Stability of characters and construction of phylogenetic trees.
Stability of characters and construction of phylogenetic trees.
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性状稳定性和系统发育树的构建。
DOI：
10.1089/cmb.2007.r001
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发表时间：
2007
期刊：
影响因子：
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通讯作者：
Przytycka,Teresa
中科院分区：
文献类型：
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作者：
Przytycka,Teresa
简约法通过最小化解释观察到的性状状态所需的性状变化来推断系统发育树。从简约方法的适用性来看，评估用于推断系统发育的特征是否可能提供正确的树是很重要的。我们引入了一个图理论表征，它有助于评估给定的字符集是否适合与简约方法一起使用。给定一组字符和一组分类群，我们构造了一个称为字符重叠图的网络。我们展示了适合在简约方法中使用的字符的字符重叠图的特征是被称为漏洞的子网的显着代表性不足，并为这一观察结果提供了验证。这一特征解释了使用简约方法对某些特征（如蛋白质结构域）构建进化树的成功，而对其他特征（如内含子）则缺乏这种成功。在后一种情况下，对直接应用简约方法的障碍的理解使我们找到了一种检测不一致和/或噪声数据的新方法。也就是说，我们引入了稳定字符的概念，它与众所周知的成对兼容字符的概念相似，但限制较少。这种方法在内含子上的应用产生了与腔瘤假说一致的进化树。
Parsimony methods infer phylogenetic trees by minimizing number of character changes required to explain observed character states. From the perspective of applicability of parsimony methods, it is important to assess whether the characters used to infer phylogeny are likely to provide a correct tree. We introduce a graph theoretical characterization that helps to assess whether given set of characters is appropriate to use with parsimony methods. Given a set of characters and a set of taxa, we construct a network called character overlap graph. We show that the character overlap graph for characters that are appropriate to use in parsimony methods is characterized by significant under-representation of subnetworks known as holes, and provide a validation for this observation. This characterization explains success in constructing evolutionary trees using parsimony method for some characters (e.g., protein domains) and lack of such success for other characters (e.g., introns). In the latter case, the understanding of obstacles to applying parsimony methods in a direct way has lead us to a new approach for detecting inconsistent and/or noisy data. Namely, we introduce the concept of stable characters which is similar but less restrictive than the well known concept of pairwise compatible characters. Application of this approach to introns produces the evolutionary tree consistent with the Coelomata hypothesis.