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BMC Biol. 2018 Apr 13;16(1):39. doi: 10.1186/s12915-018-0499-2.

A phylogenomic framework and timescale for comparative studies of tunicates.

Author information

1
ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France. Frederic.Delsuc@umontpellier.fr.
2
Centre for Biodiversity Theory and Modelling, UMR CNRS 5321, Station d'Ecologie Théorique et Expérimentale, Moulis, France.
3
Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montréal, Canada.
4
ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.
5
School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
6
Center for Advanced Studies of Blanes (CEAB, CSIC), Girona, Spain.
7
Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, USA.
8
Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237, CNRS, Université de Montpellier, Montpellier, France.

Abstract

BACKGROUND:

Tunicates 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.

RESULTS:

Phylogenetic 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.

CONCLUSIONS:

Our 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.

KEYWORDS:

Evo-devo; Molecular dating; Phylogenomics; Thaliacea; Transcriptomes; Tunicata

PMID:
29653534
PMCID:
PMC5899321
DOI:
10.1186/s12915-018-0499-2
[Indexed for MEDLINE]
Free PMC Article

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