How rivers and historical climate oscillations impact on genetic structure in Chinese Muntjac (Muntiacus reevesi)

Aim The characterization of the genetic structure and demographic dynamics of a species can shed light on the impacts of natural landscapes, historical climate change and human activities, thus enabling us to develop appropriate protection and management strategies. In this study, we aimed to characterize how the above-mentioned factors shaped the genetic structure and demographic history of the Chinese muntjac (Muntiacus reevesi). Location The reaches of the Yangtze River, China. Methods Using mtDNA control region sequences and 15 nuclear microsatellite loci as genetic markers, we analysed population genetic structure with a factorial correspondence analysis (FCA), AMOVA, F-ST estimates and Bayesian cluster analysis. In addition, we estimated the demographic history using Bayesian skyline plot (BSP) analysis and MSVAR simulation. Results High genetic diversity was detected in Chinese muntjac populations. Population structure analysis strongly suggesting three genetic clusters (QL/BA/WLS, DB and JLS/WN/WYS). The demographic analyses showed that Chinese muntjac experienced population fluctuation during the late Pleistocene, followed by bottleneck during the Holocene. Main conclusions The extant Chinese muntjac populations harbour a surprisingly high genetic diversity despite of the bottleneck they went through. The populations show significant population structure separating populations in the upper, middle and lower regions of the Yangtze River, supporting the presence of three independent management units (QL/BA/WLS, DB and JLS/WN/WYS). The population demography of the Chinese muntjac presents high concordance with the rotation of glacial-interglacial in late Pleistocene. In addition, our study identified that the Chinese muntjac's recent population history may have been influenced by early human activities (8,509-1,605 years ago).