Bininda-Emonds O R
Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom.
Mol Phylogenet Evol. 2000 Jul;16(1):113-26. doi: 10.1006/mpev.2000.0772.
Phylogenetic reconstruction has undergone numerous developments in tree selection criteria (e.g., phenetics, cladistics, maximum-likelihood), available data sources (morphology versus molecules, and subsets of the latter), and practical limits on study size. Together with study age, I examined the effects of these variables on inferences of phylogeny for the mammalian order Carnivora. The raw data comprised 274 source trees spread among 13 carnivore taxa (generally families), which I divided into categories for each variable and combined using the supertree technique matrix representation with parsimony analysis. Incongruence between the resultant tree topologies or the underlying data was assessed using four comparison measures, each with slightly different properties: the triplet measures "do not conflict" and "explicitly agree," the partition metric, and the incongruence length difference metric. Except for a few cases reflecting historical problem areas in carnivore systematics, no significant differences in incongruence levels were found among the different categories within each variable, between the variables themselves, or between the taxa. Thus, most estimates of carnivore phylogeny cannot be distinguished from one another (and may even point toward the same solution) regardless of the methodology or data source employed. This conclusion held regardless of the comparison measure used.
系统发育重建在树选择标准（如数值分类学、分支系统学、最大似然法）、可用数据源（形态学与分子数据，以及分子数据的子集）和研究规模的实际限制方面经历了众多发展。我结合研究年代，研究了这些变量对食肉目哺乳动物系统发育推断的影响。原始数据包括分布在13个食肉动物分类单元（通常为科）中的274棵源树，我将其按每个变量进行分类，并使用简约分析的超树技术矩阵表示法进行组合。使用四种比较方法评估所得树形拓扑结构或基础数据之间的不一致性，每种方法的属性略有不同：三元组度量“不冲突”和“明确一致”、划分度量以及不一致长度差异度量。除了少数反映食肉动物系统学中历史问题区域的情况外，在每个变量内的不同类别之间、变量本身之间或分类单元之间，未发现不一致水平存在显著差异。因此，无论采用何种方法或数据源，大多数食肉动物系统发育的估计结果都无法相互区分（甚至可能指向相同的解决方案）。无论使用何种比较方法，这一结论都成立。
