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

Mollusks 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. 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. The supertrees presented here were not constructed to provide yet another hypothesis of molluscan relationships, but rather to algorithmically evaluate the relationships present in the disparate published topologies. Based on the totality of available evidence, certain patterns of relatedness among constituent taxa become clear. The internodal distance is consistently short between a few taxon pairs, particularly supporting the relatedness of Monoplacophora and the chitons, Polyplacophora. Other taxon pairs are rarely or never found in close proximity, such as the vermiform Caudofoveata and Bivalvia. Our results have specific utility for guiding constructive research planning in order to better test relationships in Mollusca as well as other problematic groups. Taxa with consistently proximate relationships should be the focus of a combined approach in 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.

软体动物门（Mollusca）是现存动物界中形态差异最为显著的类群，其物种已辐射分化至所有生境，并拥有漫长的化石记录。该类群现存的8个纲的单系性与分类界定均无争议，但这些类群间的系统发育关系以及早期辐射演化模式始终悬而未决。传统形态学系统发育研究的争论多围绕少数拓扑学概念展开，但往往未考虑各纲类群间的亲缘远近关系。与之相反，分子生物学研究则提出了大量截然不同、本质上相互矛盾且颇具争议的姊妹群关系假说。本研究整合了42份已发表的、互不重复的软体动物系统发育关系树数据集。本研究借助这些数据集，以由8个终端分类单元构成的单系集合所构建的随机树变异零模型为参照，针对软体动物系统发育的解析现状提出了若干科学问题。尽管通过形态学推演已提出27株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。在已发表的分子系统发育拓扑结构中，截至目前仅有4项研究纳入了深海类群单板纲（Monoplacophora）；但所有系统发育树中有36.4%在统计学上无显著差异。本研究还构建了基于2种数据分区与3种分析方法的超树，整合了所有已发表的软体动物分子系统发育研究结果，该超树将为后续的假说验证提供研究基础。本次构建的超树并非旨在提出新的软体动物亲缘关系假说，而是通过算法评估已发表的各类系统发育拓扑结构中所呈现的类群间亲缘关系。基于现有全部证据，软体动物组成类群间的部分亲缘关系模式已逐渐明晰。若干分类单元对之间的节点间距始终较短，这尤其支持单板纲（Monoplacophora）与多板纲（Polyplacophora，石鳖）之间的亲缘关系。另有一些分类单元对则极少甚至从未被发现存在较近亲缘关系，比如蠕形的尾腔纲（Caudofoveata）与双壳纲（Bivalvia）。本研究结果可为构建针对性的研究规划提供具体参考，以更好地验证软体动物门以及其他存在分类争议的类群的系统发育关系。亲缘关系始终较近的类群，可作为联合分析的重点对象，以协同评估其潜在的遗传与解剖学同源性；而亲缘关系明确较远的类群，则可作为高阶系统发育基因组学分析中样本选择的最优参照。