DOI: 10.5061/dryad.8333
title: Data from: An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

description: BACKGROUND: Tunicates have been recently revealed to be the closest living
 relatives of vertebrates. Yet, with more than 2500 described species,
 details of their evolutionary history are still obscure. From a molecular
 point of view, tunicate phylogenetic relationships have been mostly
 studied based on analyses of 18S rRNA sequences, which indicate several
 major clades at odds with the traditional class-level arrangements.
 Nonetheless, substantial uncertainty remains about the phylogenetic
 relationships and taxonomic status of key groups such as the
 Aplousobranchia, Appendicularia, and Thaliacea. RESULTS: Thirty new
 complete 18S rRNA sequences were acquired from previously unsampled
 tunicate species, with special focus on groups presenting high
 evolutionary rate. The updated 18S rRNA dataset has been aligned with
 respect to the constraint on homology imposed by the rRNA secondary
 structure. A probabilistic framework of phylogenetic reconstruction was
 adopted to accommodate the particular evolutionary dynamics of this
 ribosomal marker. Detailed Bayesian analyses were conducted under the
 non-parametric CAT mixture model accounting for site-specific
 heterogeneity of the evolutionary process, and under RNA-specific doublet
 models accommodating the occurrence of compensatory substitutions in stem
 regions. Our results support the division of tunicates into three major
 clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2)
 Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia
 could not be firmly resolved. Our study additionally reveals that most
 Aplousobranchia evolve at extremely high rates involving changes in
 secondary structure of their 18S rRNA, with the exception of the family
 Clavelinidae, which appears to be slowly evolving. This extreme rate
 heterogeneity precluded resolving with certainty the exact phylogenetic
 placement of Aplousobranchia. Finally, the best fitting
 secondary-structure and CAT-mixture models suggest a sister-group
 relationship between Salpida and Pyrosomatida within Thaliacea.
 CONCLUSION: An updated phylogenetic framework for tunicates is provided
 based on phylogenetic analyses using the most realistic evolutionary
 models currently available for ribosomal molecules and an unprecedented
 taxonomic sampling. Detailed analyses of the 18S rRNA gene allowed a clear
 definition of the major tunicate groups and revealed contrasting
 evolutionary dynamics among major lineages. The resolving power of this
 gene nevertheless appears limited within the clades composed of
 Phlebobranchia + Thaliacea + Aplousobranchia and Pyuridae + Styelidae,
 which were delineated as spots of low resolution. These limitations
 underline the need to develop new nuclear markers in order to further
 resolve the phylogeny of this keystone group in chordate evolution.
description: Tsagkogeorga-BMCEvolBiol2010-Tunicata_18S_88taxaSecondary structure-based 18S rRNA alignment for 88 taxaTsagkogeorga-BMCEvolBiol2010-Tunicata_18S_88taxa_2nd_structureSecondary structure-based 18S rRNA alignment for 88 taxaTsagkogeorga-BMCEvolBiol2010-Tunicata_18S_110taxaSecondary structure-based 18S rRNA alignment for 110 taxaTsagkogeorga-BMCEvolBiol2010-Tunicata_18S_110taxa_2nd_structureSecondary structure-based 18S rRNA alignment for 110 taxa