Matsen Frederick A, Steel Mike
Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand.
Syst Biol. 2007 Oct;56(5):767-75. doi: 10.1080/10635150701627304.
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data are generated by a mixture model has stimulated considerable recent debate. Much of the controversy stems from simulations of mixture model data on a given tree topology for which reconstruction algorithms output a tree of a different topology; these findings were held up to show the shortcomings of particular tree reconstruction methods. In so doing, the underlying assumption was that mixture model data on one topology can be distinguished from data evolved on an unmixed tree of another topology given enough data and the "correct" method. Here we show that this assumption can be false. For biologists, our results imply that, for example, the combined data from two genes whose phylogenetic trees differ only in terms of branch lengths can perfectly fit a tree of a different topology.
系统发育混合模型用于模拟数据中常见的非均匀分子进化。在混合模型生成基础数据的情况下,系统发育重建方法的性能引发了近期相当多的争论。许多争议源于在给定树拓扑结构上对混合模型数据的模拟,对于这些模拟,重建算法输出了不同拓扑结构的树;这些发现被用来表明特定树重建方法的缺点。这样做时,潜在的假设是,给定足够的数据和“正确”的方法,一种拓扑结构上的混合模型数据可以与在另一种拓扑结构的非混合树上进化的数据区分开来。在这里,我们表明这个假设可能是错误的。对于生物学家来说,我们的结果意味着,例如,来自两个系统发育树仅在分支长度方面不同的基因的组合数据可以完美地拟合不同拓扑结构的树。