Influence of finite-sites mutation, population subdivision and sampling schemes on patterns of nucleotide polymorphism for species with molecular hyperdiversity
Influence of finite-sites mutation, population subdivision and sampling schemes on patterns of nucleotide polymorphism for species with molecular hyperdiversity
复制标题
有限位点突变、群体细分和抽样方案对分子超多样性物种核苷酸多态性模式的影响
DOI：
10.1111/j.1365-294x.2012.05475.x
复制
发表时间：
2012-03-01
影响因子：
4.9
通讯作者：
Peng, Yue
中科院分区：
文献类型：
--
作者：
Cutter, Asher D.;Wang, Guo-Xiu;Peng, Yue
分子高度多样性已在病毒、原核生物和真核生物中得到记录。这种生物体破坏了无限位点突变模型的假设，因为一个位点的多个突变事件包含多态性的不可忽略的部分。此外，来自细分种群的物种的个体的不同采样方案可以深刻地影响分子变异的结果模式和解释。受到线虫 Caenorhabditis sp 分子高度多样性的启发。如图 5 所示，同义位点之间的平均成对差异 > 5% 以及适度的群体结构，我们通过合并模拟研究了有限位点突变 (FSM) 过程和群体细分对变异频谱的联合影响。从通过垫脚石迁移模型互连的许多群体中，我们构建了来自单个群体的局部样本、来自多个群体的汇集样本以及来自多个群体的单个个体的分散样本。与平衡状态下的单个恐慌群体相比，我们发现在 FSM 模型下，高群体突变率会导致稀有变异（Tajimas D 阳性）的缺乏。当迁移较高时，种群结构也会导致本地样本出现这种偏差，而当迁移较低时，种群结构也会导致混合样本出现这种偏差。 C. sp. 采样方案的对比5 意味着高突变输入和高迁移。我们建议，利用根据不同抽样方案分析序列时表现出的部分不同的多态性模式，对细分种群的物种的局部、汇集和分散样本进行联合分析，提供了一种改进人口统计历史推断的方法。
Molecular hyperdiversity has been documented in viruses, prokaryotes and eukaryotes. Such organisms undermine the assumptions of the infinite-sites mutational model, because multiple mutational events at a site comprise a non-negligible portion of polymorphisms. Moreover, different sampling schemes of individuals from species with subdivided populations can profoundly influence resulting patterns and interpretations of molecular variation. Inspired by molecular hyperdiversity in the nematode Caenorhabditis sp. 5, which exhibits average pairwise differences among synonymous sites of >5% as well as modest population structure, we investigated via coalescent simulation the joint effects of a finite-sites mutation (FSM) process and population subdivision on the variant frequency spectrum. From many demes interconnected through a stepping-stone migration model, we constructed local samples from a single deme, pooled samples from several demes and scattered samples of a single individual from numerous demes. Compared with a single panmictic population at equilibrium, we find that high population mutation rates induce a deficit of rare variants (positive Tajimas D) under a FSM model. Population structure also induces such a skew for local samples when migration is high and for pooled samples when migration is low. Contrasts of sampling schemes for C. sp. 5 imply high mutational input coupled with high migration. We propose that joint analysis of local, pooled and scattered samples for species with subdivided populations provides a means of improving inference of demographic history, by virtue of the partially distinct patterns of polymorphism that manifest when sequences are analyzed according to differing sampling schemes.