Data from: Exploring the potential of small RNA subunit and ITS sequences for resolving phylogenetic relationships within the phylum Ctenophora

Ctenophores are a phylum of non-bilaterian marine (mostly planktonic)
animals, characterised by several unique synapomorphies (e.g. comb rows,
apical organ). Relationships between and within the nine recognised
ctenophore orders are far from understood, notably due to a paucity of
phylogenetically-informative anatomical characters. Previous attempts to
address ctenophore phylogeny using molecular data (18S rRNA) led to poorly
resolved trees but demonstrated the paraphyly of the order Cydippida. Here
we compiled an updated 18S rRNA data set, notably including a few
newly-sequenced species representing previously unsampled families
(Lampeidae, Euryhamphaeidae), and we built up an additional more
rapidly-evolving ITS1+5.8SrRNA+ITS2 alignment. These data sets have been
analysed separately and in combination under a probabilistic framework,
using different methods (Maximum Likelihood, Bayesian inference) and
models (e.g. doublet model to accommodate secondary structure; data
partitioning). An important lesson from our exploration of these datasets
is that the fast-evolving ITS regions are useful markers for
reconstructing high-level relationships within ctenophores. Our results
confirm the paraphyly of the order Cydippida (and thus a “cyddipid-like”
ctenophore common ancestor) and suggest that the family Mertensiidae could
be the sister-group of all other ctenophores. The family Lampeidae (also
part of the former “Cydippida”) is probably the sister-group of the order
Platyctenida (benthic ctenophores). The order Beroida might not be
monophyletic, due to the position of Beroe abyssicola outside of a clade
grouping the other Beroe species and members of the “Cydippida” family
Haeckeliidae. Many relationships (i.e. between Pleurobrachiidae, Beroida,
Cestida, Lobata, Thalassocalycida) remain unresolved. Future progress in
understanding ctenophore phylogeny will come from the use of additional
rapidly-evolving markers and improvement of taxonomic sampling.