Data from: Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda

Background: Evaluating patterns of genetic variation is important to
identify conservation units (i.e., evolutionarily significant units
[ESUs], management units [MUs], and adaptive units [AUs]) in endangered
species. While neutral markers could be used to infer population history,
their application in the estimation of adaptive variation is limited. The
capacity to adapt to various environments is vital for the long-term
survival of endangered species. Hence, analysis of adaptive loci, such as
the major histocompatibility complex (MHC) genes, is critical for
conservation genetics studies. Here, we investigated 4 classical MHC class
I genes (Aime-C, Aime-F, Aime-I, and Aime-L) and 8 microsatellites to
infer patterns of genetic variation in the giant panda (Ailuropoda
melanoleuca) and to further define conservation units. Results: Overall,
we identified 24 haplotypes (9 for Aime-C, 1 for Aime-F, 7 for Aime-I, and
7 for Aime-L) from 218 individuals obtained from 6 populations of giant
panda. We found that the Xiaoxiangling population had the highest genetic
variation at microsatellites among the 6 giant panda populations and
higher genetic variation at Aime-MHC class I genes than other larger
populations (Qinling, Qionglai, and Minshan populations). Differentiation
index (FST)-based phylogenetic and Bayesian clustering analyses for
Aime-MHC-I and microsatellite loci both supported that most populations
were highly differentiated. The Qinling population was the most
genetically differentiated. Conclusions: The giant panda showed a
relatively higher level of genetic diversity at MHC class I genes compared
with endangered felids. Using all of the loci, we found that the 6 giant
panda populations fell into 2 ESUs: Qinling and non-Qinling populations.
We defined 3 MUs based on microsatellites: Qinling, Minshan-Qionglai, and
Daxiangling-Xiaoxiangling-Liangshan. We also recommended 3 possible AUs
based on MHC loci: Qinling, Minshan-Qionglai, and
Daxiangling-Xiaoxiangling-Liangshan. Furthermore, we recommend that a
captive breeding program be considered for the Qinling panda population.