title: Phylogeography of red muntjacs reveals three distinct mitochondrial lineages.
abstract: The members of the genus Muntiacus are of particular interest to evolutionary biologists due to their extreme chromosomal rearrangements and the ongoing discussions about the number of living species. Red muntjacs have the largest distribution of all muntjacs and were formerly considered as one species. Karyotype differences led to the provisional split between the Southern Red Muntjac (Muntiacus muntjak) and the Northern Red Muntjac (M. vaginalis), but uncertainties remain as, so far, no phylogenetic study has been conducted. Here, we analysed whole mitochondrial genomes of 59 archival and 16 contemporaneous samples to resolve uncertainties about their taxonomy and used red muntjacs as model for understanding the evolutionary history of other species in Southeast Asia.
  
  
  
  We found three distinct matrilineal groups of red muntjacs: Sri Lankan red muntjacs (including the Western Ghats) diverged first from other muntjacs about 1.5 Mya; later northern red muntjacs (including North India and Indochina) and southern red muntjacs (Sundaland) 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. Interestingly, we 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.
  
  
  
  Our results provide new insights into the evolution of species in South and Southeast Asia as we found clear genetic differentiation in a widespread and generalist species, corresponding to two known biogeographical barriers: The Isthmus of Kra and the central Indian dry zone. In addition, our molecular data support either the delineation of three monotypic species or three subspecies, but more importantly these data highlight the conservation importance of the Sri Lankan/South Indian red muntjac.
authors.affiliation: Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany. martins@izw-berlin.de.
authors.forename: Renata F
authors.initials: RF
authors.lastname: Martins
authors.affiliation: Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.|Potsdam University, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 22-24, 14476, Potsdam-Golm, Germany.
authors.forename: Jörns
authors.initials: J
authors.lastname: Fickel
authors.affiliation: Faculty of Environmental Science, Hanoi University of Science, Vietnam National University, 334 Nguyen Trai Road, Hanoi, Vietnam.|Centre for Natural Resources and Environmental Studies, Vietnam National University, 19 Le Thanh Tong Street, Hanoi, Vietnam.
authors.forename: Minh
authors.initials: M
authors.lastname: Le
authors.affiliation: Centre for Natural Resources and Environmental Studies, Vietnam National University, 19 Le Thanh Tong Street, Hanoi, Vietnam.
authors.forename: Thanh
authors.initials: T
authors.lastname: van Nguyen
authors.affiliation: Centre for Natural Resources and Environmental Studies, Vietnam National University, 19 Le Thanh Tong Street, Hanoi, Vietnam.|Present address: U.S. Agency for International Development, Governance for Inclusive Growth Program, Chemonics International Inc, 115 Tran Hung Dao Street, Hanoi, Vietnam.
authors.forename: Ha M
authors.initials: HM
authors.lastname: Nguyen
authors.affiliation: , 1123 Monroe Street, Evanston, IL, 60202, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Timmins
authors.affiliation: School of Science, Monash University Malaysia, 47500, Bandar Sunway, Malaysia.|Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, 47500, Bandar Sunway, Malaysia.
authors.forename: Han Ming
authors.initials: HM
authors.lastname: Gan
authors.affiliation: Department of Wildlife and National Parks (DWNP) Peninsular Malaysia, National Wildlife Forensic Laboratory (NWFL), 56100, Kuala Lumpur, Malaysia.
authors.forename: Jeffrine J
authors.initials: JJ
authors.lastname: Rovie-Ryan
authors.affiliation: Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
authors.forename: Dorina
authors.initials: D
authors.lastname: Lenz
authors.affiliation: Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
authors.forename: Daniel W
authors.initials: DW
authors.lastname: Förster
authors.affiliation: Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Wilting
mesh_terms: D000818:Animals; D001210:Asia, Southeastern; D004272:DNA, Mitochondrial; D019143:Evolution, Molecular; D007194:India; D007621:Karyotyping; D008928:Mitochondria / Q000235:genetics*; D058889:Molecular Typing; D018668:Muntjacs / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D058974:Phylogeography
chemical_list: D004272:DNA, Mitochondrial
keywords: Archival DNA; Muntjac; Phylogeography; Southeast Asia; Species complex