The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection.
The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection.
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DOI：
10.1371/journal.pgen.1002660
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Nakhleh L
中科院分区：
文献类型：
--
作者：
Yu Y;Degnan JH;Nakhleh L
基因树拓扑结构已被证明是一个强大的数据源，用于各种任务，包括物种树推理和物种定界。因此，用于计算物种树内的基因树的概率的方法已经被开发并广泛用于概率推理框架中。所有这些方法都假设一个潜在的多物种结合模型。然而，当网状进化事件，如杂交发生时，这些方法是不够的，因为它们没有考虑到这样的事件。在计算基因树拓扑结构的概率时考虑杂交和深度合并的方法目前存在于非常有限的情况下。然而，没有这样的方法存在的一般情况下，主要是由于这样一个事实，即目前还不知道如何计算的概率的基因树拓扑结构内的分支系统发育网络。在这里，我们提出了一种新的方法来计算概率的基因树拓扑结构的系统发育网络，并证明其应用的推理杂交的存在下，不完整的谱系排序。我们重新分析了酵母属物种的数据集，多个分析已经收敛在一个物种树候选人。使用我们的方法，虽然，我们表明，在这组涉及杂交的进化假说有更好的支持比严格的分歧。对一组三种果蝇的类似再分析表明，数据与杂交一致。此外，使用广泛的模拟研究，我们证明了权力的基因树拓扑结构在获得准确的估计分支长度和杂交概率的一个给定的系统发育网络。最后，我们讨论了可识别性问题与检测杂交，特别是在涉及灭绝或不完整的类群采样的情况下。物种树描述了物种如何分裂和分化。在物种树的分支中，描述物种中不同基因组区域的进化历史的基因树生长。对密切相关的生物体的基因组的进化分析突出了这样一种现象，即基因树可能彼此不一致，也可能由于深度合并而与包含它们的物种树不一致。此外，对于一些生物群体来说，杂交在它们的进化和多样化中起着重要作用。这一进化事件也导致基因树的不一致，并产生了一个物种的进化，这是一个网络。因此，推断已知或怀疑杂交在进化中起作用的生物群体的进化历史，需要同时处理杂交和基因树不一致的其他来源。目前，还没有方法可以在一般的混合情况下做到这一点。在本文中，我们提出了第一种方法，这项任务，并证明其性能。我们重新分析了一组酵母物种和另一种果蝇物种，并表明，进化历史涉及杂交有更高的支持比严格分歧的进化历史估计时，不纳入杂交分析。
Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa. Species trees depict how species split and diverge. Within the branches of a species tree, gene trees, which depict the evolutionary histories of different genomic regions in the species, grow. Evolutionary analyses of the genomes of closely related organisms have highlighted the phenomenon that gene trees may disagree with each other as well as with the species tree that contains them due to deep coalescence. Furthermore, for several groups of organisms, hybridization plays an important role in their evolution and diversification. This evolutionary event also results in gene tree incongruence and gives rise to a species phylogeny that is a network. Thus, inferring the evolutionary histories of groups of organisms where hybridization is known, or suspected, to play an evolutionary role requires dealing simultaneously with hybridization and other sources of gene tree incongruence. Currently, no methods exist for doing this with general scenarios of hybridization. In this paper, we propose the first method for this task and demonstrate its performance. We revisit the analysis of a set of yeast species and another of Drosophila species, and show that evolutionary histories involving hybridization have higher support than the strictly diverging evolutionary histories estimated when not incorporating hybridization in the analysis.
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影响因子：
10.7
作者：
DeGiorgio, Michael;Degnan, James H.
通讯作者：
Degnan, James H.
影响因子：
6.5
作者：
Knowles, L. Lacey;Carstens, Bryan C.
通讯作者：
Carstens, Bryan C.
影响因子：
6.8
作者：
AKAIKE, H
通讯作者：
AKAIKE, H
DOI：
10.1073/pnas.0607004104
发表时间：
2007-04-03
影响因子：
11.1
作者：
Edwards, Scott V.;Liu, Liang;Pearl, Dennis K.
通讯作者：
Pearl, Dennis K.
影响因子：
3
作者：
Linder, CR;Rieseberg, LH
通讯作者：
Rieseberg, LH