Data from: Combined analysis of extant Rhynchonellida (Brachiopoda) using morphological and molecular data

Independent molecular and morphological phylogenetic analyses have often produced discordant results for certain groups which, for fossil-rich groups, raises the possibility that morphological data might mislead in those groups for which we depend upon morphology the most. Rhynchonellide brachiopods, with more than 500 extinct genera but only 19 extant genera represented today, provide an opportunity to explore the factors that produce contentious phylogenetic signal across datasets, as previous phylogenetic hypotheses generated from molecular sequence data bear little agreement with those constructed using morphological characters. Using a revised matrix of 66 morphological characters, and published ribosomal DNA sequences, we performed a series of combined phylogenetic analyses to identify conflicting phylogenetic signals. We completed a series of parsimony-based and Bayesian analyses, varying the data used, the taxa included, and the models used in the Bayesian analyses. We also performed simulation-based sensitivity analyses to assess whether the small size of the morphological data partition relative to the molecular data influenced the results of the combined analyses. In order to compare and contrast a large number of phylogenetic analyses and their resulting summary trees, we developed a measure for the incongruence between two topologies, and simultaneously ignore any differences in phylogenetic resolution. Phylogenetic hypotheses generated using only morphological characters differed amongst each other, and with previous analyses, while molecular-only and combined Bayesian analyses produced extremely similar topologies. Characters historically associated with traditional classification in the Rhynchonellida have very low consistency indices on the topology preferred by the combined Bayesian analyses. Overall, this casts doubt on the use of morphological systematics to resolve relationships among the crown rhynchonellide brachiopods. However, expanding our dataset to a larger number of extinct taxa with intermediate morphologies is necessary to exclude the possibility that the morphology of extant taxa is not dominated by convergence along long branches.

针对多个类群开展的独立分子与形态学系统发育分析时常得出相悖结果；对于化石记录丰富的类群而言，这意味着在我们最为依赖形态学数据的类群中，形态学数据可能存在误导性。穿孔贝目腕足动物（Rhynchonellide brachiopods）现已知有超过500个灭绝属，但现今仅存19个属，为探究不同数据集间产生争议性系统发育信号的成因提供了理想研究对象——此前基于分子序列数据构建的系统发育假说，与利用形态学特征得到的结果几乎毫无共识。本研究使用经过修订的66项形态学特征矩阵，结合已发表的核糖体DNA序列，开展了一系列联合系统发育分析以识别冲突的系统发育信号。我们完成了多组基于简约法和贝叶斯的分析，调整了所用数据、纳入类群以及贝叶斯分析采用的演化模型。此外，我们还开展了基于模拟的敏感性分析，以评估相较于分子数据分区，形态学数据分区规模较小是否会对联合分析结果产生影响。为对比大量系统发育分析及其生成的总结树，我们构建了一种衡量两个拓扑结构间不一致性的指标，同时忽略系统发育分辨率上的差异。仅使用形态学特征生成的系统发育假说不仅彼此间存在分歧，与既往分析结果也不尽一致；而仅基于分子数据的分析与联合数据分析的贝叶斯分析所得到的拓扑结构高度相似。在联合贝叶斯分析所支持的拓扑结构上，与穿孔贝目传统分类体系相关的经典形态学特征，其一致性指数极低。综上，这一结果对利用形态学系统学方法解决冠群穿孔贝目腕足动物的系统发育关系提出了质疑。不过，若要排除现生类群的形态特征未受长支趋同演化主导这一可能性，我们需要将数据集扩展至包含更多具有中间形态的灭绝类群。