Clitellata is a major clade of Annelida comprising nearly all freshwater and terrestrial annelids as well as several marine species. We investigated clitellate phylogenetic relationships using transcriptomes sampled from 74 taxa (64 clitellates and 10 polychaetes), including multiple representatives of nearly all major clitellate higher taxa (Branchiobdellida, Capilloventridae, Crassiclitellata, Enchytraeidae, Haplotaxidae, Hirudinida, Lumbriculida, Moniligastridae, Naididae, Parvidrilidae, Phreodrilidae, Propappidae and Randiellidae). We used a number of filtered data matrices and phylogenetic analyses to examine the effects of data partitioning, missing data and compositional and branch‐length heterogeneity and used the resulting phylogenies for divergence time estimation and ancestral habitat reconstructions. All analyses and filtering methods produced a consistent, strongly supported topology in which (a) Enchytraeidae, Hirudinida, Hirudinea (here, Branchiobdellida plus Hirudinida), Lumbriculida, Lumbriculata (Lumbriculida plus Hirudinea), Phreodrilidae and Naididae are monophyletic, (b) a Parvidrilidae + Randiellidae clade is sister to the rest of Clitellata, (c) Phreodrilidae is sister to Naididae, (d) Haplotaxidae is non‐monophyletic, with some haplotaxids grouping with Crassiclitellata + Moniligastridae, (e) the Phreodrilidae + Naididae clade is sister to all other clitellates except Parvidrilidae + Randiellidae and Capilloventridae, and (f) Lumbriculata is sister to the Crassiclitellata + Moniligastridae + Haplotaxidae (in part) clade. Ancestral habitat reconstructions and divergence time analysis suggested that the most recent common ancestor of Clitellata lived in freshwater during the Devonian (419–359 million years ago) and that all major extant clitellate lineages arose over the next ~150 million years, with multiple lineages subsequently returning to marine habitats or invading land. This study provides a phylogenetic framework for further investigation of the geological, environmental and biotic forces and genomic changes that may have impacted clitellate evolution and enabled several major habitat transitions within this group.

中文翻译：

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系统生物学分析揭示了古生代辐射并支持淡水来源的带菌类无脊椎动物。

Clitellata是Annelida的主要进化枝，几乎包括所有淡水和陆生鱼类，以及几种海洋物种。我们使用从74个类群（64个小类和10个多毛类）中取样的转录组研究了种质系统发生的关系，包括几乎所有主要的小类高等分类群（Branchiobdellida，Capilloventridae，Crassiclitellata，Enchytraeidae，Haplotaxidae，Hirudinida，Naidstridae，Lundriculidae）的多个代表re科，Pro科和兰科。我们使用了许多过滤后的数据矩阵和系统发育分析来检查数据分区，丢失数据以及成分和分支长度异质性的影响，并将所得系统发育用于发散时间估计和祖先栖息地重建。祖先的栖息地重建和发散时间分析表明，克里特雷塔山脉的最新共同祖先生活在泥盆纪时期（419-359百万年前），在接下来的约1.5亿年里，所有主要现存的斜纹世系都出现了，随后又出现了多个世系返回海洋栖息地或入侵土地。这项研究为进一步研究可能影响气候演化并促成该群体内几个主要生境过渡的地质，环境和生物力以及基因组变化提供了系统发育框架。