Robust analysis of phylogenetic tree space

Phylogenetic analyses often produce large numbers of trees. Mapping trees’ distribution in “tree space” can illuminate the behavior and performance of search strategies, reveal distinct clusters of optimal trees, and expose differences between different data sources or phylogenetic methods—but the high-dimensional spaces defined by metric distances are necessarily distorted when represented in fewer dimensions. Here, I explore the consequences of this transformation in phylogenetic search results from 128 morphological data sets, using stratigraphic congruence—a complementary aspect of tree similarity—to evaluate the utility of low-dimensional mappings. I find that phylogenetic similarities between cladograms are most accurately depicted in tree spaces derived from information-theoretic tree distances or the quartet distance. Robinson–Foulds tree spaces exhibit prominent distortions and often fail to group trees according to phylogenetic similarity, whereas the strong influence of tree ...

系统发育分析（phylogenetic analyses）常产生大量树结构。将树在“树空间（tree space）”中的分布进行映射，可阐明搜索策略的行为与性能、揭示最优树的不同聚类，并暴露不同数据源或系统发育方法（phylogenetic methods）间的差异——但由度量距离（metric distances）定义的高维空间在以较少维度表示时必然会发生扭曲。本文基于128个形态学数据集（morphological data sets）的系统发育搜索结果，探究这种变换的后果；通过地层一致性（stratigraphic congruence）——树相似性（tree similarity）的一个互补方面——评估低维映射（low-dimensional mappings）的效用。研究发现，分支图（cladograms）间的系统发育相似性在基于信息论树距离（information-theoretic tree distances）或四分体距离（quartet distance）的树空间中得到最准确的呈现；Robinson–Foulds树空间存在显著扭曲，且常无法依据系统发育相似性对树进行分组，而树的强烈影响...