Data from: Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny

BACKGROUND: Tunicates represent a key metazoan group as the sister-group
of vertebrates within chordates. The six complete mitochondrial genomes
available so far for tunicates have revealed distinctive features.
Extensive gene rearrangements and particularly high evolutionary rates
have been evidenced with regard to other chordates. This peculiar
evolutionary dynamics has hampered the reconstruction of tunicate
phylogenetic relationships within chordates based on mitogenomic data.
RESULTS: In order to further understand the atypical evolutionary dynamics
of the mitochondrial genome of tunicates, we determined the complete
sequence of the solitary ascidian Herdmania momus. This genome from a
stolidobranch ascidian presents the typical tunicate gene content with 13
protein-coding genes, 2 rRNAs and 24 tRNAs which are all encoded on the
same strand. However, it also presents a novel gene arrangement,
highlighting the extreme plasticity of gene order observed in tunicate
mitochondrial genomes. Probabilistic phylogenetic inferences were
conducted on the concatenation of the 13 mitochondrial protein-coding
genes from representatives of major metazoan phyla. We show that whereas
standard homogeneous amino acid models support an artefactual sister
position of tunicates relative to all other bilaterians, the CAT and
CAT+BP site- and time-heterogeneous mixture models place tunicates as the
sister-group of vertebrates within monophyletic chordates. Moreover, the
reference phylogeny indicates that tunicate mitochondrial genomes have
experienced a drastic acceleration in their evolutionary rate that equally
affects protein-coding and ribosomal-RNA genes. CONCLUSION: This is the
first mitogenomic study supporting the new chordate phylogeny revealed by
recent phylogenomic analyses. It illustrates the beneficial effects of an
increased taxon sampling coupled with the use of more realistic amino acid
substitution models for the reconstruction of animal phylogeny.