Which random processes describe the tree of life?: A large-scale study of phylogenetic tree imbalance
Which random processes describe the tree of life?: A large-scale study of phylogenetic tree imbalance
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DOI：
10.1080/10635150600889625
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发表时间：
2006-08-01
影响因子：
6.5
通讯作者：
Francois, Olivier
中科院分区：
文献类型：
--
作者：
Blum, Michael G. B.;Francois, Olivier
系统发育研究的激增不仅提供了生物多样性的清晰快照，而且使推断多样性是如何产生的成为可能(例如，见Purvis和Hector，2000；Harvey等人，1996；Nee等人，1996；Mace等人，2003)。为此，通过它们在系统发育树形状上的签名，研究了物种形成和灭绝率的变化(Mooers和Hed，1997)。这个问题非常重要，因为将随机模型与树木数据进行匹配将有助于理解潜在的宏观进化过程。虽然流行的观点认为它不能很好地代表系统发育，但最流行的系统发育树模型是Yule提出的分支过程，在这个过程中，谱系随机分裂(Yule，1924)。在这里，我们报告了使用Yule模型和其他几个模型对一个主要的已发表的系统发育数据库进行的研究。我们的结果证实了先前的观察结果，即Yule模型不足以描述系统发育树数据。此外，他们还支持这样一种假设，即许多树木与Aldous在1996年首次考虑的简单树枝分裂模型是一致的。对系统发育树形状的随机模型的分析始于1924年的Yule，在20世纪70年代中期由伍兹霍尔小组恢复(Raup等人，1973；古尔德等人，1977)。他们基于模型的方法得出的结论是，血统多样化的潜力各不相同。由于他们的工作，最近在理解上投入了很大的努力
The explosion of phylogenetic studies not only provides a clear snapshot of biodiversity, but also makes it possible to infer how the diversity has arisen (see, for example, Purvis and Hector, 2000; Harvey et al., 1996; Nee et al., 1996; Mace et al., 2003). To this aim, variation in speciation and extinction rates have been investigated through their signatures in the shapes of phylogenetic trees (Mooers and Heard, 1997). This issue is of great importance, as fitting stochastic models to tree data would help to understand underlying macroevolutionary processes. Although the prevailing view is that it does not represent phylogenies so well, the most popular model of phylogenetic trees is a branching process introduced by Yule, in which lineages split at random (Yule, 1924). Here we report the study of one major database of published phylogenies using the Yule model as well as several other models. Our results confirm the previous observation that the Yule model is inadequate to describe phylogenetic tree data. In addition, they support the hypothesis that many trees are consistent with a simple branch split model first considered by Aldous in 1996. The analysis of stochastic models of phylogenetic tree shape, which began with Yule in 1924, was revived in the mid-1970s by the Woods Hole Group (Raup et al., 1973; Gould et al., 1977). Their model-based approach yielded the conclusion that lineages have varied in their potential for diversification. As a result of their work, much effort has recently been placed on understanding