Inferring phylogenetic networks by the maximum parsimony criterion: A case study
Inferring phylogenetic networks by the maximum parsimony criterion: A case study
复制标题
DOI：
10.1093/molbev/msl163
复制
发表时间：
2007-01-01
影响因子：
10.7
通讯作者：
Tuller, Tamir
中科院分区：
文献类型：
--
作者：
Jin, Guohua;Nakhleh, Luay;Tuller, Tamir
水平基因转移（HGT）可能会导致基因的进化历史彼此不一致，也与物种树不一致。在这种情况下，协调物种和基因树会产生一个关系网络，称为物种集合的“系统发育网络”。一个系统发育网络，结合HGT包括一个潜在的物种树，捕捉垂直遗传和一组边缘模型的“水平”转移的遗传物质。Nakhleh及其同事最近在一系列论文中提出了系统发育网络的最大简约性（MP）准则，提供了一系列计算效率高的算法和算法，并在模拟数据上证明了该准则的可行性。我们的研究结果表明，MP是非常有前途的，当它的应用扩展到系统发育网络重建和HGT检测领域。在我们研究的所有情况下，MP标准检测到正确的HGT事件的数量，需要映射到物种的进化历史的基因数据集。此外，我们的研究结果表明，该标准是强大的不完全分类单元采样和使用不同的网站替代矩阵。最后，我们的研究结果表明，MP标准是非常有前途的检测HGT嵌合基因，其进化历史是一个混合的垂直和水平的进化。除了MP的性能分析之外，我们的研究结果还为4个生物数据集的进化提供了新的见解，并为HGT场景在其进化历史中的新的可能解释。
Horizontal gene transfer (HGT) may result in genes whose evolutionary histories disagree with each other, as well as with the species tree. In this case, reconciling the species and gene trees results in a network of relationships, known as the "phylogenetic network" of the set of species. A phylogenetic network that incorporates HGT consists of an underlying species tree that captures vertical inheritance and a set of edges which model the "horizontal" transfer of genetic material. In a series of papers, Nakhleh and colleagues have recently formulated a maximum parsimony (MP) criterion for phylogenetic networks, provided an array of computationally efficient algorithms and heuristics for computing it, and demonstrated its plausibility on simulated data.In this article, we study the performance and robustness of this criterion on biological data. Our findings indicate that MP is very promising when its application is extended to the domain of phylogenetic network reconstruction and HGT detection. In all cases we investigated, the MP criterion detected the correct number of HGT events required to map the evolutionary history of a gene data set onto the species phylogeny. Furthermore, our results indicate that the criterion is robust with respect to both incomplete taxon sampling and the use of different site substitution matrices. Finally, our results show that the MP criterion is very promising in detecting HGT in chimeric genes, whose evolutionary histories are a mix of vertical and horizontal evolution. Besides the performance analysis of MP, our findings offer new insights into the evolution of 4 biological data sets and new possible explanations of HGT scenarios in their evolutionary history.