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Acoelomorph flatworms are deuterostomes related to Xenoturbella
Hervé Philippe, Henner Brinkmann, Richard R. Copley, Leonid L. Moroz, Hiroaki Nakano, Albert J. Poustka, Andreas Wallberg, Kevin J. Peterson & Maximilian J. Telford Nature 470, 255–258 (10 February 2011) Received 04 August 2010 2011 Xenoturbellida and Acoelomorpha are marine worms with contentious ancestry. Both were originally associated with the flatworms (Platyhelminthes), but molecular data have revised their phylogenetic positions, generally linking Xenoturbellida to the deuterostomes1, 2 and positioning the Acoelomorpha as the most basally branching bilaterian group(s)3, 4, 5, 6. Recent phylogenomic data suggested that Xenoturbellida and Acoelomorpha are sister taxa and together constitute an early branch of Bilateria7. Here we assemble three independent data sets—mitochondrial genes, a phylogenomic data set of 38,330 amino-acid positions and new microRNA (miRNA) complements—and show that the position of Acoelomorpha is strongly affected by a long-branch attraction (LBA) artefact. When we minimize LBA we find consistent support for a position of both acoelomorphs and Xenoturbella within the deuterostomes. The most likely phylogeny links Xenoturbella and Acoelomorpha in a clade we call Xenacoelomorpha. The Xenacoelomorpha is the sister group of the Ambulacraria (hemichordates and echinoderms). We show that analyses of miRNA complements 8 have been affected by character loss in the acoels and that both groups possess one miRNA and the gene Rsb66 otherwise specific to deuterostomes. In addition, Xenoturbella shares one miRNA with the ambulacrarians, and two with the acoels. This phylogeny makes sense of the shared characteristics of Xenoturbellida and Acoelomorpha, such as ciliary ultrastructure and diffuse nervous system, and implies the loss of various deuterostome characters in the Xenacoelomorpha including coelomic cavities, through gut and gill slits. Subject terms: Evolution Zoology doi:10.1038/nature09676 Published online 09 February
Accepted 16 November 2010
In contrast to previous results1, 2, 4, 9, 10 (Fig. 1a), two recent phylogenomic studies have suggested a sister group relationship between Acoelomorpha and Xenoturbella. These studies disagree over where this clade might be placed, either at the base of Bilateria 7 (Fig. 1b) or with the deuterostomes11 (Fig. 1c). The acoelomorph genes studied, however, show extremely high rates of sequence evolution. This bias could result in susceptibility to the LBA artefact: a systematic error that may be compounded by the short internal branches around the origin of the Bilateria12. Overcoming this potential artefact requires the analysis of large molecular data sets comprising many species and using a complex model of sequence evolution designed to reduce the impact of systematic errors12. Figure 1: Alternative phylogenetic positions of Acoela, Nemertodermatida and Xenoturbellida with implied evolution of different characters.
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X. We assembled a largely complete set of mitochondrial protein sequences from four acoels using expressed sequence tag (EST) databases. c. Protein RSB66 and deuterostome mitochondrial gene order are also indicated. Tree based on analyses of ref. and refs 1 and 2 for position of Xenoturbella. Complete trees are shown in Supplementary Figs 10–14. and cross validation13 shows that the CATmodel with a general time reversible (GTR) exchange rate matrix and gamma correction (CAT+ GTR+ Γ) fits best. ambulacrarians and the Xenoturbella/acoel group is unresolved (PP = 0.).99) (Fig. miamia (photographs by M.T. Losses and gains of miRNAs are shown on each branch. the relationship between chordates. followed by GTR+ Γ then CAT+ Γ. b. The minimum number of total steps to explain miRNA distribution is shown above trees. A notable feature of Fig. Xenambulacraria and Xenacoelomorpha are shown in red. acoels are the sister-group of Xenoturbella (posterior probability (PP) of 0. Figure 2: Animal phylogeny based on mitochondrial proteins reconstructed using the CAT + GTR + Γ model under a Bayesian analysis. In the phylogeny inferred with the best model. bocki and H. miRNAs representing possible synapomorphies of Deuterostomia.J. which are nevertheless grouped with the slow-evolving Xenoturbella. Tree based on refs 6 and 9 for positions of nemertodermatids and acoels.47).a.99) within deuterostomes (PP = 0. However.W. Tree based on the results from this paper. 2). Bottom left. 2 of 13 . 7. Better-fitting models of molecular evolution are expected to be less sensitive to systematic errors. 2 is the extremely fast evolutionary rate of acoels. and A.
finally ruling out a close relationship between acoels and rhabditophoran platyhelminthes3 (Supplementary Fig. 1). We also constructed a large alignment from EST and genome data (66 species. the acoelomorph clade is sister to the slow-evolving Xenoturbella (BS = 80%). 3 of 13 . 30% missing data) including all major animal phyla represented by slowly evolving species (Supplementary Tables 1 and 2). Using GTR+ Γ we recover acoels + Xenoturbella (PP = 1.) with high support (generally a bootstrap support (BS) of 100%).We exaggerated the effect of LBA by using the less-fit models (Supplementary Fig. etc. Xenoturbella plus Acoelomorpha are sister to Ambulacraria (BS = 78%) within deuterostomes. Ecdysozoa.65). Acoels are seen to be very fast evolving and are the sister group of the nemertodermatids (BS = 55%). 38. 2). Lophotrochozoa. 3) recovers all expected clades (Bilateria. the acoel Symsagittifera roscoffensis does not possess a protostome-type mitochondrial NAD5 gene 15. For this new data set.99). 197 genes. The phylogeny inferred under CAT+ Γ (Fig. Figure 3: Phylogeny of 66 animal species based on EST sequences.0) as basal deuterostomes (PP = 0. Only using the least fit model (CAT+ Γ) do we find that the acoels are located as basal bilaterians (PP = 0. these analyses provide evidence for grouping acoels and Xenoturbella together with deuterostomes. The fast evolutionary rate of acoels is therefore likely to be responsible for their early emergence revealed in previous studies 14.330 positions. Interestingly. Despite the limited size and heterogeneous evolutionary rates of mitochondrial genomes. As in the mitochondrial analyses. CAT+ Γ has a better fit than GTR + Γ (CAT+ GTR+ Γ was not investigated as the computation is too time-consuming) 13.
Tree was reconstructed using the CAT + Γ model under a Bayesian analysis. 38. but in no case are acoelomorphs basal to Bilateria (Supplementary Fig. The fast-evolving Nemertodermatida are consistently found as a sister-group to Ambulacraria.195 ±127). Major accepted metazoan clades (for example. in contrast. our topology differs from the recent phylogenomic analysis of Hejnol et al. Level of bootstrap support is indicated. Nemertodermatida and Ambulacraria. deuterostomes are paraphyletic when Xenoturbella is absent (Supplementary Fig. Lophotrochozoa. 30% missing data. we therefore assembled an alignment of 145 genes (with 4 of 13 . Acoela and Nemertodermatida within deuterostomes. To test the possibility that the fast evolutionary rate of Acoelomorpha might have an effect on phylogenetic inference due to LBA. which itself is significantly better than the GTR+ Γ model (ΔlnL = 3.Analysis of 197 genes. The backbone topology inferred with the CAT+ Γ model is unchanged when the number of taxa is reduced (Supplementary Fig. 5a). even with the least-fit GTR+ Γ model. Although the analysis of ESTs is congruent with the mitochondrial genome result. Protostomia) are supported. and the very fast-evolving Acoela are either grouped with Nemertodermatida and Xenoturbella or basal to deuterostomes (Supplementary Fig. 3). Scale bar. Regardless of the species sampling. The sub-optimal site-heterogeneous CAT+ Γ model yields results that are more difficult to interpret: for example. is the result of an LBA artefact stemming from the use of a sub-optimal site-homogeneous model 7. we pruned our data set to 37 species and compared alternative models (including CAT+ GTR+ Γ) and different taxon sampling schemes aimed at lessening or exaggerating a potential LBA artefact. Computational constraints prevented the analysis of the original data set (94 species and 270. Cross-validation demonstrates that the site-heterogeneous CAT+ GTR+ Γ model has a significantly better fit than the CAT+ Γ model (ΔlnL = 490 ±48). Similar support is obtained when jack-knifing 50% of the genes (Supplementary Fig. 9). Xenoturbella plus Acoelomorpha are monophyletic and sister to Chordata + Ambulacraria (Supplementary Fig. When the very-fast-evolving Acoela are removed. 1b). We propose that the basal emergence of Xenoturbella plus Acoelomorpha observed by Hejnol et al. 3a and Fig. Interestingly. leads to variable positions of the members of Acoelomorpha. reflecting the expected behaviour of a method sensitive to LBA artefacts. Xenoturbella and Acoelomorpha are sister groups (phylum Xenacoelomorpha). 5).330 unambiguously aligned positions. the best available model (CAT+ GTR+ Γ) locates Xenoturbella. The least-fit site-homogeneous GTR + Γ model. 3b. 3). Xenacoelomorpha is the sister taxon of Ambulacraria (Xenambulacraria) within the deuterostomes. showing that the very-fast-evolving Acoela is the only group that is difficult to locate and that its placement requires the use of complex models to avoid artefactual results. Ecdysozoa.580 positions. even GTR+ Γ recovers the monophyly of Xenoturbella. 7 (Fig. substitutions per position.or fast-evolving representatives are included (Supplementary Fig. 4a–f). Acoela and Nemertodermatida are sister groups (Acoelomorpha). depending on whether slow. with 84% missing data) with the site-heterogeneous CAT+ Γ model. d).
we propose the name Xenacoelomorpha for this clade. coding for the sperm protein RSB66. inevitably. 1 and Supplementary Fig. roscoffensis library (Supplementary Table 3). Limited additional support for our tree comes from this unique deuterostomian miRNA (miR-103/107/2013). 22. 1 and Supplementary Fig. we find that Xenoturbella and acoels share two miRNAs found in no other animals: a novel miRNA family (XANov-1) and a paralogue of miR-92 (XANov-2) (Supplementary Fig. in particular from Symsagittifera. Furthermore.Xenoturbella (see also Supplementary Figs 7–9). suggesting that their absence cannot be considered a credible contra-indication of deuterostome affinity. 14). Alternative interpretations of these data assuming monophyly of acoels and based either on the results of refs 1. We suggest that miR-103/107/2013 is a plausible synapomorphy of Xenoturbella. Locating Acoelomorpha and Xenoturbella inside Deuterostomia. To examine this conclusion we have constructed and sequenced libraries of small RNAs from a second acoel. Numerous miRNAs must have been lost from at least some Acoels. From the Hofstenia library we found ten miRNAs that were not detected in the S. 14 (Supplementary Fig. miR-2012 (Fig. The Xenacoelomorpha are excluded from the deuterostome phyla of Hemichordata. yet outside Chordata or Ambulacraria. Bilateria))) (Supplementary Figs 10 and 11). in addition to their two novel miRNAs and their eight shared miRNA losses. 14) imply large-scale losses of miRNAs. 1 and Supplementary Fig. 6. 15). this. Symsagittifera roscoffensis. possesses a second miRNA. Xenoturbella has all but ten of the miRNAs typically found in bilaterian genomes 16. uniquely in the genomes of Ambulacraria. we have detected an additional gene. Echinodermata and Chordata and hence constitute an independent fourth phylum of 5 of 13 . 21. 16). fitting a picture of miRNA evolution occurring through continuous addition and mosaic loss 16. are not highly supported results. means almost all possible losses are of bilaterian level characters—there is only a single known deuterostome specific miRNA—and this is exactly what we observe. From Xenoturbella we detected reads from all ten of these miRNAs. 2. Finally. This result rather implausibly implies non-monophyly of Acoela. which we find in both acoels and in Xenoturbella (Fig. The most parsimonious tree derived from an analysis of miRNA data places the two species of acoels and Xenoturbella as three independent branches basal to the Bilateria (Symsagittifera (Hofstenia (Xenoturbella. Ambulacraria and Chordata and that miR-2012 is a likely synapomorphy of Xenambulacraria. 15). or the tree of Hejnol et al. The Rsb66 genes of acoelomorphs and Xenoturbella share a small and rather variable insertion relative to Chordata and Ambulacraria. has supported the idea that the acoels are a basal clade relative to other Bilateria 8. Hofstenia miamia and from Xenoturbella bocki. 9. gives further support to the idea that they are sister taxa (Fig. at least. 12). as well as eight additional miRNAs found in Bilateria. Chordata. 18. Xenoturbella. the paucity of bilaterian miRNAs in one acoel. (Supplementary Fig. Acoelomorpha and Xenoturbella (Fig. 1 and Supplementary Fig. Acoelomorpha. Our three independent data sources indicate a sister group relationship between the acoelomorphs and Xenoturbella 17. 13) or on our tree (Supplementary Fig. 19 within the deuterostomes. noting that a deuterostome affinity for both Xenoturbella and Acoelomorpha has been previously suggested based on morphological considerations 20. 14). Difficult phylogenetic questions such as that addressed here must ultimately be solved by the congruent patterns emerging from what. previously found only in Ambulacraria.
ncbi. Phylogenomic data.nlm. we predict that more deuterostome characters will be discovered in the morphology.ncbi. b5 = half). SCaFOS was allowed to create chimaerical operational taxonomic units by merging partial sequences from closely related species (Supplementary Table 1) when full-length sequences were not available. through-gut and protonephridia) as well as the homologous attributes of Ambulacraria and Chordata (deuterostomy. Information about the names of the 197 selected genes. 28 and Dunn et al. Finally.nih.mcmaster. 32). Nucleotides from each gene were aligned using TranslatorX33 with the appropriate genetic code and using ClustalW34 for the amino-acid alignment.nlm.ncbi. Although it is clear that certain of these characters have been lost in the living Xenacoelomorpha. the deuterostome affinity of the Xenacoelomorpha implies that they have lost characters present in the common ancestor of deuterostomes. species with fewer 6 of 13 .nlm. We first discarded seven species because of their incompleteness (that is.gov/Traces/) at the National Center for Biotechnology Information. Concatenations of single gene alignments into supermatrices were performed with SCaFoS38.ca/ogre/).characteristics were present in Precambrian bilaterians .physics. This ancestor must have possessed pan-bilaterian apomorphies (for example. Ambiguously aligned regions were detected and removed with Gblocks37 (b2 = 75%. b3 = 5. 35 were updated with new sequences from GenBank (http://www. Neochildia fusca and Symsagittifera roscoffensis from the Trace Archive (http://www. embryology or genomes of members of the Xenacoelomorpha. this automated selection was slightly refined by eye using Net (also from MUST). caudatus using Genewise 31. Multiple positives from a given species were then assembled into a contig using CAP3 (ref. To minimize the amount of missing data. their size and the distribution of missing data are available in Supplementary Table 2.gov /Traces/) at the National Center for Biotechnology Information.nih. Open reading frames of positive hits were identified by aligning ESTs to the homologous protein sequence from P. Metazoan mitochondrial protein coding genes were downloaded from OGRE (http://drake. Methods Phylogenetic data assembly Mitochondrial data. To assemble acoel partial genomes we used TBLASTN against EST collections from Convolutriba longifissura. dbEST (http://www. When multiple orthologous sequences were available for a particular operational taxonomic unit.nih. The amount of missing data per gene was limited to 25 species out of 66. gill slits and endostylar tissue27). b4 = 5.nih. Our strategy for selecting taxa for elimination was as follows.gov/dbEST/) and the Trace Archive (http://www.nlm.gov/sites/entrez?db=protein). Phylogenetic analyses were performed on the amino-acid translations. We used Priapulus caudatus mitochondrial proteins as a BLAST query. SCaFoS helped to select the slowest-evolving sequence as determined from ML distances computed under a WAG + F model with TREE-PUZZLE39. Alignments from Philippe et al. enterocoely.ncbi. Single gene alignments were assembled using new features of the program Ed from the MUST software package36. To produce a data set that was tractable for the most time-consuming CAT+GTR + Γ model we reduced the number of taxa from 66 to 37.
118 positions) and a reduced EST-based alignment (37 species.632 unambiguously aligned positions. and jack-knife supports are very similar to bootstrap supports. for large data sets.000 was sufficient). Cnidaria. time-consuming. 41. each data set was analysed with PhyloBayes. for most data sets. PhyloBayes analyses were performed with the CAT+ Γ 4 mixture model. This strategy. Mollusca. 9) is identical to the tree based on the complete gene sample (Fig. To test the robustness of our results to gene sampling. saved every ten cycles.100) being discarded as burn-in. JTT or LG. which are generally used—are special cases of the GTR model. This model is implemented in an MCMC framework by the program PhyloBayes version 3.2 (ref. we applied a standard. 30% missing data). while making the data set of a size that permits the use of the best (and most time-consuming) models. Annelida. the CAT+ Γ 4 model and the GTR + Γ 4 model using cross-validation tests as described in ref. We first performed statistical comparisons of the CAT+ GTR+ Γ 4 model.100 cycles. MCMC were run for 1. finally.330 amino-acid positions. yielding a set of 145 genes (24. Ten replicates were run: 9/10 of the positions randomly drawn from the alignment were used as the learning set and the remaining 1/10 as the test set.100) cycles with the mitochondrial (EST) alignment. 600 (1. bootstrap procedure42: 100 pseudo-replicates were generated with SEQBOOT43. Arthropoda.000 cycles (250 topological moves per cycle) with the same operators as in Lartillot et al. we also performed a jack-knife analysis of genes. For the mitochondrial alignment (32 species and 2. 20.600 (2. 100 being discarded as burn-in.330 positions. 3).000 cycles were necessary. a consensus tree was inferred from these 100 consensus trees using CONSENSE to compute the bootstrap support values for each node. the amount of data available is generally sufficient to learn the 190 free parameters of the GTR model40. 7. however. For the CAT+ Γ 4 and CAT+ GTR+ Γ 4 models. about three species per major phylum Porifera. Other matrix based models—WAG. 40). For the alignment of 66 species and 38. and the posterior consensus was computed on the 500 (900 for mitochondrial alignments) remaining trees.000 points were discarded as burn-in for all the data sets (expect for the mitochondrial alignments where a burn-in of 1. only genes for which sequences were available for at least 55 species out of 94 were retained. for the super-matrix of 94 species. The consensus trees obtained from all the post-burn-in trees (Supplementary Fig. trees were collected after the initial burn-in period and a consensus tree was computed by PhyloBayes. The first 5. 38. we verified by cross-validation that the GTR+ Γ 4 model had a better fit to our data set than the WAG + Γ 4 7 of 13 . Vertebrata). we also used the site-homogeneous GTR+ Γ 4 and the time-consuming site-heterogeneous CAT+ GTR+ Γ 4. Another data set was assembled from the set of genes with the taxon sampling of Hejnol et al. MCMC were run for 1. We randomly sampled 50% of our 197 genes and for each of the ten replicates a PhyloBayes analysis was done using the CAT+ Γ 4 model. For the GTR + Γ 4 model. Two independent runs were performed with a total length of 10. In that case. also allowed us to reduce the proportion of missing data from 30% (66 species) to 22% (37 species). Phylogenetic inference For mitochondrial and phylogenomic data sets.taxon sampling (that is. This accounts for across-site heterogeneities in the amino-acid replacement process29. 22% missing data). 41.
7 demonstrates that the amino-acid compositions of Xenoturbella. Dayhoff. urochordates. In one taxon sample (that excluding nemertodermatids). some minor rearrangements within Porifera. and the observation that the acoelomorph and Xenoturbella code (invertebrate code) differs from all of these makes the deuterostome affinity observed in our analyses conservative. We expect minor. at least in a reasonable time (that is. Instead. This problem is particularly difficult because of the extreme rate heterogeneity in the tree (the distance between Porifera and Anthozoa is smaller than the distances within Echinodermata). Supplementary Fig. we used the Dayhoff coding46 in which the amino acids are recoded according to the six classes defined by M. only the position of Trichoplax varies in some cases. all the topologies found by PhyloBayes were also found among the bootstrap replicates of RAxML (corresponding to bootstrap support between 10 and 20%). we do not see any tree reconstruction artefact that would erroneously cluster the fast-evolving acoels with the slow-evolving Xenoturbella (whereas the fast rate of Aurelia 8 of 13 . Importantly. Our inference thus does not seem to be biased by compositional heterogeneity. various chains of PhyloBayes failed to converge towards the same topology.2 using the CAT+ Γ 4 model. The resulting compositional biases may impede correct reconstruction of relationships within the deuterostomes1. To verify that amino-acid compositional heterogeneity does not bias our inference. under the same conditions as previously. Lophotrochozoa. 3. 8) is almost identical to the tree of Fig. as implemented in the R package. we cannot use the time-heterogeneous CAT-BP45 because of the intractable computational burden. This indicates that the various topologies have very similar likelihoods and that PhyloBayes is unable to switch readily among these various local minima. and even no. The mitochondrial analysis is complicated to an unknown extent by the existence of multiple variants of the genetic code within deuterostomes. This matrix was then displayed as a two-dimensional plot in a principal component analysis. The resulting phylogeny (Supplementary Fig. cephalochordates. The recoded alignments were analysed with PhyloBayes 3.using RAxML and PhyloBayes. differing only by the position of Acoela (which corresponds to bootstrap support close to 30%). differences between the ML and Bayesian inference because the same model is used (priors are known to have an effect on Bayesian analysis. The non-monophyly of Cnidaria observed in the mitochondrial tree is likely to be incorrect. interestingly. several months of computation). Vertebrata and Xenacoelomorpha correspond to poorly supported groups. In five of these taxon samples. Different mitochondrial genetic codes are found in vertebrates. This heterogeneity is coupled with a change in the properties of the evolutionary process47. but bootstrap supports for the placement of Trichoplax are around 50%. Compositional heterogeneity The amino-acid composition of the 66 species EST-based data set was visualized by assembling a 20 ! 66 matrix containing the frequency of each amino acid per species using the program Net from the MUST package36. the RAxML and PhyloBayes topologies are identical. but it should be very small given the large size of the data set). Nemertodermatida and Acoela are not similar and therefore that their monophyly is not likely to be due to a compositional artefact. echinoderms and hemichordates.
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Biol (in the press) Download references Acknowledgements We thank N. 2005) 44. & Lartillot. A. Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. and E. Natural Sciences and Engineering Research Council and Réseau Québécois de Calcul de Haute Performance for computational resources: more than 220. Département de Biochimie. 1).Kristineberg. Bioinformatics 22. 783–791 (1985) 43.(Suppl. BMC Evol. Stamatakis. Sperling for help with small RNA library construction. Seattle. Montréal. were part-funded by the Biotechnology and Biological Sciences Research Council SYNTAX scheme. Université de Montréal. UK Richard R. Copley The Whitney Laboratory for Marine Biosciences and Department of Neuroscience. 842–858 (2008) 46. I.J. Blanquart. S4 (2007) 42. & Philippe. K.000 central processing unit (CPU)–hours were used producing at least 7 tonnes of CO2 excluding grey energy. 2688–2690 (2006) 45. A site.V. Felsenstein. Roosevelt Drive. A. Univ.J.P. was also supported by a Wellcome Trust core award.C. R.R. Evolution 39. H. 618–622 (2004) 47. Florida 32080.J. Washington. Evol. University of Florida. 25. J.T. Hrdy. Biol. R. St Augustine and Gainesville. Oxford OX3 7BN. Succursale Centre-Ville.P. Sterrer for helping collect material. was funded by Inez Johanssons Stiftelse and Stiftelsen Lars Hiertas Minne.W. et al.P. J.and time-heterogeneous model of amino acid replacement.C. Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference. is supported by the National Science Foundation and NASA Ames. USA Leonid L. Author information Affiliations Centre Robert-Cedergren. grant number 075491/Z/04. Nature 432. is funded by Canada Research Chairs. Felsenstein. and M. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. S. B. Canada Hervé Philippe & Henner Brinkmann Wellcome Trust Centre for Human Genetics. PHYLIP (Phylogeny Inference Package) version 3. Roure. H. W. University of Gothenburg. A. Québec H3C 3J7. Moroz Department of Marine Ecology.R. was supported by the Max-Planck Society for the Advancement of Sciences e. Mol. 450 34 11 of 13 . Confidence limits on phylogenies: an approach using the bootstrap.69 (Department of Genome Sciences. Lartillot for reading the manuscript. N.
J. Supplementary information PDF files 1. Supplementary Information (2.3M) The file contains Supplementary Figures 1-16 with legends and Supplementary Tables 1-3. H.W. A. produced Xenoturbella genomic data. All authors commented on the manuscript. Gower Street. and A. Shimoda. and K. assembled mitochondrial data. M.J.M.T. Evolution and Environment. Supplementary Information (2. 2. and A. collected Xenoturbella for genomic and miRNA data.P.J.J.T.P. University of Tsukuba. Supplementary Information (1.C.P. Competing financial interests The authors declare no competing financial interests. Supplementary Information (66K) This file contains the aligned and concatenated mitochondrial genes used in phylogenetic analyses.T.Department of Biology. Text files 1.P.R. assembled and analysed the miRNA matrix. and M. Corresponding author Correspondence to: Maximilian J.J. and H. USA Kevin J. New Hampshire 03755. Shizuoka.P.4M) This file contains the aligned and concatenated nuclear genes used in phylogenetic analyses.org and can be found in the Supplementary Information.J. M. performed preliminary phylogenomic analyses.P. Darwin Building.W. R. L. M. M. K. Hanover.P.R. drafted the paper with H. Japan.mirbase.J. 3.J. Telford MicroRNA sequences are deposited in http://www. conceived and designed the study. UK Maximilian J. Hiroaki Nakano Contributions H. collected Hofstenia.2M) 12 of 13 . University College London.T. Telford Present address: Shimoda Marine Research Center. H. Peterson Department of Genetics. 415-0025. produced Xenoturbella and Hofstenia miRNA libraries.J.. and R.B. London WC1E 6BT.T. K.N.C.L. assembled EST data and performed phylogenetic analyses of ESTs and mitochondrial genomes. Dartmouth College..
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