Accuracy and Precision of Species Trees: Effects of Locus, Individual, and Base Pair Sampling on Inference of Species Trees in Lizards of the Liolaemus darwinii Group (Squamata, Liolaemidae)
Accuracy and Precision of Species Trees: Effects of Locus, Individual, and Base Pair Sampling on Inference of Species Trees in Lizards of the Liolaemus darwinii Group (Squamata, Liolaemidae)
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DOI：
10.1093/sysbio/syr105
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发表时间：
2012-03-01
影响因子：
6.5
通讯作者：
Sites, Jack W., Jr.
中科院分区：
文献类型：
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作者：
Camargo, Arley;Avila, Luciano J.;Sites, Jack W., Jr.
分子遗传学已经进入了一个新的时代，在这个时代，物种树是从一系列基因树中估计出来的，使用的方法是适应它们的异质性和与物种树的不一致性。对树种的经验评价是评估性能所必需的（即，准确性和精确度），这些方法与真实的数据，其中包括基因谱系可能形成不同的历史和人口统计过程。利用 *BEAST软件分析了达氏蜥蜴种组16种南美蜥蜴的20个基因座，构建了物种树，并比较了该方法在不同基因座、个体和序列长度取样策略下的性能。我们发现，随着基因座数量的增加，物种树的准确性和精确度增加，但对于任何数量的基因座，准确性大幅下降，只有当每个物种只使用一个个体或25%的全长序列长度（类似于147 bp）。此外，位点的“信息量”是一个重要的因素，在物种树的准确性/精度时，使用几个位点，但它变得越来越不相关的附加位点。我们的实证结果结合以前的模拟研究表明，有一个最佳范围的采样努力的位点，个人和序列长度为一个给定的物种形成的历史和信息内容的数据。未来的研究应进一步评估其他因素，可以影响树种的表现，包括基因流，基因座的“信息”，树形，缺失的数据，和错误的物种界定。
Molecular phylogenetics has entered a new era in which species trees are estimated from a collection of gene trees using methods that accommodate their heterogeneity and discordance with the species tree. Empirical evaluation of species trees is necessary to assess the performance (i.e., accuracy and precision) of these methods with real data, which consists of gene genealogies likely shaped by different historical and demographic processes. We analyzed 20 loci for 16 species of the South American lizards of the Liolaemus darwinii species group and reconstructed a species tree with *BEAST, then compared the performance of this method under different sampling strategies of loci, individuals, and sequence lengths. We found an increase in the accuracy and precision of species trees with the number of loci, but for any number of loci, accuracy substantially decreased only when using only one individual per species or 25% of the full sequence length (similar to 147 bp). In addition, locus "informativeness" was an important factor in the accuracy/precision of species trees when using a few loci, but it became increasingly irrelevant with additional loci. Our empirical results combined with the previous simulation studies suggest that there is an optimal range of sampling effort of loci, individuals, and sequence lengths for a given speciation history and information content of the data. Future studies should be directed toward further assessment of other factors that can impact performance of species trees, including gene flow, locus "informativeness," tree shape, missing data, and errors in species delimitation.