Unguided species delimitation using DNA sequence data from multiple Loci.
Unguided species delimitation using DNA sequence data from multiple Loci.
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DOI：
10.1093/molbev/msu279
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发表时间：
2014-12
影响因子：
10.7
通讯作者：
Rannala B
中科院分区：
文献类型：
--
作者：
Yang Z;Rannala B
提出了一种利用多物种融合模型同时进行物种定界和物种发生贝叶斯推断的方法。该方法消除了用户指定的指导树在物种划界的需要，并将系统发育的不确定性贝叶斯框架。最近邻交换算法被适配为提出对物种树的改变，在提议中改变多个位点的基因树以避免与新提出的物种树冲突。我们还修改了我们以前的计划，指定先验的物种划界模型，以构建联合先验的物种划界和物种的进化模型。在我们早期的方法中，修改后的算法集成了基因树，考虑到基因树拓扑结构和分支长度给定的序列数据的不确定性。我们进行了模拟研究，以检查该方法的统计特性，使用六个种群（每个两个序列）和三个物种的真实数量，与分歧时间和祖先的人口规模的值是现实的最近分歧的物种。结果表明，该方法趋于保守，高后验概率是物种状态的可靠指标。模拟结果还表明，权力的方法来界定物种的增加，在物种树的分歧时间的增加，并与基因座的数量增加。重新分析的两个数据集的洞穴鱼和海岸角蜥蜴提出相当大的系统发育的不确定性，即使数据是翔实的物种划分。讨论了先验对物种定界和物种发生模型的影响，以及先验对种群大小参数（θ）对贝叶斯物种定界的影响。
A method was developed for simultaneous Bayesian inference of species delimitation and species phylogeny using the multispecies coalescent model. The method eliminates the need for a user-specified guide tree in species delimitation and incorporates phylogenetic uncertainty in a Bayesian framework. The nearest-neighbor interchange algorithm was adapted to propose changes to the species tree, with the gene trees for multiple loci altered in the proposal to avoid conflicts with the newly proposed species tree. We also modify our previous scheme for specifying priors for species delimitation models to construct joint priors for models of species delimitation and species phylogeny. As in our earlier method, the modified algorithm integrates over gene trees, taking account of the uncertainty of gene tree topology and branch lengths given the sequence data. We conducted a simulation study to examine the statistical properties of the method using six populations (two sequences each) and a true number of three species, with values of divergence times and ancestral population sizes that are realistic for recently diverged species. The results suggest that the method tends to be conservative with high posterior probabilities being a confident indicator of species status. Simulation results also indicate that the power of the method to delimit species increases with an increase of the divergence times in the species tree, and with an increased number of gene loci. Reanalyses of two data sets of cavefish and coast horned lizards suggest considerable phylogenetic uncertainty even though the data are informative about species delimitation. We discuss the impact of the prior on models of species delimitation and species phylogeny and of the prior on population size parameters (θ) on Bayesian species delimitation.
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影响因子：
6.5
作者：
Zhang C;Rannala B;Yang Z
通讯作者：
Yang Z
影响因子：
6.5
作者：
De Queiroz, Kevin
通讯作者：
De Queiroz, Kevin
影响因子：
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作者：
Rannala, Bruce;Yang, Ziheng
通讯作者：
Yang, Ziheng
影响因子：
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作者：
Pons, Joan;Barraclough, Timothy G.;Vogler, Alfried P.
通讯作者：
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影响因子：
1
作者：
Green, PJ;Richardson, S
通讯作者：
Richardson, S