Quartet-based methods to reconstruct phylogenetic networks.
Quartet-based methods to reconstruct phylogenetic networks.
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DOI：
10.1186/1752-0509-8-21
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发表时间：
2014-02-20
影响因子：
--
通讯作者：
Wan XF
中科院分区：
文献类型：
--
作者：
Yang J;Grünewald S;Xu Y;Wan XF
系统发生网络被用来可视化一组核苷酸序列、基因或物种之间的进化关系，当认为涉及杂交、重组、重组和水平基因转移等网状事件时。与传统的基于距离的方法相比，基于四元组的方法在重建过程中考虑了更多的信息，因此具有更准确的潜力。我们介绍了QuartetSuite，其中包括一组新的基于四分之一的方法，即QuartetS，QuartetA和QuartetM，从核苷酸序列重建系统发育网络。我们在两个模拟的核苷酸序列数据集上测试了它们的性能，并将它们与其他流行的方法进行了比较：一个数据集由树拓扑生成，另一个数据集由包含三个网状事件的复杂进化历史生成。我们进一步验证了这些方法对两个真实的数据集：一个细菌数据集，由36个细菌物种的7个串联基因组成，并在中国最近出现的H7 N9低致病性禽流感病毒相关的流感数据集。QuartetS、QuartetA和QuartetM具有准确重建从简单分支树到包含许多网状事件的复杂网络的进化场景的潜力。这些方法可以为理解复杂的生物进化过程，如细菌分类学和流感病毒的抗性提供见解。
Phylogenetic networks are employed to visualize evolutionary relationships among a group of nucleotide sequences, genes or species when reticulate events like hybridization, recombination, reassortant and horizontal gene transfer are believed to be involved. In comparison to traditional distance-based methods, quartet-based methods consider more information in the reconstruction process and thus have the potential to be more accurate. We introduce QuartetSuite, which includes a set of new quartet-based methods, namely QuartetS, QuartetA, and QuartetM, to reconstruct phylogenetic networks from nucleotide sequences. We tested their performances and compared them with other popular methods on two simulated nucleotide sequence data sets: one generated from a tree topology and the other from a complicated evolutionary history containing three reticulate events. We further validated these methods to two real data sets: a bacterial data set consisting of seven concatenated genes of 36 bacterial species and an influenza data set related to recently emerging H7N9 low pathogenic avian influenza viruses in China. QuartetS, QuartetA, and QuartetM have the potential to accurately reconstruct evolutionary scenarios from simple branching trees to complicated networks containing many reticulate events. These methods could provide insights into the understanding of complicated biological evolutionary processes such as bacterial taxonomy and reassortant of influenza viruses.
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