Novel methodology for construction and pruning of quasi-median networks.
Novel methodology for construction and pruning of quasi-median networks.
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DOI：
10.1186/1471-2105-9-115
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发表时间：
2008-02-25
影响因子：
3
通讯作者：
Brown TA
中科院分区：
文献类型：
--
作者：
Ayling SC;Brown TA
可视化一组序列的进化历史是分子系统发育学面临的挑战。一种方法是使用无向图，如中位网络，来可视化系统发育，其中网状关系，如重组或同质，显示为循环。中值网络包含作为节点的序列的二进制表示，其中连接这些序列的边在一个字符上不同；调用假设的祖先节点以生成包含所有最简约树的连接网络。准中值网络是中值网络的推广，它不限于二进制数据，尽管包含在多态位置内的系统发育信息可能在数据的预处理过程中丢失。当一组样本的历史包含频繁的同态或重组事件时，准中值网络将具有复杂的拓扑结构。图缩减或剪枝方法已被用来降低网络复杂性，但其中一些方法不适用于发生重组的数据集，而另一些方法过程复杂和/或导致网络断开。我们解决了在构造和简化准中值网络时所固有的问题。我们描述了一种生成准中值网络的新方法，该方法使用所有字符，包括二进制和多态，而不强制对多态分区进行任意排序。我们还描述了一种剪枝机制，它在观察到的序列之间保持至少一条最短路径，在保持连通图的同时显示所有序列对之间的潜在关系。将该方法应用于海甜菜的5S rDNA序列数据，产生了一个修剪网络，在该网络中，种群之间的遗传隔离是明显的，这表明了该方法在探索进化关系方面的价值。
Visualising the evolutionary history of a set of sequences is a challenge for molecular phylogenetics. One approach is to use undirected graphs, such as median networks, to visualise phylogenies where reticulate relationships such as recombination or homoplasy are displayed as cycles. Median networks contain binary representations of sequences as nodes, with edges connecting those sequences differing at one character; hypothetical ancestral nodes are invoked to generate a connected network which contains all most parsimonious trees. Quasi-median networks are a generalisation of median networks which are not restricted to binary data, although phylogenetic information contained within the multistate positions can be lost during the preprocessing of data. Where the history of a set of samples contain frequent homoplasies or recombination events quasi-median networks will have a complex topology. Graph reduction or pruning methods have been used to reduce network complexity but some of these methods are inapplicable to datasets in which recombination has occurred and others are procedurally complex and/or result in disconnected networks. We address the problems inherent in construction and reduction of quasi-median networks. We describe a novel method of generating quasi-median networks that uses all characters, both binary and multistate, without imposing an arbitrary ordering of the multistate partitions. We also describe a pruning mechanism which maintains at least one shortest path between observed sequences, displaying the underlying relations between all pairs of sequences while maintaining a connected graph. Application of this approach to 5S rDNA sequence data from sea beet produced a pruned network within which genetic isolation between populations by distance was evident, demonstrating the value of this approach for exploration of evolutionary relationships.
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影响因子：
10.7
作者：
Bryant, D;Moulton, V
通讯作者：
Moulton, V
影响因子：
3.8
作者：
Raybould, AF;Mogg, RJ;Clarke, RT
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16.8
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影响因子：
1.1
作者：
Bandelt, HJ;Huber, KT;Moulton, V
通讯作者：
Moulton, V
影响因子：
3.8
作者：
Raybould, AF;Mogg, RJ;Clarke, RT
通讯作者：
Clarke, RT