Homoplasy and Clade Support
Homoplasy and Clade Support
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DOI：
10.1093/sysbio/syp019
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发表时间：
2009-04-01
影响因子：
6.5
通讯作者：
McGuire, Jimmy A.
中科院分区：
文献类型：
--
作者：
Brandley, Matthew C.;Warren, Dan L.;McGuire, Jimmy A.
区分系统发育信号与同源性（类群之间的共同相似性不是由共同祖先产生的）是任何系统发育研究的隐含目标。大量的同质性可能会干扰准确的树推断，并且可以预期，包括自举比例和贝叶斯后验概率在内的常见枝支持度量也应该在一定程度上受到同质性的影响。通过对38个经验数据集的数据模拟和分析，我们表明，大量的同质性将以依赖于支系大小的方式影响支系支持的所有测量。更具体地说，在无根树拓扑结构中，相对于中等大小的分支，最小的分类单元双分区将得到更高的支持，即使所有分支都得到相同数量的数据支持。我们确定了这种影响的最终原因是在bootstrap重采样和Markov chain Monte Carlo （MCMC）拓扑搜索过程中包含随机树（由于同质性），以及小分类群双分区（即2或3个分类群）相对于大分类群双分区的相对比例较高。然而，使用基于显式模型的方法，特别是贝叶斯MCMC方法，即使存在非常少量的系统发育信号，也能有效地克服这种进化支大小效应。我们开发了一个事后统计，支系差异指数（CDI），以衡量支系大小效应的相对大小及其统计显著性。在模拟和经验数据的分析中，CDI值表明贝叶斯MCMC分析比最大简约和最大似然自举分析更有可能估计出与进化支大小无关的进化支支持值，因此受同质性的影响较小。这些结果可能与“深层”系统发育问题特别相关，比如重建生命之树，因为它们代表了时间和进化速度的最大可能极端，这是导致同质性的两个因素。
Distinguishing phylogenetic signal from homoplasy (shared similarities among taxa that do not arise by common ancestry) is an implicit goal of any phylogenetic study. Large amounts of homoplasy can interfere with accurate tree inference, and it is expected that common measures of clade support, including bootstrap proportions and Bayesian posterior probabilities, should also be impacted to some degree by homoplasy. Through data simulation and analysis of 38 empirical data sets, we show that high amounts of homoplasy will affect all measures of clade support in a manner that is dependent on clade size. More specifically, the smallest taxon bipartitions in an unrooted tree topology will receive higher support relative to clades of intermediate sizes, even when all clades are supported by the same amount of data. We determine that the ultimate causes of this effect are the inclusion of random trees (due to homoplasy) during bootstrap resampling and Markov chain Monte Carlo (MCMC) topology searching and the higher relative proportion of small taxon bipartitions (i.e., 2 or 3 taxa) to larger sized bipartitions. However, the use of explicit model-based methods, especially Bayesian MCMC methods, effectively overcomes this clade size effect even when very small amounts of phylogenetic signal are present. We develop a post hoc statistic, the clade disparity index (CDI), to measure both the relative magnitude of the clade size effect and its statistical significance. In analyses of both simulated and empirical data, CDI values indicate that Bayesian MCMC analyses are substantially more likely to estimate clade support values that are uncorrelated with clade size than are maximum parsimony and maximum likelihood bootstrap analyses and thus less affected by homoplasy. These results may be especially relevant to "deep" phylogenetic problems, such as reconstructing the tree of life, as they represent the largest possible extremes of time and evolutionary rates, 2 factors that cause homoplasy.