiversity hotspots.