Next-generation sequencing for molecular ecology: a caveat regarding pooled samples

We develop a model based on the Dirichlet-compound multinomial distribution (CMD) and Ewens sampling formula to predict the fraction of SNP loci that will appear fixed for alternate alleles between two pooled samples drawn from the same underlying population. We apply this model to next-generation sequencing (NGS) data from Baltic Sea herring recently published by (Corander et al., , Molecular Ecology, 2931–2940), and show that there are many more fixed loci than expected in the absence of genetic structure. However, we show through coalescent simulations that the degree of population structure required to explain the fraction of alternatively fixed SNPs is extraordinarily high and that the surplus of fixed loci is more likely a consequence of limited representation of individual gene copies in the pooled samples, than it is of population structure. Our analysis signals that the use of NGS on pooled samples to identify divergent SNPs warrants caution. With pooled samples, it is hard to ...我们构建了一种基于狄利克雷复合多项式分布（Dirichlet-compound multinomial distribution）与Ewens抽样公式（Ewens sampling formula）的模型，用于预测从同一基础种群中抽取的两份混合样本间，会固定为变异等位基因的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点比例。我们将该模型应用于Corander等近期发表于《Molecular Ecology》（第2931–2940页）的波罗的海鲱下一代测序（Next-Generation Sequencing, NGS）数据，结果显示固定位点的数量远多于无遗传结构情形下的预期值。然而通过溯祖模拟（coalescent simulations）我们发现，要解释该变异等位基因固定SNP位点的比例，所需的种群结构程度极高；且相较于种群结构因素，混合样本中单个基因拷贝的代表性不足更可能是固定位点过剩的诱因。本研究表明，利用混合样本的下一代测序数据识别分化SNP位点时需谨慎。对于混合样本而言，很难……