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

Background: Earthworms (Crassiclitellata) are 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, another terrestrial annelid group thought to be closely related to Crassiclitellata. 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：蚯蚓（Crassiclitellata）是一类多样性丰富的环节动物（Annelida），兼具重要的生态与经济价值。蚯蚓主要为陆生底内动物，自然扩散能力相对有限，因此其近乎全球的分布格局，实则反映出一段古老且极可能复杂的演化历史。尽管学界对该类群的研究已有悠久历史，但其主要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套全新转录组（transcriptome）数据与公开可用的转录组数据，对蚯蚓（Crassiclitellata）的系统发育关系展开评估。本研究的数据覆盖了几乎所有现存蚯蚓科类群，同时纳入了巨蚓科（Moniligastridae）的代表类群——该类群是另一类被认为与蚯蚓（Crassiclitellata）亲缘关系密切的陆生环节动物。我们采用一系列经过差异化过滤的数据矩阵与分析方法，系统探究了数据分区、缺失数据、组成异质性与支系长度异质性，以及外类群（outgroup）选取对系统发育分析结果的影响。 结果与讨论：无论采用何种分析方法，本研究均得到了一致且支持度极高的内类群（ingroup）拓扑结构。该拓扑结构支持将蚯蚓划分为两大主要支系，每一支系均分别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相关假说高度契合：即南北半球的支系分化，源于超级大陆盘古大陆（Pangaea）的解体。 结论：本研究结果支持近期多项针对蚯蚓经典系统发育认知的修订方案，揭示了两大与盘古大陆分布格局相符的主要支系，并为蚯蚓演化关系的后续研究提出了新的科学问题。