Résumé
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.