Data from: Consensus and confusion in Molluscan trees: evaluating morphological and molecular phylogenies

Molluscs are the most morphologically disparate living animal phylum, they have diversified into all habitats, and have a deep fossil record. Monophyly and identity of their eight living classes is undisputed, but relationships between these groups and patterns of their early radiation have remained elusive. Arguments about traditional morphological phylogeny focus on a small number of topological concepts but often without regard to proximity of the individual classes. In contrast, molecular studies have proposed a number of radically different, inherently contradictory, and controversial sister-relationships. Here, we assembled a dataset of 42 unique published trees describing molluscan interrelationships. We used these data to ask several questions about the state of resolution of molluscan phylogeny compared to a null model of the variation possible in random trees constructed from a monophyletic assemblage of eight terminals. Although 27 different unique trees have been proposed from morphological inference, the majority of these are not statistically different from each other. Within the available molecular topologies, only four studies to date have included the deep-sea class Monoplacophora; but 36.4% of all trees are not significantly different. Based on the totality of available evidence, certain patterns of relatedness among constituent taxa become clear. The inter-nodal distance is consistently close between a few taxon pairs, particularly supporting the relatedness of Monoplacophora and the chitons, Polyplacophora. Others have rare or non-existent occurrence of proximate placement, such as the vermiform Caudofoveata and Bivalvia. We also present supertrees derived from 2 data partitions and 3 methods, including all available molecular molluscan phylogenies, which will form the basis for future hypothesis testing. Our results have specific utility for guiding constructive research planning in order to better test relationships in molluscs as well as other problematic groups. Taxa with consistently proximate relationships should be the focus of a combined approach to address a concerted assessment of potential genetic and anatomical homology, while unequivocally distant taxa will make the most constructive choices for exemplar selection in higher-level phylogenomic analyses.

软体动物（Molluscs）是现生动物界中形态多样性最高的门类，其类群已辐射适应所有生境，且拥有悠久的化石记录。目前学界对其现生8个纲的单系性与分类界定已达成共识，但这些类群间的系统发育关系以及该门类早期辐射演化的模式仍悬而未决。传统形态学系统发育研究的争论多聚焦于少数拓扑学框架，但往往未考虑各单纲间的亲缘远近。与之形成鲜明对比的是，分子生物学研究提出了一系列截然不同、本质上相互矛盾且颇具争议的姊妹群关系。本研究整合了42套已发表的、互不重复的软体动物类群亲缘关系系统发育树数据集，以此为基础探讨软体动物系统发育学的解析现状，并与基于8个单系群终端类群构建的随机树变异零模型进行对比。尽管形态学推导已提出27套互不重复的系统发育树，但其中绝大多数在统计学上并无显著差异。在现有分子拓扑结构研究中，截至目前仅有4项研究纳入了深海类群试腔纲（Monoplacophora），但所有分子树中36.4%的拓扑结构在统计学上无显著差异。基于现有全部证据的综合分析，软体动物各类群间的部分亲缘关系模式已逐渐明晰：少数类群对的节点间距离始终较近，尤其支持试腔纲与多板纲（Polyplacophora，石鳖）的亲缘关系；而另有一些类群则几乎未出现或完全未出现近缘聚类的情况，比如蠕虫状的尾腔纲（Caudofoveata）与双壳纲（Bivalvia）。本研究还基于2种数据分区与3种构建方法，整合所有已发表的软体动物分子系统发育研究生成了超树，该超树将为后续的假说验证提供核心基础。本研究结果在指导针对性研究规划方面具有明确应用价值，可用于更好地解析软体动物及其他疑难类群的亲缘关系：对于始终呈现近缘关系的类群，应采用联合研究策略开展协同评估，以验证其潜在的遗传与解剖学同源性；而明确存在远缘关系的类群，则可作为高阶系统基因组学分析中选择模式类群的最优参考。