Article a Transcriptomic Approach to Ribbon Worm
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MBE Advance Access published September 18, 2014 ATranscriptomicApproachtoRibbonWormSystematics (Nemertea): Resolving the Pilidiophora Problem , ,1 2 3 4 5 Sonia C. S. Andrade,* z Horacio Montenegro, Malin Strand, Megan L. Schwartz, Hiroshi Kajihara, Jon L. Norenburg,6 James M. Turbeville,7 Per Sundberg,8 and Gonzalo Giribet1 1Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University 2Departamento de Entomologia, ESALQ-USP, Piracicaba, Sa˜oPaulo,Brazil 3Swedish Species Information Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden 4Division of Science and Mathematics, University of Washington, Tacoma 5Faculty of Science, Hokkaido University, Sapporo, Japan 6Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC 7Department of Biology, Virginia Commonwealth University 8Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden zPresent address: Departamento de Zootecnia, ESALQ-USP, Piracicaba, Sa˜oPaulo,Brazil *Corresponding author: E-mail: [email protected]. Associate editor: Gregory Wray Downloaded from Abstract Resolving the deep relationships of ancient animal lineages has proven difficult using standard Sanger-sequencing approaches with a handful of markers. We thus reassess the relatively well-studied phylogeny of the phylum http://mbe.oxfordjournals.org/ Nemertea (ribbon worms)—for which the targeted gene approaches had resolved many clades but had left key phylo- genetic gaps—by using a phylogenomic approach using Illumina-based de novo assembled transcriptomes and automatic orthology prediction methods. The analysis of a concatenated data set of 2,779 genes (411,138 amino acids) with about 78% gene occupancy and a reduced version with 95% gene occupancy, under evolutionary models accounting or not for site-specific amino acid replacement patterns results in awell-supportedphylogenythatrecoversallmajoraccepted nemertean clades with the monophyly of Heteronemertea, Hoplonemertea, Monostilifera, being well supported. Significantly, all the ambiguous patterns inferred from Sanger-based approaches were resolved, namely the monophyly of Palaeonemertea and Pilidiophora. By testing for possible conflict in the analyzed supermatrix, we observed at Harvard Library on November 26, 2014 that concatenation was the best solution, and the results of the analyses should settle prior debates on nemertean phylogeny. The study highlights the importance, feasibility, and completeness of Illumina-based phylogenomic data matrices. Key words: phylogeny, Palaeonemertea, Neonemertea, Pilidiophora, supermatrix, concatenation, Illumina. Article Introduction Of all the animal phyla, nemerteans are unique in presenting The classification of nemerteans has been in flux for an excretory system similar to that of some acoelomates decades but a consensus has arisen with the relatively while possessing true coeloms, the rhynchocoel and the recent use of molecular systematics (e.g., Sundberg et al. closed circulatory system (see Turbeville 2002). This taxon 2001; Thollesson and Norenburg 2003; Sundberg and includes about 1,280 species (Gibson 1995; Kajihara et al. Strand 2007; Andrade et al. 2012; Kvist et al. 2014). The tra- 2008), which is more than many other well-known animal ditional classification system of nemerteans for most of the phyla, but it is still considered a “minor” phylum by some, last 100 years followed largely Stiasny-Wijnhoff (1936), which despite inhabiting marine, freshwater and some terrestrial accepted as classes Schultze’s (1851) division of nemerteans environments. The phylum includes what is considered to into Anopla and Enopla. Stiasny-Wijnhoff (1936) divided be the longest metazoan ever recorded, Lineus longissimus, Anopla into Palaeonemertea and Heteronemertea, which can reach more than 30 m in length (McIntosh 1873– and Enopla into Hoplonemertea and Bdellonemertea. 1874), but many species are small, and some even micro- Hoplonemertea was further subdivided into Monostilifera scopic. Most nemertean species are carnivorous or scaven- and Polystilifera. Recent accounts of the systematics of gers, using their unique proboscis apparatus for capturing Nemertea were provided by Andrade et al. (2012) and Kvist prey. et al. (2014).Inthosestudies,theauthorsproduceda ß The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: [email protected] Mol. Biol. Evol. doi:10.1093/molbev/msu253 Advance Access publication August 27, 2014 1 Andrade et al. doi:10.1093/molbev/msu253 MBE comprehensive analysis of ribbon worm relationships based number of assembled base pairs. This indicates that transcrip- on six molecular markers obtained by Sanger sequencing for a tome quality may not be directly correlated to the number of large taxon sample, including all major lineages. Although raw reads or the number of used reads, but instead with many relationships were conclusive, and the major groupings library quality and diversity. (e.g., Heteronemertea and Hoplonemertea) were well We obtained a total of 42,730 clusters from the ortholog supported, their relationship to Palaeonemertea and clustering analyses, from which 7,581 had five taxa or more. Hubrechtidae, and the monophyly of Palaeonemertea were Although previous studies have compared alternative matri- not satisfactorily resolved. Andrade et al. (2012) therefore ces (e.g., Hejnol et al. 2009; Smith et al. 2011), this was done to concluded their study with a plea for Next Generation compare results between large numbers of genes (which Sequence data to resolve the deepest nodes in the tree, as came with low matrix completeness) and more complete phylogenomic matrices assembled this way have proven matrices. The most densely populated matrix from Hejnol informative at resolving basal metazoan and protostome et al. (2009),withonly53genes,wasonly50%complete. relationships (e.g., Dunn et al. 2008; Hejnol et al. 2009; Pick Likewise, the “small” matrix of Smith et al. (2011),consisting et al. 2010; Kocot et al. 2011; Smith et al. 2011; Struck et al. of 301 genes, has 50% gene occupancy and 27% character 2011; von Reumont et al. 2012; Fernandez, Laumer, et al. occupancy, whereas the “big” matrix consists of 1,185 genes 2014). with 40% gene occupancy and 21% character occupancy. Our Nemertean transcriptomic data are scarce and based on original gene occupancy threshold is much higher than any of Downloaded from Sanger data for the species Cerebratulus lacteus (Heterone- these matrices, and we obtained 89% and 80% of character mertea) and Carinoma mutabile (Palaeonemertea) (Dunn occupancy for the reduced and large matrices, respectively. As et al. 2008). More recently, two additional species have support is optimal for almost all nodes, we did not find it been sequenced using Illumina, Cephalothrix hongkongiensis necessary to evaluate more than two alternative matrices (Palaeonemertea) and C. marginatus (Heteronemertea) with more or less occupancy (fig. 1). The number of ortholog http://mbe.oxfordjournals.org/ (Riesgo, Andrade, et al. 2012), both included in this study. groups represented per taxon ranged from 704 to 2,613 for Here, we use an RNA-seq approach to generate new tran- the large matrix and from 247 to 458 for the reduced matrix scriptomes for 11 nemertean species with Illumina (including (table 2). the ones from Riesgo, Andrade, et al. 2012)andRoche-454to The maximum likelihood (ML) tests using the two alter- address four outstanding questions in nemertean phylogeny. native models, LG and LG4X, produced an identical topology We selected species from all the major ribbon-worm lineages, on the best-scoring trees. The log-likelihood score for them spanning their entire diversity, and obtained fresh RNA from was 6,056,455.0098 and 5,973,224.5499, respectively. For live or RNAlater preserved specimens. Our aims were to 1) the reducedÀ matrix, only theÀ LG4X model was used, and the at Harvard Library on November 26, 2014 test the monophyly of Palaeonemertea by including a best-scoring tree had a log-likelihood value of member of each of the three lineages obtained by Andrade 1,236,158.9849. The phylogenetic analyses of our two data et al. (2012);(2)testthemonophylyofAnopla,whichhas matricesÀ yielded identical topologies for the ML analysis using been falsified by most phylogenetic analyses; 3) test the po- apartitionedmodelapproachandfortheBayesiananalyses sition of Heteronemertea, which has remained in flux in most (fig. 2), the only differences being in the internal resolution of studies; and 4) address the position of Hubrechtidae, a family Palaeonemertea and in one of the outgroup taxa. Each node of uncertain affinities, originally classified in Palaeonemertea, in the nemertean tree received 100% bootstrap support or a but more recently found to be the possible sister group of posterior probability of 1.00, with the exception of the Heteronemertea, thus forming a clade named Pilidiophora for sister group relationship of Carinoma and Cephalothrix,not the presence of a pilidium larva which occurs in both taxa supported in the small data matrix. Monophyly of (Thollesson and Norenburg 2003). Nemertea, Palaeonemertea, Neonemertea, Hoplonemertea, Monostilifera, Pilidiophora, and Heteronemertea are thus Results found in all analyses with maximum support. One result evi- The number of sequence reads, used reads, contigs, and other dent in