Data from: Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

Gastropods are a highly diverse clade of molluscs that includes many familiar animals, such as limpets, snails, slugs, and sea slugs. It is one of the most abundant groups of animals in the sea and the only molluscan lineage that has successfully colonised land. Yet the relationships among and within its constituent clades have remained in flux for over a century of morphological, anatomical and molecular study. Here we re-evaluate gastropod phylogenetic relationships by collecting new transcriptome data for 40 species and analysing them in combination with publicly available genomes and transcriptomes. Our datasets include all five main gastropod clades: Patellogastropoda, Vetigastropoda, Neritimorpha, Caenogastropoda and Heterobranchia. We use two different methods to assign orthology, subsample each of these matrices into three increasingly dense subsets, and analyse all six of these supermatrices with two different models of molecular evolution. All twelve analyses yield the same unrooted network connecting the five major gastropod lineages. This reduces deep gastropod phylogeny to three alternative rooting hypotheses. These results reject the prevalent hypothesis of gastropod phylogeny, Orthogastropoda. Our dated tree is congruent with a possible end-Permian recovery of some gastropod clades, namely Caenogastropoda and some Heterobranchia subclades.

腹足类（Gastropods）是一类高度多样的软体动物支系，涵盖诸多为人熟知的类群，如帽贝、蜗牛、蛞蝓以及海蛞蝓。它是海洋中物种丰度最高的动物类群之一，也是唯一成功登陆的软体动物支系。然而，一个多世纪以来，尽管已有形态学、解剖学与分子生物学相关研究，其内部各组成支系间的演化关系始终处于变动之中。
本研究通过采集40个物种的全新转录组数据，并结合公开可用的基因组与转录组数据，重新评估腹足类的系统发育关系。我们的数据集涵盖腹足类全部5个主要支系：笠形腹足亚纲（Patellogastropoda）、古腹足亚纲（Vetigastropoda）、蜑形亚纲（Neritimorpha）、新进腹足亚纲（Caenogastropoda）以及异鳃亚纲（Heterobranchia）。我们采用两种不同的方法进行直系同源聚类，将每个矩阵亚采样为三个密度逐渐升高的子集，并使用两种不同的分子演化模型对全部六个超级矩阵开展分析。所有十二项分析均得到了连接五个主要腹足类支系的一致无根网络。这将腹足类深层系统发育的候选假说缩减为三种可供选择的定根假说。本研究结果驳斥了当前主流的腹足类系统发育假说——直腹足类假说（Orthogastropoda）。我们的定年树与部分腹足类支系（即新进腹足亚纲及部分异鳃亚纲支系）在二叠纪末的复苏事件相吻合。