Data from: Genetic structuring and recent demographic history of red pandas (Ailurus fulgens) inferred from microsatellite and mitochondrial DNA

Clarification of the genetic structure and population history of a species
can shed light on impacts of landscapes, historical climate change and
contemporary human activities, and thus enables evidence-based
conservation decisions for endangered organisms. The red panda (Ailurus
fulgens) is an endangered species distributing at the edge of the
Qinghai-Tibetan Plateau and is currently subject to habitat loss,
fragmentation and population decline, thus representing a good model to
test the influences of the above factors on a plateau edge species. We
combined nine microsatellite loci and 551 bp of mitochondrial control
region (mtDNA CR) to explore the genetic structure and demographic history
of this species. 123 individuals were sampled from 23 locations across
five populations. High levels of genetic variation were identified for
both mtDNA and microsatellites. Phylogeographic analyses indicated little
geographic structure, suggesting historically wide gene flow. However,
microsatellite-based Bayesian clustering clearly identified three groups
(Qionglai-Liangshan, Xiaoxiangling and Gaoligong-Tibet). A significant
isolation-by-distance pattern was detected only after removing
Xiaoxiangling. For mtDNA data there was no statistical support for a
historical population expansion or contraction for the whole sample or any
population except Xiaoxiangling where a signal of contraction was
detected. However, Bayesian simulations of population history using
microsatellite data did pinpoint population declines for Qionglai,
Xiaoxiangling and Gaoligong, demonstrating significant influences of human
activity on demography. The unique history of the Xiaoxiangling population
plays a critical role in shaping the genetic structure of this species,
and large-scale habitat loss and fragmentation is hampering gene flow
among populations. The implications of our findings for the biogeography
of the Qinghai-Tibetan Plateau, subspecies classification and conservation
of red pandas are discussed.