title: Patterns of adaptive and neutral diversity identify the Xiaoxiangling mountains as a refuge for the giant panda.
abstract: Genetic variation plays a significant role in maintaining the evolutionary potential of a species. Comparing the patterns of adaptive and neutral diversity in extant populations is useful for understanding the local adaptations of a species. In this study, we determined the fine-scale genetic structure of 6 extant populations of the giant panda (Ailuropoda melanoleuca) using mtDNA and DNA fingerprints, and then overlaid adaptive variations in 6 functional Aime-MHC class II genes (DRA, DRB3, DQA1, DQA2, DQB1, and DQB2) on this framework. We found that: (1) analysis of the mtDNA and DNA fingerprint-based networks of the 6 populations identified the independent evolutionary histories of the 2 panda subspecies; (2) the basal (ancestral) branches of the fingerprint-based Sichuan-derived network all originated from the smallest Xiaoxiangling (XXL) population, suggesting the status of a glacial refuge in XXL; (3) the MHC variations among the tested populations showed that the XXL population exhibited extraordinary high levels of MHC diversity in allelic richness, which is consistent with the diversity characteristics of a glacial refuge; (4) the phylogenetic tree showed that the basal clades of giant panda DQB sequences were all occupied by XXL-specific sequences, providing evidence for the ancestor-resembling traits of XXL. Finally, we found that the giant panda had many more DQ alleles than DR alleles (33∶13), contrary to other mammals, and that the XXL refuge showed special characteristics in the DQB loci, with 7 DQB members of 9 XXL-unique alleles. Thus, this study identified XXL as a glacial refuge, specifically harboring the most number of primitive DQB alleles.
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, PR China.
authors.forename: Yi-Yan
authors.initials: YY
authors.lastname: Chen
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhu
authors.forename: Qiu-Hong
authors.initials: QH
authors.lastname: Wan
authors.forename: Ji-Kang
authors.initials: JK
authors.lastname: Lou
authors.forename: Wen-Jing
authors.initials: WJ
authors.lastname: Li
authors.forename: Yun-Fa
authors.initials: YF
authors.lastname: Ge
authors.forename: Sheng-Guo
authors.initials: SG
authors.lastname: Fang
mesh_terms: D000220:Adaptation, Biological; D000483:Alleles; D000818:Animals; D005075:Biological Evolution; D004272:DNA, Mitochondrial / Q000235:genetics; D005787:Gene Frequency; D005802:Genes, MHC Class II; D014644:Genetic Variation; D005838:Genotype; D062305:Geographic Mapping; D006239:Haplotypes; D008969:Molecular Sequence Data; D010802:Phylogeny; D012641:Selection, Genetic; D001503:Ursidae / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial
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