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.
Highlights
Genetic variability plays an important role in maintaining the evolutionary potential of a species
Based on the well-developed genotyping techniques of these AimeMHC genes, the second objective of this study was to understand how the patterns of major histocompatibility complex (MHC)-based adaptive variation vary in relation to the patterns of neutral genetic variation within wild populations, and what adaptation strategies are adopted by the giant panda compared to other carnivores
The causes of death were mostly natural; a few deaths were due to infectious diseases such as ascariasis, pneumonia, and tick-borne diseases. These nature reserves (NRs) obtained permission from China Giant Panda Protection and Management Office (CGPPMO) to collect these samples as genetic resources and delivered them to SCCGREWC for preservation
Summary
Genetic variability plays an important role in maintaining the evolutionary potential of a species. Due to habitat loss from increasing and human continuing activities, the species is currently isolated as 6 extant populations in the Qinling (QLI), Minshan (MSH), Qionglai (QLA), Daxiangling (DXL), Xiaoxiangling (XXL), and Liangshan (LSH) mountain ranges on the edge of the Tibetan plateau in China [4] (Figure 1A). The sizes of these giant panda populations range from 29 to 708, with ,1,600 total individuals [5], making it one of the world’s most endangered species
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