Data from: The effect of close relatives on unsupervised Bayesian clustering algorithms in population genetic structure analysis

The inference of population genetic structures is essential in many research areas in population genetics, conservation biology and evolutionary biology. Recently, unsupervised Bayesian clustering algorithms have been developed to detect a hidden population structure from genotypic data, assuming among others that individuals taken from the population are unrelated. Because of this hypothesis, markers in a sample taken from a subpopulation can be considered to be in Hardy-Weinberg and linkage equilibrium. However, close relatives might be sampled from the same subpopulation, and consequently, might cause Hardy-Weinberg and linkage disequilibrium and thus bias a population genetic structure analysis. In this study, we used simulated and real data to investigate the impact of close relatives in a sample on Bayesian population structure analysis. We also showed that, when close relatives were identified by a pedigree reconstruction approach and removed, the accuracy of a population genetic structure analysis can be greatly improved. The results indicate that unsupervised Bayesian clustering algorithms cannot be used blindly to detect genetic structure in a sample with closely related individuals. Rather, when closely related individuals are suspected to be frequent in a sample, these individuals should be first identified and removed before conducting a population structure analysis.

种群遗传结构推断在种群遗传学、保护生物学与进化生物学的诸多研究领域中均具有核心重要性。近年来，学界已开发出无监督贝叶斯聚类算法（unsupervised Bayesian clustering algorithms），用于从基因型数据中挖掘隐藏的种群结构，其默认假设之一为：采集自目标种群的所有个体均无亲缘关系。基于该假设，从亚种群中获取的样本内的遗传标记可被认为处于哈迪-温伯格平衡（Hardy-Weinberg equilibrium）与连锁平衡（linkage equilibrium）状态。然而，若同一亚种群内的近缘个体被纳入采样，将可能引发哈迪-温伯格失衡与连锁不平衡（linkage disequilibrium），进而对种群遗传结构分析引入偏倚。本研究借助模拟数据与真实实验数据，系统探究了样本中的近缘个体对贝叶斯种群结构分析的影响。研究同时证实，若通过谱系重建方法（pedigree reconstruction approach）识别并移除样本中的近缘个体，种群遗传结构分析的准确性可得到大幅提升。研究结果表明，不可盲目将无监督贝叶斯聚类算法用于包含近缘个体的样本的遗传结构检测。反之，当怀疑样本中存在大量近缘个体时，应先对其进行识别并移除，再开展种群遗传结构分析。