Discordance of species trees with their most likely gene trees.
Discordance of species trees with their most likely gene trees.
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DOI：
10.1371/journal.pgen.0020068
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发表时间：
2006-05
期刊：
影响因子：
4.5
通讯作者：
Rosenberg NA
中科院分区：
文献类型：
--
作者：
Degnan JH;Rosenberg NA
由于谱系在物种形成过程中排序的随机方式，基因树在拓扑结构上可能彼此不同，也可能与物种树不同。令人惊讶的是，假设遗传谱系遵循种内进化的结合模型，我们发现，对于任何具有五个或更多个物种的物种树拓扑结构，存在基因树不一致的分支长度是如此常见，以至于最有可能沿着物种树的分支沿着进化的基因树拓扑结构不同于物种的进化。这个违反直觉的结果意味着，在结合多个位点的数据，使用最频繁观察到的基因树拓扑结构作为物种树拓扑结构的估计的简单程序可以渐近保证产生不正确的估计。我们的结论与建议，可以帮助克服这一新的障碍，准确的基因组推断的物种benchgenies。沿着物种关系树的分支沿着进化的不同基因组区域可以具有不同的进化历史。因此，从遗传数据中估计物种树可能会受到分析中使用的基因组区域的特定选择的影响。最近的工作重点是通过结合来自多个地区的信息来规避这个问题，试图产生准确的树种估计。作者表明，使用多个基因组区域进行物种树推断会遇到一个令人惊讶的新困难，即“异常基因树”问题。不仅单个基因或基因组区域可以具有与物种树在形状或拓扑上不同的系谱历史，最可能进化的基因树拓扑也可以与物种树拓扑不同。因此，随着更多基因的添加，使用最常观察到的基因树拓扑作为物种树拓扑估计的“民主投票”程序可能会收敛到错误的物种树。随着同时研究基因组的多个区域变得更加可行，物种树推理算法将需要开始考虑异常基因树的问题。
Because of the stochastic way in which lineages sort during speciation, gene trees may differ in topology from each other and from species trees. Surprisingly, assuming that genetic lineages follow a coalescent model of within-species evolution, we find that for any species tree topology with five or more species, there exist branch lengths for which gene tree discordance is so common that the most likely gene tree topology to evolve along the branches of a species tree differs from the species phylogeny. This counterintuitive result implies that in combining data on multiple loci, the straightforward procedure of using the most frequently observed gene tree topology as an estimate of the species tree topology can be asymptotically guaranteed to produce an incorrect estimate. We conclude with suggestions that can aid in overcoming this new obstacle to accurate genomic inference of species phylogenies. Different genomic regions evolving along the branches of a tree of species relationships can have different evolutionary histories. Consequently, estimates of species trees from genetic data may be influenced by the particular choice of genomic regions used in an analysis. Recent work has focused on circumventing this problem by combining information from multiple regions to attempt to produce accurate species tree estimates. The authors show that the use of multiple genomic regions for species tree inference is subject to a surprising new difficulty, the problem of “anomalous gene trees.” Not only can individual genes or genomic regions have genealogical histories that differ in shape, or topology, from a species tree, the gene tree topology most likely to evolve can differ from the species tree topology. As a result, the “democratic vote” procedure of using the most frequently observed gene tree topology as an estimate of the species tree topology can converge on the wrong species tree as more genes are added. As it becomes more feasible to simultaneously investigate many regions of a genome, species tree inference algorithms will need to begin taking the problem of anomalous gene trees into consideration.
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影响因子：
4.1
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