Data from: Bayesian clustering analyses for genetic assignment and study of hybridization in oaks: effects of asymmetric phylogenies and asymmetric sampling schemes

Bayesian clustering methods have been widely used for studying species delimitation and genetic introgression. In order to test the effect of phylogenetic relationships and sampling scheme on the inferred clustering solution and on the performance of Bayesian clustering analysis, I simulated genotypes of the interfertile oak species Quercus robur, Quercus petraea, and Quercus pubescens and I run analyses using two popular software programs, STRUCTURE and BAPS. First, based on purebred simulations, I compared clustering solutions resulting from different sample size configurations. While clustering solution generally reflected the taxonomic relationships when equal samples of each species were included, spurious partition was inferred by STRUCTURE when some species were represented by larger and others by smaller samples. In very unbalanced configurations, STRUCTURE failed to identify the three species, even if three subpopulations were assumed. By contrast, BAPS could properly identify the three species under any sampling scheme. Second, based on simulations of purebreds and hybrids, I tested the performance of individual assignments with variable number of loci. This analysis showed that STRUCTURE can detect introgressed individuals more efficiently than BAPS. However, BAPS could assign purebreds more efficiently with a lower number of loci. Method performance also depended on phylogenetic relationships. In the case of Q. petraea, Q. pubescens, and their hybrids, method performance was lower due to their phylogenetic affinity. Inclusion of three instead of two species into the analysis led to reduction of performance, and to misclassification of hybrids, which often reflected the phylogenetic affinity between Q. petraea and Q. pubescens.

贝叶斯聚类方法已被广泛应用于物种界定与基因渐渗的研究中。为探究系统发育关系与采样方案对聚类推断结果及贝叶斯聚类分析性能的影响，本研究对三个可杂交的栎属物种——夏栎（Quercus robur）、无梗花栎（Quercus petraea）以及柔毛栎（Quercus pubescens）的基因型进行了模拟，并采用两款主流软件STRUCTURE与BAPS开展分析。
首先，基于纯种个体的模拟数据，本研究对比了不同样本量配置下得到的聚类结果。当各物种样本量均等时，聚类结果通常能够反映类群的分类学关系；但当部分物种样本量较大、其余物种样本量较小时，STRUCTURE会推断出虚假的聚类分区。在样本量极不均衡的配置下，即使预设存在3个亚种群，STRUCTURE也无法正确区分这三个物种。相比之下，BAPS在任意采样方案下均能正确识别这三个物种。
其次，基于纯种与杂交个体的模拟数据，本研究测试了不同位点数量下的个体归属分析性能。分析结果表明，STRUCTURE对渐渗个体的检出效率高于BAPS。但在使用较少位点时，BAPS对纯种个体的归属判定效率更高。分析方法的性能同样受系统发育关系的影响：针对无梗花栎、柔毛栎及其杂交个体的分析中，由于二者系统发育亲缘关系较近，方法的整体性能有所下降。当分析中纳入3个物种而非2个物种时，分析性能会出现下降，且杂交个体的错分率升高，这一现象通常源于无梗花栎与柔毛栎之间的系统发育亲缘关系。