Revisiting the phylogeny of phylum Ctenophora: a molecular perspective

Abstract

The phylogenetic relationships of deep metazoans, specifically in the phylum Ctenophora (inside and outside the phylum), are not totally understood. Several loci (protein coding and ribosomal RNA) from organisms belonging to this phylum are currently available on public databases (e.g. GenBank). Previous studies take into account the ribosomal data and the protein data separately. In this study, we perform a meta-analysis of previously published data together. The published data of this phylum have been used in previous phylogenetic analyses inside the phylum and consist in nuclear ribosomal data, such as 18S, 5.8S, ITS1, ITS2, and protein-coding markers such as NFP (non-fluorescent protein).Previous studies concentrate their efforts toward the analyses of ribosomal data or the protein-coding marker separately. Now we take into account these markers together for an upgrade of the phylogenetic analysis of this phylum. We also test several markers such as 28S, IPNS, Tyrosine aminotransferase and HLH domaincontaining protein for the improvement of the study. This markers were analyzed by Bayesian Inference (MrBayes) and Maximum Likelihood (Garli and RAxML), individually and concatenated, showing improvement in the orders placement and presenting new interesting relationship between the paraphyletic order Cydippida and the other ctenophores. These analyses also include sequences from undescribed species that have been reported in GenBank which improved the alignment matrices and support values of some nodes. Adding the undescribed species suggests interesting and well supported clades, the posterior identification of this species would led to an improvement on the ctenophore's taxonomy. Amendments from Version 1We revised the manuscript and performed the following changes according the suggestions made by the referees for the last version of the manuscript:1. Here we present the meta-analysis combining amino acid and nucleotide data to resconstruct a single tree (instead of one per dataset). As a consequence of this we redrawed our conclusions.2. We perform phylogenetic reconstructions using the combined dataset by Bayesian Inference and Maximum Likelihood, but for ML we used RAxML in addition to GARLI.3. We included a new Figure 1 to replace the one in the former version. 4.Rooted trees for each analysis (RAxML, GARLI and MrBayes) have been included in Supplementary material. 5.As suggested by the reviewers we excluded IPNS as a marker for the analysis since it is a duplicated gene, and not informative for phylogenetic reconstriction. We included 2 protein coding genes (tyrosine aminotransferase and HLH domain containing protein) to the analysis to solve this problem.6. We included to the analysis sequenced from undescribed species and other taxa not included in the previous version.