Data from: The phylogenetic trunk: maximal inclusion of taxa with missing data in an analysis of the Lepospondyli (Vertebrata, Tetrapoda)

The importance of fossils to phylogenetic reconstruction is well established. However, analyses of fossil data sets are confounded by problems related to the less complete nature of the specimens. Taxa that are incompletely known are problematic because of the uncertainty of their placement within a tree, leading to a proliferation of most parsimonious solutions and wild card behavior. Problematic taxa are commonly deleted based on a priori criteria of completeness. Paradoxically, a taxon's problematic behavior is tree dependent, and levels of completeness are not directly associated with problematic behavior. Exclusion of taxa based on completeness eliminates real character conflict and, by not allowing incomplete taxa to determine tree topology, the phylogenetic hypothesis is diminished. The phylogenetic trunk approach is proposed to allow optimization of taxonomic inclusion and tree stability. This method is used in an analysis of the Paleozoic Lepospondyli. A single most parsimonious tree, or trunk, is found after removal of one taxon identified as being problematic. The 38 trees found one additional step from this primary trunk are reduced to two by removal of one additional taxon. These trunks are compared to the trees found by excluding taxa with various degrees of completeness. Effects of incomplete taxa are explored in light of the trunk. Correlated characters associated with limblessness are discussed regarding the assumption of character independence, but inclusion of intermediate taxa is found to be the single best method for breaking down long branches.化石对于系统发育重建（phylogenetic reconstruction）的重要性已得到学界广泛认可。然而，化石数据集的分析却因标本保存完整性不足的问题而受到干扰。对于信息不完全的分类群（taxon）而言，其在系统发育树中的系统位置存在不确定性，这会导致最简约树数量激增并引发随意摆位现象。当前学界通常依据完整性的先验标准剔除存在问题的分类群。但矛盾的是，某一分类群的随意摆位行为依赖于具体的系统发育树，且分类群的完整性水平与其是否表现出此类问题行为并无直接关联。基于完整性标准剔除分类群，会丢失真实的性状冲突信号；若不允许信息不完全的分类群参与确定系统发育树的拓扑结构，则会削弱所构建的系统发育假说的可信度。为此，本文提出系统发育主干法（phylogenetic trunk approach），以优化分类群的纳入策略并提升系统发育树的稳定性。该方法被应用于古生代壳椎亚纲（Lepospondyli）的系统发育分析：研究人员首先剔除1个被判定为存在问题的分类群，得到唯一一棵最简约树，即系统发育主干树；在该主干树基础上多1个进化步数的38棵树，可通过再剔除1个分类群缩减为2棵。随后将这些主干树与依据不同完整性程度剔除分类群所得到的系统发育树进行对比分析。同时，基于系统发育主干法探讨了信息不完全分类群对分析结果的影响，并围绕性状独立性假设讨论了与无肢性相关的关联性状；研究最终发现，纳入中间过渡分类群是打破长分支效应的最优单一方法。