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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.

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