taxonID	type	description	language	source
B62A87D64F0D4F4E066BFFD7FD63C6EB.taxon	description	By and large, relationships among the outgroups, and between them and Clitellata, are inconsistently resolved and with low support (Figure 1 and Supplementary Materials %. Nevertheless, in ten of the twelve RAxML BKL trees, the sister group to Clitellata is a strongly supported pair comprising Hrabeiella periglandulata and Aeolosoma sp. In the 75 % TreSpEx-and-BaCoCa-filtered RAxML and PhyloBayes trees, the polychaete Sternapsis is recovered as sister to Aeolosoma + Hrabeiella, but with low bootstrap support (59 %% in the BKL tree.	en	Erséus, Christer, Williams, Bronwyn W., Horn, Kevin M., Halanych, Kenneth M., Santos, Scott R., James, Samuel W., Châtelliers, Michel Creuzé des, Anderson, Frank E. (2020): Phylogenomic analyses reveal a Palaeozoic radiation and support a freshwater origin for clitellate annelids. Zoologica Scripta 49 (5): 614-640, DOI: 10.1111/zsc.12426, URL: https://doi.org/10.1111/zsc.12426
B62A87D64F0D4F4E0533FE1FFAD3C136.taxon	description	The 15 species analysed represent six of the ten naidid subfamilies recognized by the WoRMS database (www. marinespecies. org %, that is, excluding Opistocystinae, Telmatodrilinae and Rhyacodriloidinae, as well as the enigmatic Branchiura (Branchiurinae, likely to be Tubificinae; see Erséus, Envall, Marchese, & Gustavsson, 2010; Martin, Martínez-Ansemil, & Sambugar, 2010 % and Paranadrilus, the latter of which with unsettled classification. Our naidid lineage is fully resolved, with all internal nodes maximally supported (Figure 1 %. Analyses of all data matrices yielded this topology, with one exception — on the 75 % MARE-filtered tree, Albanidrilus sp. was recovered as sister to Limnodriloides sp., but on all other trees, it was sister to Olavius + Heterodrilus. Pristininae (Pristina % and Limnodriloidinae (Limnodriloides % are represented only by one species each. Naidinae (Paranais and Chaetogaster % and Tubificinae (Aulodrilus, Troglodrilus and Potamothrix % are monophyletic, whereas Phallodrilinae (Bathydrilus, Olavius and Albanidrilus % and Rhyacodrilinae (Rhyacodrilus, Heronidrilus, Bothrioneurum and Heterodrilus % are not. Members of Rhyacodrilinae (as currently defined % are found in three positions: Heronidrilus and Bothrioneurum form the sister to the rest of Naididae, while Rhyacodrilus is sister to Naidinae, and Heterodrilus is sister to a part of Phallodrilinae. Pristininae is sister to Rhyacodrilinae s. str. (i. e. here Rhyacodrilus only % + Naidinae, and Tubificinae is sister to Limnodriloidinae. Bathydrilus, previously regarded as a member of Phallodrilinae, is placed as sister to a clade containing the sister groups [Heterodrilus + Phallodrilinae (part %] and [Limnodriloidinae + Tubificinae].	en	Erséus, Christer, Williams, Bronwyn W., Horn, Kevin M., Halanych, Kenneth M., Santos, Scott R., James, Samuel W., Châtelliers, Michel Creuzé des, Anderson, Frank E. (2020): Phylogenomic analyses reveal a Palaeozoic radiation and support a freshwater origin for clitellate annelids. Zoologica Scripta 49 (5): 614-640, DOI: 10.1111/zsc.12426, URL: https://doi.org/10.1111/zsc.12426
B62A87D64F0D4F480533F9DCFE50C173.taxon	description	These two families are generally recovered as sisters (e. g. Figure 1 %, but with low support, and in a few trees, Propappus is sister either to a clade comprising Lumbriculida, Hirudinea, Crassiclitellata and two haplotaxids (Figure S 3 % or to a larger clade comprising the aforementioned clade plus Enchytraeidae (Supplementary Materials; Figures S 1 and S 5 %. Propappidae is monotypic (= Propappus %, while the four genera representing Enchytraeidae (out of its> 30 genera % are resolved. However, Guaranidrilus is usually recovered as sister to Grania + Enchytraeus (Figure 1 %, but sometimes recovered as sister to Mesenchytraeus (e. g. Figures 2 and 3; Supplementary Materials %.	en	Erséus, Christer, Williams, Bronwyn W., Horn, Kevin M., Halanych, Kenneth M., Santos, Scott R., James, Samuel W., Châtelliers, Michel Creuzé des, Anderson, Frank E. (2020): Phylogenomic analyses reveal a Palaeozoic radiation and support a freshwater origin for clitellate annelids. Zoologica Scripta 49 (5): 614-640, DOI: 10.1111/zsc.12426, URL: https://doi.org/10.1111/zsc.12426
B62A87D64F084F4A0660F911FEB9C6AE.taxon	description	Relationships within Crassiclitellata closely match those recovered in Anderson et al. (2017 %, despite the smaller taxonomic sample used here. As seen in that study, the positions of the moniligastrid Drawida sp. and the haplotaxid Pelodrilus sp. vary somewhat across analyses. In most trees, Drawida sp. is sister to a clade comprising all sampled crassiclitellates and Pelodrilus sp., but Pelodrilus is sister to a subclade comprising the North American taxa Komarekiona and Sparganophilus and Kynotus from Madagascar (Figure 1 %. In two trees (25 % MARE and 75 % TreSpEx-and-BaCoCa-filtered %, Pelodrilus is sister to a clade comprising all crassiclitellates plus Drawida sp., with Drawida sp. recovered as sister to a large clade comprising all crassiclitellates except Komarekiona, Kynotus and Sparganophilus. In two trees (50 % MARE and 75 % MARE %, Pelodrilus is sister to the Komarekiona + Kynotus + Sparganophilus clade, with Drawida sister to a clade comprising all other crassiclitellates. The only other relationships within Crassiclitellata that vary across trees involve Eudrilus eugeniae; in most trees, it is sister to a clade comprising three members of Megascolecoidea (Acanthodrilus, Dichogaster and Pontodrilus % and two ocnerodrilids (Kerriona and an unidentified worm from Madagascar %, with a clade comprising Andiorrhinus, Areco and Pontoscolex then being sister to that group. By contrast, Eudrilus is recovered as sister to Andiorrhinus sp. in the 75 % MARE tree (Figure S 3 %.	en	Erséus, Christer, Williams, Bronwyn W., Horn, Kevin M., Halanych, Kenneth M., Santos, Scott R., James, Samuel W., Châtelliers, Michel Creuzé des, Anderson, Frank E. (2020): Phylogenomic analyses reveal a Palaeozoic radiation and support a freshwater origin for clitellate annelids. Zoologica Scripta 49 (5): 614-640, DOI: 10.1111/zsc.12426, URL: https://doi.org/10.1111/zsc.12426
B62A87D64F174F560533F974FE05C506.taxon	description	Naididae today embraces ca. 1,000 species, but only a few of them have been available for DNA studies to date. In this study, we have 15 representatives, representing six of the eight subfamilies in current use by the first author. Other authors (Schmelz & Timm 2008; Timm 2009 %, accepting paraphyly in diagnostically / morphologically distinct taxa, advocate familial rank, that is, the names Tubificidae, ‘ Naididae (s. str. % ’, Pristinidae and Opistocystidae, for parts together corresponding to ‘ Naididae (s. lat. % ’. Nevertheless, there is consensus that this complex is monophyletic, with marine and freshwater species mixed in most major lineages. Our current analyses yielded a fully resolved Naididae, and despite the limited taxon sample, three main conclusions about the subfamilies can be drawn with stronger confidence than before: 1. Limnodriloidinae (Limnodriloides % and Tubificinae (Aulodrilus, Troglodrilus, Potamothrix % are both monophyletic and sister taxa (Erséus, Envall, et al., 2010; Liu et al., 2017; Marotta et al., 2008; Sjölin et al., 2005 %. 2. Phallodrilinae requires taxonomic revision. First, a core group (Phallodrilinae sensu stricto % must contain the type genus (Phallodrilus, not yet molecularly studied %. As inferred from an analysis of morphology (Erséus, 1992 %, Phallodrilinae is herein represented by Albanidrilus and Olavius. The placement of the marine genus Bathydrilus (an alleged phallodriline; Erséus, 1979 % in or near this group is neither corroborated here nor in other studies (Envall et al., 2006; Erséus, Envall, et al., 2010; Martin et al., 2010; Mejlon et al., 2015; Rousset et al., 2008 %. Another marine taxon, Duridrilus Erséus, 1983, also first classified in Phallodrilinae, may be closely related to Bathydrilus (Erséus, 1983 %. Molecular studies underway support this (CE, unpublished data %. On the other hand, the notion that Phallodrilinae (i. e. sensu stricto % is sister to the large genus Heterodrilus (e. g. Envall et al., 2006; Erséus et al., 2002; Mejlon et al., 2015 % is again, and now maximally, supported. However, Heterodrilus (placed in Rhyacodrilinae due to its diffuse prostates and conspicuous coelomocytes; Erséus, 1981 % differs morphologically from Phallodrilus s. str. (with solid prostate gland and inconspicuous coelomocytes; Erséus, 1993 % in such a way that treating it as a subfamily of its own could be advantageous from a diagnostic point of view. 3. Rhyacodrilinae also requires revision. A distinct clade with four of our naidid species represents three subfamilies (Figure 1 %: Pristininae (Pristina %, Rhyacodrilinae sensu stricto (Rhyacodrilus % and Naidinae (Paranais, Chaetogaster %. This lineage, albeit with a different (and less strongly supported % internal topology, was recovered before (Envall et al., 2006; Erséus, Envall, et al., 2010; Rousset et al., 2008; Sjölin et al., 2005 %; in the Erséus, Envall et al. study also with a fourth subfamily, Opistocystinae recovered as sister to Pristininae. Therefore, in a recent multilocus analysis of Naidinae, species of Rhyacodrilinae s. str., Pristininae and Opistocystidae were used as outgroups (Erséus et al., 2017 %. From these earlier studies, we know that other ‘ rhyacodriline’ taxa (Monopylephorus, Epirodrilus and some Ainudrilus % are also part of this lineage, but there is still no strong evidence that they all form a monophyletic group (i. e. a hypothetical Rhyacodrilinae s. str. % with Rhyacodrilus. To make matters worse, two other ‘ rhyacodriline’ taxa, Heronidrilus (marine % and Bothrioneurum (freshwater % are rooted in a more basal part of the naidid tree in the present study as well as in all other studies mentioned here. Here, they appear as sisters and together they are the sister to the rest of Naididae (Figure 1 %, but in some previous studies, they occur in other positions. Undersampling may be one reason for these incongruencies. To summarize, Rhyacodrilinae ‘ sensu lato’ must be heavily pruned and divided into smaller subfamily-level taxa following extended molecular sampling.	en	Erséus, Christer, Williams, Bronwyn W., Horn, Kevin M., Halanych, Kenneth M., Santos, Scott R., James, Samuel W., Châtelliers, Michel Creuzé des, Anderson, Frank E. (2020): Phylogenomic analyses reveal a Palaeozoic radiation and support a freshwater origin for clitellate annelids. Zoologica Scripta 49 (5): 614-640, DOI: 10.1111/zsc.12426, URL: https://doi.org/10.1111/zsc.12426
B62A87D64F154F560533FED9FA64C265.taxon	description	This is an assemblage of freshwater clitellates with a complex taxonomic history and a distribution covering all continents except Antarctica. It comprises ca. 20 species in eight genera (Martin et al., 2007 %, occasionally suggested to represent an ancestral stage in clitellate evolution as a whole (e. g. Brinkhurst, 1992 %, but more recently recovered as a non-monophyletic taxon close to the base of Crassiclitellata (Anderson et al., 2017; Martínez-Ansemil et al., 2012 %. In the present study, we included transcriptomes of three species, that is, data also used by Anderson et al.; two of those species, but with other data, were treated by Martínez-Ansemil et al. The conclusion that Haplotaxidae as currently defined is not monophyletic is maintained. We found Haplotaxis (= Haplotaxidae sensu stricto), with maximum support, as sister to the lineage containing Lumbriculata, Moniligastridae, Crassiclitellata and the two other ‘ haplotaxids’ (Delaya and Pelodrilus % (Figures 1 – 3 %. In the present study, Delaya and Pelodrilus are outside, but close to, Crassiclitellata (as currently defined; see below %, but this is not maximally supported. In Anderson et al. (2017, Figure 1 %, on the other hand, they are in paraphyly, that is, adjacent to each other, and with full support. However, our representation of Haplotaxidae s. lat. is limited, and a final conclusion must be based on molecular data from a much larger sample of taxa. In an ongoing study using legacy markers, a greater number of samples of alleged haplotaxids from North America, Europe, Asia, Africa and Australia will be assessed in more detail (Martinsson, Fend, Klinth, Martin, Torii, Erséus, in prep. %.	en	Erséus, Christer, Williams, Bronwyn W., Horn, Kevin M., Halanych, Kenneth M., Santos, Scott R., James, Samuel W., Châtelliers, Michel Creuzé des, Anderson, Frank E. (2020): Phylogenomic analyses reveal a Palaeozoic radiation and support a freshwater origin for clitellate annelids. Zoologica Scripta 49 (5): 614-640, DOI: 10.1111/zsc.12426, URL: https://doi.org/10.1111/zsc.12426
B62A87D64F154F510533FA6FFEC4C18E.taxon	description	Lumbriculata, a clade comprising lumbriculidans and hirudineans, was maximally supported in our analyses, consistent with previous molecular investigations, even though they largely had poor support (Erséus & Källersjö, 2004; Marotta et al., 2008; Martin, 2001; Rousset et al., 2008; Siddall et al., 2001 %. Spermatozoan ultrastructure provided support for Lumbriculata as well (Ferraguti et al., 1999 %. However, in all studies to date (including the present one % the monophyly of Lumbriculida has been based on a limited sample of taxa. The hirudinean lineage has been more extensively studied, and its monophyly is well documented (Tessler et al., 2018 %. There is also a growing consensus about a basal dichotomy between the crayfish worms (Branchiobdellida % and the more typical leech-like group, comprising Acanthobdellida and the ‘ true leeches’ (Hirudinida %. In the current study, Branchiobdellida is recovered as sister to Hirudinida with strong support across all analyses. Acanthobdellida was not sampled for this study, though recent studies have placed it as sister to Hirudinida (Phillips et al., 2019; Tessler et al., 2018 %. Within Hirudinida, we consistently recovered a monophyletic Rhynchobdellida and Arhynchobdellida, generally with strong support, in agreement with a recent phylogenomic study of relationships within Hirudinea (Phillips et al., 2019 %. This contrasts with previous molecular phylogenetic studies based on molecular markers like COI and 18 S, but also 16 S, ND 1, 28 S and ITS (either analysed individually or in various combinations %, which recover a paraphyletic Rhynchobdellida, with either Glossiphoniidae (e. g. Helobdella and Theromyzon % (Apakupakul et al., 1999; Borda & Siddall, 2004; Siddall & Burreson, 1998 % or Oceanobdelliformes (e. g. Glyptonotobdella and Piscicolidae sp. % as sister to all other leeches (Tessler et al., 2018 %. However, it is concordant with traditional taxonomy and cladistic analysis of morphological data (Siddall & Burreson, 1995 % (though unlike Siddall and Burreson, we recover a monophyletic Piscicolidae, as do Williams & Burreson, 2006 %. This conflict over the status of Rhynchobdellida appears to be a rooting problem. If on our phylogeny, Hirudinida had been rooted on the branch leading to Piscicolidae sp. and Glyptonotobdella instead of on the branch between Arhynchobdellida (Erpobdella, Haemopis and Cylicobdellidae sp. % and Rhynchobdellida (Helobdella, Theromyzon, Piscicolidae sp. and Glyptonotobdella %, our leech topology would match that of Tessler et al. Leeches, branchiobdellidans and acanthobdellidans are well known for their relatively high molecular substitution rates (Martin, Kaygorodova, Sherbakov, & Verheyen, 2000 % (see our Figures 1 and 3 %, which can make phylogenetic inference and rooting challenging (Anderson & Swofford, 2004; Felsenstein, 1978; Hendy & Penny, 1989; Huelsenbeck & Hillis, 1993 %. Although this is one of the first phylogenomic studies to include dozens to hundreds of loci sampled from representatives of multiple leech suborders, our limited taxonomic sampling within leeches (particularly including no representatives of Americobdelliformes % and allied taxa (e. g. Acanthobdellida % implies that additional taxonomic sampling will be needed before a final verdict on this topic can be rendered.	en	Erséus, Christer, Williams, Bronwyn W., Horn, Kevin M., Halanych, Kenneth M., Santos, Scott R., James, Samuel W., Châtelliers, Michel Creuzé des, Anderson, Frank E. (2020): Phylogenomic analyses reveal a Palaeozoic radiation and support a freshwater origin for clitellate annelids. Zoologica Scripta 49 (5): 614-640, DOI: 10.1111/zsc.12426, URL: https://doi.org/10.1111/zsc.12426
B62A87D64F154F56066BFDCCFA40C63B.taxon	description	The freshwater genus Propappus Michaelsen, 1905 was initially regarded as a ‘ primitive’ member of Enchytraeidae, but several of its morphological features (chaetae with bifid tips, glands associated with chaetae, spermathecae in segment IV, thickened vasa deferentia in XII and ovaries in XIII % were considered different enough to justify its elevation to a monotypic family, Propappidae, by Coates (1986 %. Gustavsson, Ferraguti, & Marotta, (2008 % found support for these families being closely related after studying the cuticular ultrastructure and spermatozoa of Propappus, but Gorgón, Krodkiewska and Światek (2015 % found the ovary ultrastructure and oogenesis of this genus similar to those known for other aquatic clitellates and clearly different from corresponding features in Enchytraeidae. In the first molecular studies involving Propappus, both Erséus and Källersjö (2004 % and Rousset et al. (2007 % found Propappus to be sister to Haplotaxis, but with low support. The Propappidae + Enchytraeidae group was, however, recovered by Marotta et al. (2008: Figure 3 %, but again with low support. The long branch of Propappus in our tree (Figure 1 % manifests a genetic gap between Propappidae and Enchytraeidae, and our analyses sometimes place Propappus as sister to a clade comprising Enchytraeidae, Lumbriculata and Metagynophora (along with some haplotaxids % (Figures 2 and 3 and Figure S 3; Supplementary Materials %. Enchytraeidae is a large family with species from both terrestrial and aquatic habitats. Its monophyly was verified, and its internal phylogeny was analysed, by Erséus, Rota, et al. (2010 % and Martinsson, Dózsa-Farkas, Rota, and Erséus (2017 %. In our tree, the ingroup topology (i. e. with Grania nearest to Enchytraeus % conforms better with the tree of Martinsson et al. than with Erséus et al. ’ s results, where Grania is nearer to Mesenchytraeus than to Enchytraeus. However, with ca. 700 enchytraeid species (in ca. 30 genera % worldwide, it is possible that the six species we sampled, representing only four genera, are not enough to robustly resolve the relationships within this family. Our results suggest that either a clade comprising Propappidae and Enchytraeidae, or Enchytraeidae alone, is sister to all the remaining groups discussed below. This refutes a previous hypothesis that enchytraeids are closely related to earthworms, that is, Metagynophora (see Erséus, 2005 %.	en	Erséus, Christer, Williams, Bronwyn W., Horn, Kevin M., Halanych, Kenneth M., Santos, Scott R., James, Samuel W., Châtelliers, Michel Creuzé des, Anderson, Frank E. (2020): Phylogenomic analyses reveal a Palaeozoic radiation and support a freshwater origin for clitellate annelids. Zoologica Scripta 49 (5): 614-640, DOI: 10.1111/zsc.12426, URL: https://doi.org/10.1111/zsc.12426
