Understanding the diversification pattern of three subspecies of swamp deer (Rucervus duvaucelii) during the Pleistocene–Holocene based on mitochondrial and Y chromosome markers

Abstract

The Quaternary period played a vital role in the creation of new ecological and vegetation zones, which shaped the diversification and distribution of species. The present study aimed to document, for the first time, phylogeography of three reported subspecies/populations of swamp deer, Rucervus duvaucelii duvaucelii (northern), R. d. ranjitsinhi (eastern) and R. d. branderi (central), using a fragment of the mitochondrial cyt b gene and the Y chromosome DBY-7. Inferred phylogenetic relationships revealed the presence of three genetically distinct lineages using both historic and contemporary samples. Sequence divergence between the northern and eastern populations was less (1.5%) than between the northern and central populations (1.8%). Molecular dating based on the cyt b gene suggests that swamp deer split into two (northern-eastern and central) major clades from the common ancestor before 1.3 Million years ago. Demography based on Bayesian skyline plot suggested a slight decline in one population (R. d. duvaucelii) but a stable population size in the other two populations (R. d. ranjitsinhi and R. d. branderi). The observed shallow split of the northern population into the Jhilmil Tal Wildlife Conservation Reserve and Dudhwa National Park subpopulations may have been due to extreme climatic fluctuations during the Quaternary period (Holocene) and the subsequent increased human footprint. We also review and discuss the significance of past climatic and vegetation changes due to human settlement and of paleoenvironmental and biogeographic events that may have facilitated the diversification and distribution of habitat-specific swamp deer into small patches across the Indian subcontinent and of the congeneric species, R. schomburgki, from the southeastern area in Thailand with related conservation implications.