Data from: Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms

Background: Crassiclitellata, or earthworms, comprise a diverse group of annelids of substantial ecological and economic importance. Earthworms are primarily terrestrial infaunal animals, and as such are probably rather poor natural dispersers. Therefore, the near global distribution of earthworms reflects an old and likely complex evolutionary history. Despite a long-standing interest in Crassiclitellata, relationships among and within major clades remain unresolved. Methods: In this study, we evaluate crassiclitellate phylogenetic relationships using 38 new transcriptomes in combination with publicly available transcriptome data. Our data include representatives of nearly all extant earthworm families, and a representative of Moniligastridae, a non-crassiclitellate 'earthworm.' We use a series of differentially filtered data matrices and analyses to examine the effects of data partitioning, missing data, compositional and branch-length heterogeneity, and outgroup inclusion. Results and Discussion: We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology. The topology supports two major earthworm clades, each of which consists of a Northern Hemisphere subclade and a Southern Hemisphere subclade. Divergence time analysis results are concordant with the hypothesis that these north-south splits are the result of the breakup of the supercontinent Pangaea. Conclusions: These results support several recently proposed revisions to the classical understanding of earthworm phylogeny, reveal two major clades that seem to reflect Pangaean distributions, and raise new questions about earthworm evolutionary relationships.研究背景：巨蚓类（Crassiclitellata）俗称蚯蚓，是一类物种多样性丰富的环节动物类群，在生态系统服务与经济利用层面均具有重要价值。蚯蚓多为陆生底内动物，其自然扩散能力相对有限，因此其近乎全球的分布格局反映出一段古老且大概率复杂的演化历史。尽管学界对巨蚓类的研究已有较长历史，但主要演化支之间及内部的系统发育关系仍未得到明确解析。 研究方法：本研究结合38个全新转录组（transcriptome）数据与公开可用的转录组数据，对巨蚓类的系统发育关系进行解析。本研究的数据覆盖了几乎所有现生蚯蚓科类群，同时纳入1个链胃蚓科（Moniligastridae）类群——该类群属于非巨蚓类的“蚯蚓”。我们通过一系列经过差异化筛选的数据矩阵与分析方法，探究了数据分区、缺失数据、组成异质性与支长异质性以及外类群纳入对系统发育分析结果的影响。 结果与讨论：本研究得到了一致且高支持度的内类群系统发育拓扑结构，且该结果不受分析方法差异的影响。该拓扑结构支持蚯蚓分为两大主要演化支，每一支均包含一个北半球亚支与一个南半球亚支。分化时间分析结果与“南北分化源于超大陆盘古大陆（Pangaea）裂解”的假说相符。 研究结论：本研究结果支持近期多项针对蚯蚓系统发育经典认知的修订方案，揭示了两大与盘古大陆分布格局相关的主要演化支，并为蚯蚓演化关系研究提出了新的科学问题。