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.

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（annelid），具有重要的生态与经济价值。蚯蚓多为陆生底内动物，其自然扩散能力较弱。因此，蚯蚓近乎全球的分布格局，反映出其古老且可能极为复杂的演化历史。尽管学界对巨蚓类的研究已有悠久历史，但其各大支系内部及支系间的系统发育关系仍未得到明确解析。
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开展解析。本研究的数据覆盖了几乎所有现生蚯蚓科类群，同时纳入了非巨蚓类的“蚯蚓”——巨形蚓科（Moniligastridae）代表物种。我们通过一系列经差异化过滤的数据矩阵与分析方案，探究了数据分区、缺失数据、碱基组成与分支长度异质性以及外类群选取对系统发育分析结果的影响。
结果与讨论：无论分析方法存在何种差异，我们均获得了一致且得到强力支持的内类群拓扑结构。该拓扑结构支持两大蚯蚓支系，每一支系均包含北半球亚支与南半球亚支。分化时间分析结果与“南北分异格局源于超大陆盘古大陆（Pangaea）解体”的假说高度一致。
结论：本研究结果支持近期提出的对经典蚯蚓系统发育认知的若干修订，揭示了两大反映盘古大陆分布格局的支系，并为蚯蚓演化关系研究提出了新的科学问题。