Data from: Resolving the evolutionary relationships of molluscs with phylogenomic tools

Molluscs (snails, octopuses, clams, and relatives) have great body plan disparity, and among animals only arthropods surpass them in species number. This diversity has made Mollusca one of the best-studied groups of animals, yet their evolutionary relationships remain poorly resolved. Open questions have important implications for the origin of Mollusca and morphological evolution within the group. These include whether the shell-less vermiform aplacophoran molluscs diverged prior to the origin of the shelled molluscs (Conchifera), or secondarily lost their shell. Monoplacophora were not included in molecular studies until recently , when it was proposed that they constitute a clade with chitons named Serialia, reflecting the serial repetition of body organs in both groups. Attempts to understand the early evolution of molluscs become even more complex when considering the large diversity of Cambrian fossils. These can have multiple dorsal shell plates and sclerites, or be shell-less but with a typical molluscan radula and serially repeated gills. In order to better resolve the relationships among molluscs we generated transcriptome data for 15 molluscs that, in combination with existing data, represent for the first time all major molluscan groups. We analysed multiple data sets containing up to 216,402 sites and 1185 gene regions using multiple models and methods. Our results support a clade Aculifera, containing the three molluscan groups with spicules but without true shells, as well as the monophyly of Conchifera—the shelled molluscs. Monoplacophora are not the sister group to other Conchifera, but constitute the sister group to the highly modified cephalopods. Strong support is found for a clade comprised of Scaphopoda (tusk shells), Gastropoda, and Bivalvia, with most analyses placing Scaphopoda and Gastropoda as sister groups. This well-resolved tree will constitute a framework for further studies in mollusc evolution, development and anatomy.

软体动物（Mollusca）涵盖蜗牛、章鱼、蛤蜊及其近缘类群，其躯体构型多样性极高；在动物界中，仅节肢动物（Arthropoda）的物种数量超越软体动物。这种多样性使得软体动物成为研究最为深入的动物类群之一，但其演化亲缘关系至今仍未得到清晰解析。现存的诸多悬而未决的问题，对软体动物的起源及其类群内部的形态演化具有重要研究价值。这些问题包括：无壳、蠕虫状的无板纲（Aplacophora）软体动物，究竟是在有壳类（Conchifera）起源之前就已分化，还是次生丢失了外壳？直至近年，单板纲（Monoplacophora）才被纳入分子生物学研究；当时有研究提出，单板纲与多板纲（石鳖，Polyplacophora）共同构成一个演化支，被命名为串行类（Serialia），这一分类反映了两类群体内器官的串行重复特征。若考虑到寒武纪化石类群的高度多样性，解析软体动物早期演化的尝试将变得更为复杂。这些化石类群可能拥有多块背侧壳板与骨片（sclerites），也可能无壳，但具备典型的软体动物齿舌（radula）与串行重复的鳃。为了更好地解析软体动物的亲缘关系，本研究对15种软体动物进行了转录组测序；结合已有数据后，本次研究首次覆盖了软体动物门的所有主要类群。本研究采用多种模型与分析方法，对包含最多216402个位点、1185个基因区域的多套数据集进行了系统发育分析。研究结果支持有针类（Aculifera）演化支的存在，该类群包含3类具有骨针但无真正外壳的软体动物类群；同时也证实了有壳类（Conchifera，即带壳软体动物）的单系性。单板纲并非其他有壳类的姊妹群，而是与高度特化的头足类（Cephalopoda）构成姊妹群。本研究为掘足纲（Scaphopoda，又称象牙贝）、腹足纲（Gastropoda）与双壳纲（Bivalvia）构成的演化支提供了强有力的支持，多数分析结果显示掘足纲与腹足纲为姊妹群。这一解析度较高的系统发育树，将为软体动物演化、发育与解剖学的后续研究提供核心框架。