Phylogeography of red muntjacs reveals three distinct mitochondrial lineages

Muntjacs are studied for their dramatic variation in chromosome numbers, but taxonomic concordance within this genus has not been achieved yet due to lack of molecular studies combined with limited morphological or ecological differences. The genus is mainly composed of endemics and species with small regional distributions, with two exceptions: Reeve's muntjac and the red muntjacs. Red muntjacs have the largest distributions of all muntjacs, ranging from the Indian subcontinent to the Indochinese Peninsula and southeastern China, and across the Malay Peninsula towards all the major islands of Sundaland. Red muntjacs occur in a wide range of habitats, from deciduous to evergreen forests, and also in secondary forests, exotic commercial plantations, grasslands, shrubland savannahs, croplands, and in altitudes commonly up to 1500 m asl. Although habitat loss and hunting have caused significant population declines throughout their range, red muntjacs seem to be more resilient to habitat modifications and hunting compared to other ungulates in South and Southeast Asia. Through most of the 20th century, red muntjacs were generally classified as a single species, Muntiacus muntjak, although some authors noted that some forms might be better treated as distinct species. The classification of red muntjacs has been revised in recent years, with some studies suggesting the presence of multiple species within the "red muntjac group". However, these classifications have not been universally adopted, and the taxonomy of red muntjacs remains uncertain. To address these taxonomic uncertainties, a phylogeographic study was conducted to investigate the geographic distribution of mitochondrial lineages among red muntjac populations. The study analyzed whole mitochondrial genomes of 59 archival and 16 contemporaneous samples from red muntjacs collected from various natural history museums and field surveys. The results of the study revealed three distinct matrilineal groups of red muntjacs: Sri Lankan red muntjacs, northern red muntjacs, and southern red muntjacs. The Sri Lankan red muntjacs diverged first from other muntjacs about 1.5 Mya, while the northern and southern red muntjacs split around 1.12 Mya. The diversification of red muntjacs into these three main lineages was likely promoted by two Pleistocene barriers: one through the Indian subcontinent and one separating the Indochinese and Sundaic red muntjacs. The study also found a high level of gene flow within the populations of northern and southern red muntjacs, indicating gene flow between populations in Indochina and dispersal of red muntjacs over the exposed Sunda Shelf during the Last Glacial Maximum. The results of the study provide new insights into the evolution of species in South and Southeast Asia, highlighting the importance of considering phylogeographic patterns in understanding the mechanisms leading to the evolution and speciation of mammals in the biodiversity hotspot of this region. The study's findings also have implications for conservation efforts, as they highlight the conservation importance of the Sri Lankan/South Indian red muntjac.