Majority-rule reduced consensus trees and their use in bootstrapping
Majority-rule reduced consensus trees and their use in bootstrapping
复制标题
DOI：
10.1093/oxfordjournals.molbev.a025604
复制
发表时间：
1996-03-01
影响因子：
10.7
通讯作者：
Wilkinson, M
中科院分区：
文献类型：
--
作者：
Wilkinson, M
引导分析通常用多数规则组件共识树进行总结。这种共识方法基于复制的组件，并且像所有组件共识方法一样，它对树之间的其他类型的协议不敏感。最近开发的简化共识方法可用于总结多棵树之间假设的系统发育关系的更多共识。新方法是“严格的”，因为它们要求所有被比较的树之间达成一致，以便在共识树中表示任何关系。描述了多数规则简化共识方法，并通过假设和真实示例说明了它们在引导分析中的使用。新方法提供了所有 n-taxon 语句/分区的 bootstrap 比例的摘要，并有助于识别由高 bootstrap 比例支持的关系假设，尽管缺乏对特定组件或进化枝的支持。实际上，多数规则简化共识配置文件可能包含许多树。可以通过对所包含的树的最小引导比例和/或基数的约束来减小配置文件的大小。也可以从配置文件中事后选择多数规则简化共识树。还描述了使用广泛使用的系统发育推理软件提供的分区表或树修剪选项的多数规则简化共识方法的替代方法。这些方法旨在生成引导分析的信息更丰富的摘要，从而促进对复杂系统发育假设的优缺点进行更明智的评估。
Bootstrap analyses are usually summarized with majority-rule component consensus trees. This consensus method is based on replicated components and, like all component consensus methods, it is insensitive to other kinds of agreement between trees. Recently developed reduced consensus methods can be used to summarize much additional agreement on hypothesised phylogenetic relationships among multiple trees. The new methods are ''strict'' in the sense that they require agreement among all the trees being compared for any relationships to be represented in a consensus tree. Majority-rule reduced consensus methods are described and their use in bootstrap analyses is illustrated with a hypothetical and a real example. The new methods provide summaries of the bootstrap proportions of all n-taxon statements/partitions and facilitate the identification of hypotheses of relationships that are supported by high bootstrap proportions, in spite of a lack of support for particular components or clades. In practice majority-rule reduced consensus profiles may contain many trees. The size of the profile can be reduced by constraints on minimal bootstrap proportions and/or cardinality of the included trees. Majority-rule reduced consensus trees can also be selected a posteriori from the profile. Surrogates to the majority-rule reduced consensus methods using partition tables or tree pruning options provided by widely used phylogenetic inference software are also described. The methods are designed to produce more informative summaries of bootstrap analyses and thereby foster more informed assessment of the strengths and weaknesses of complex phylogenetic hypotheses.