Abstract
BackgroundTunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates. Their phylogeny, however, remains poorly understood, and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. To resolve their evolutionary relationships and provide a first estimate of their divergence times, we used a transcriptomic approach to build a phylogenomic dataset including all major tunicate lineages, consisting of 258 evolutionarily conserved orthologous genes from representative species.ResultsPhylogenetic analyses using site-heterogeneous CAT mixture models of amino acid sequence evolution resulted in a strongly supported tree topology resolving the relationships among four major tunicate clades: (1) Appendicularia, (2) Thaliacea + Phlebobranchia + Aplousobranchia, (3) Molgulidae, and (4) Styelidae + Pyuridae. Notably, the morphologically derived Thaliacea are confirmed as the sister group of the clade uniting Phlebobranchia + Aplousobranchia within which the precise position of the model ascidian genus Ciona remains uncertain. Relaxed molecular clock analyses accommodating the accelerated evolutionary rate of tunicates reveal ancient diversification (~ 450–350 million years ago) among the major groups and allow one to compare their evolutionary age with respect to the major vertebrate model lineages.ConclusionsOur study represents the most comprehensive phylogenomic dataset for the main tunicate lineages. It offers a reference phylogenetic framework and first tentative timescale for tunicates, allowing a direct comparison with vertebrate model species in comparative genomics and evolutionary developmental biology studies.
Highlights
Tunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates
A reference phylogenetic framework for model tunicates The evolutionary relationships of tunicates have long been a matter of debate, mainly because tunicates are characterized by an overall accelerated rate of evolution in their nuclear and mitochondrial genomes compared to other deuterostome species
The large lineage-specific variation in evolutionary rates among tunicates [16] could result in long-branch attraction (LBA) artefacts, which hamper the reliable reconstruction of their phylogenetic relationships [55,56,57]
Summary
Tunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates Their phylogeny, remains poorly understood, and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. Previous molecular phylogenetic studies relying on 18S rRNA [23,24,25,26] and mitogenomes [20, 27, 28] have proposed first delineations of major tunicate clades, revoking the traditional nineteenth century classification into the three classes Appendicularia (larvaceans), Thaliacea (salps, doliolids, and pyrosomes), and Ascidiacea (phlebobranchs, aplousobranchs, and stolidobranchs). The relationships within the latter group were left unresolved, with the position of thaliaceans relative to phlebobranchs and aplousobranchs still being debated [25, 27]
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