High-resolution species trees without concatenation
High-resolution species trees without concatenation
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DOI：
10.1073/pnas.0607004104
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发表时间：
2007-04-03
影响因子：
11.1
通讯作者：
Pearl, Dennis K.
中科院分区：
文献类型：
--
作者：
Edwards, Scott V.;Liu, Liang;Pearl, Dennis K.
绝大多数的系统发育模型集中在基因树的分辨率，尽管事实上，嵌入基因树的物种的同源性是主要的兴趣。我们分析了贝叶斯模型估计物种树，占随机变异的基因树从多个不连锁的基因座从一个单一的物种历史后，合并过程。该模型的应用程序从酵母的106个基因的数据集表明，通过统计学上承认的共享，但未知的物种树，基因树的采样恢复的一组基因树是大大减少与治疗的历史相比，每个位点独立的一个总体物种树。该分析还产生了一个集中的后验分布的酵母物种树的模式是一致的串联基因树，但可以这样做的串联方法所需的基因座的一半以下。使用模拟，我们表明，大量的基因座，高分辨率的物种树可以估计的条件下，串联的序列数据将积极误导后代，当基因树的比例匹配的物种树是
The vast majority of phylogenetic models focus on resolution of gene trees, despite the fact that phylogenies of species in which gene trees are embedded are of primary interest. We analyze a Bayesian model for estimating species trees that accounts for the stochastic variation expected for gene trees from multiple unlinked loci sampled from a single species history after a coalescent process. Application of the model to a 106-gene data set from yeast shows that the set of gene trees recovered by statistically acknowledging the shared but unknown species tree from which gene trees are sampled is much reduced compared with treating the history of each locus independently of an overarching species tree. The analysis also yields a concentrated posterior distribution of the yeast species tree whose mode is congruent with the concatenated gene tree but can do so with less than half the loci required by the concatenation method. Using simulations, we show that, with large numbers of loci, highly resolved species trees can be estimated under conditions in which concatenation of sequence data will positively mislead phylogeny, and when the proportion of gene trees matching the species tree is