Bapst David W, Schreiber Holly A, Carlson Sandra J
Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
Penn Dixie Fossil Park and Nature Reserve, 3556 Lakeshore Rd, Ste. 210 Blasdell, NY 14219, USA.
Syst Biol. 2018 Jan 1;67(1):32-48. doi: 10.1093/sysbio/syx049.
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 among each other, and with previous analyses, whereas 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.
独立的分子系统发育分析和形态系统发育分析常常会对某些类群得出不一致的结果，对于化石丰富的类群而言，这就增加了一种可能性，即形态学数据可能会在那些我们最依赖形态学的类群中产生误导。小嘴贝纲腕足动物有500多个已灭绝的属，但如今仅存19个属，这为探究跨数据集产生有争议的系统发育信号的因素提供了一个机会，因为先前从分子序列数据生成的系统发育假说与使用形态特征构建的假说几乎没有一致性。我们使用一个经过修订的包含66个形态特征的矩阵以及已发表的核糖体DNA序列，进行了一系列联合系统发育分析，以识别相互冲突的系统发育信号。我们完成了一系列基于简约法和贝叶斯法的分析，改变了所使用的数据、所包含的分类单元以及贝叶斯分析中使用的模型。我们还进行了基于模拟的敏感性分析，以评估相对于分子数据而言形态学数据分区的小尺寸是否影响了联合分析的结果。为了比较和对比大量的系统发育分析及其所得的总结树，我们开发了一种衡量两种拓扑结构之间不一致性的方法，同时忽略系统发育分辨率的任何差异。仅使用形态特征生成的系统发育假说彼此之间存在差异，并且与先前的分析也不同，而仅分子分析和联合贝叶斯分析产生了极其相似的拓扑结构。在联合贝叶斯分析所偏好的拓扑结构上，历史上与小嘴贝目的传统分类相关的特征具有非常低的一致性指数。总体而言，这对使用形态学系统分类学来解析冠小嘴贝纲腕足动物之间的关系提出了质疑。然而，有必要将我们的数据集扩展到更多具有中间形态的已灭绝分类单元，以排除现存分类单元的形态未被沿长分支的趋同现象主导的可能性。
