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.

研究背景：评估遗传变异模式，对确定濒危物种的保护单元——即进化显著单元（Evolutionarily Significant Units, ESUs）、管理单元（Management Units, MUs）与适应性单元（Adaptive Units, AUs）——具有重要意义。尽管中性标记可用于推断种群历史，但其在适应性变异评估中的应用存在局限。物种适应多样环境的能力，是濒危物种长期存续的关键。因此，针对适应性基因座（如主要组织相容性复合体（Major Histocompatibility Complex, MHC）基因）的分析，对保护遗传学研究至关重要。本研究针对4个经典MHC I类基因（Aime-C、Aime-F、Aime-I及Aime-L）与8个微卫星位点展开探究，以解析大熊猫（Ailuropoda melanoleuca）的遗传变异模式，并进一步明确其保护单元。

研究结果：总体而言，我们从6个大熊猫种群的218份个体样本中，共鉴定出24个单倍型（其中Aime-C对应9个、Aime-F对应1个、Aime-I对应7个、Aime-L对应7个）。研究发现，在6个大熊猫种群中，小相岭种群的微卫星遗传变异水平最高，且其Aime-MHC I类基因的遗传变异水平高于秦岭、邛崃、岷山这3个规模更大的种群。基于分化指数（FST）的系统发育分析与贝叶斯聚类分析，无论是针对Aime-MHC-I基因座还是微卫星位点，均证实绝大多数种群间存在显著遗传分化，其中秦岭种群的遗传分化程度最高。

研究结论：相较于濒危猫科动物，大熊猫的MHC I类基因遗传多样性水平相对更高。整合所有位点的分析结果，我们发现6个大熊猫种群可划分为2个进化显著单元：秦岭种群与非秦岭种群。基于微卫星位点，我们界定出3个管理单元：秦岭种群、岷山-邛崃种群以及大相岭-小相岭-凉山种群。此外，基于MHC基因座，我们推荐了3个潜在适应性单元：秦岭种群、岷山-邛崃种群以及大相岭-小相岭-凉山种群。最后，我们建议针对秦岭大熊猫种群开展圈养繁育计划。