Genetic structure of giant pandas across patchily distributed habitats in the Qinling Mountains

Due to geographic isolation and habitat disturbance, the Qinling giant pandas (QGPs) were divided into six habitat patches and accordingly assigned to six local populations in the Fourth National Survey on Giant Pandas. Whether the artificial division of QGP local population is of rationality and whether it is reflected by genetic structure remain unclear. To answer the questions, we conducted microsatellite marker analysis with 12 loci from 94 individuals identified via faeces samples collected from two local populations in the Qinling Mountains. Based on analysis of molecular variance (AMOVA), the genetic variation of the Xinglongling local population and Niuweihe local population mainly occurred within populations (81.22 %), with a relatively high genetic differentiation (Fst = 0.18782) and low gene flow (Nm = 0.340282) between Xinglongling and Niuweihe local population. The Mantel test revealed a significant positive correlation between pairwise genetic distance and geographic distance (R = 0.136, p = 0.001). The study reflected that the partition of two local populations is consistent with the division of habitat patches, and also confirmed the geographic distance has influences on genetic distance between QGP individuals in Qinling Mountains. These findings offer important references for effective conservation of QGPs, especially small populations, avoiding the loss of genetic diversity of the QGP population.