A Transcriptomic Approach to Ribbon Worm Systematics (Nemertea): Resolving the Pilidiophora Problem

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 Nemertea (ribbon worms)-for which the targeted gene approaches had resolved many clades but had left key phylogenetic 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 a well-supported phylogeny that recovers all major accepted 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 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.

Re-evaluating the phylogeny of Sipuncula through transcriptomics

“…1 and 2). Given our low levels of missing data and high matrix completeness (especially for the small matrix Taxon75: maximum of 23% of missing data for Phascolopsis gouldii), similar to other studies with comparable matrices and data analysis strategies (e.g., Andrade et al, 2014;Zapata et al, 2014), we think that our results should not be affected by gene occupancy or missing data artifacts. With the aim of having the most complete dataset possible, we optimized taxon sampling to represent all sipunculan families, ensuring that no major phylogenetic hypothesis was left untested for deep relationships within Sipuncula.…”

“…The systematic community has necessarily progressed from candidate genes through EST-based methods to 454 and Illumina-based transcriptome and genome datasets to resolve major relationships among the animal phyla (e.g., Dunn et al, 2008;Hejnol et al, 2009;Nosenko et al, 2013;Ryan et al, 2013;Moroz et al, 2014). Long outstanding issues have been resolved for within-phylum relationships among arthropods, molluscs, and annelids, to mention just some of the largest animal phyla (e.g., Meusemann et al, 2010;Kocot et al, 2011;Smith et al, 2011;Struck et al, 2011;von Reumont et al, 2012;Andrade et al, 2014;Weigert et al, 2014). A third wave now focuses on resolving lower-level phylogenetic questions, relying almost entirely on Illumina-based technology (e.g., Johnson et al, 2013; Kocot et al, 2013;Wheat and Wahlberg, 2013;Dell'Ampio et al, 2014;Fernández et al, 2014aFernández et al, , 2014b.…”

First record on the development of the larva of the basally branching nemertean species Carinina ochracea (Palaeonemertea)

“…They are most likely united in the monophyletic clade Neonemertea while the remaining lineages form its sister as arguably monophyletic Palaeonemertea (sensu stricto) [1,2,23]. The majority of nemertean species is assumed to develop via pelagic larvae ( [25,26,30,40], and references therein).…”

“…While being vagile, creeping adults most nemerteans develop from one of several types of pelagic larvae of which the pilidium larva might be the most well-known [24]. The pilidium larva is typical of the nemertean clade Pilidiophora comprising Heteronemertea and Hubrechtiidae the latter having formerly been classified as palaeonemertean [1,2,23,38]. The pilidium larva shows maximally indirect development with most of the juvenile developing inside the larval epidermis from distinct primordial structures termed imaginal discs.…”

Nemertea

“…In most benthic polystiliferan species (Reptantia), a gradual fusion of both openings by sharing a common atrial chamber at the tip of the head is present. Recent molecular analyses and reassessment of morphological data, however, give a different picture putting the traditional classifi cation in jeopardy Bartolomaeus and von Döhren 2010 ;Andrade et al 2012Andrade et al , 2014Kvist et al 2014 ). Of the traditional higher-ranking taxa, only Hoplonemertea and Heteronemertea are recovered ( Fig.…”