Anomalous Unrooted Gene Trees
Anomalous Unrooted Gene Trees
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DOI：
10.1093/sysbio/syt023
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发表时间：
2013-07-01
影响因子：
6.5
通讯作者：
Degnan, James H.
中科院分区：
文献类型：
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作者：
Degnan, James H.
合并和多物种合并模型使家谱随着时间的推移而回溯。通常，由于可逆突变模型、缺乏适当的外群和分子钟，根据分子序列估计的树木的时间方向是未知的。在本文中，考虑了多物种合并下无根基因树拓扑的概率。主要结果是，对于任何具有七个或更多分类单元的物种树拓扑，存在分支长度，使得存在比与物种树具有相同无根拓扑的无根基因树拓扑更有可能的无根基因树拓扑。具有这种异常无根基因树 (AUGT) 的物种树被表征为具有五个和六个分类单元的树，并探索了导致 AUGT 和有根异常基因树的分支长度模式。这些结果可能有助于理解基因树的不一致和设计模拟研究以推断具有挑战性的物种树。 【异常基因树；毛虫化；聚结；谱系排序不完整；系统发育学；罗宾逊-福兹距离；种树。]。
The coalescent and multispecies coalescent model rooted genealogies backward through time. Often, the direction of time is unknown in trees estimated from molecular sequences due to reversible mutation models, absence of an appropriate outgroup, and the absence of the molecular clock. In this article, probabilities of unrooted gene-tree topologies under the multispecies coalescent are considered. The main result is that for any species-tree topology with seven or more taxa, there exist branch lengths such that there are unrooted gene-tree topologies that are more likely than the one that has the same unrooted topology as the species tree. Species trees with such anomalous unrooted gene trees (AUGTs) are characterized for trees with five and six taxa, and patterns of branch lengths leading to AUGTs and rooted anomalous gene trees are explored. The results could be useful for understanding gene tree discordance and designing simulations studies for inferring challenging species trees. [Anomalous gene tree; caterpillarization; coalescent; incomplete lineage sorting; phylogenetics; Robinson-Foulds distance; species tree.].