title: The population genomics of a fast evolver: high levels of diversity, functional constraint, and molecular adaptation in the tunicate Ciona intestinalis.
abstract: Phylogenomics has revealed the existence of fast-evolving animal phyla in which the amino acid substitution rate, averaged across many proteins, is consistently higher than in other lineages. The reasons for such differences in proteome-wide evolutionary rates are still unknown, largely because only a handful of species offer within-species genomic data from which molecular evolutionary processes can be deduced. In this study, we use next-generation sequencing technologies and individual whole-transcriptome sequencing to gather extensive polymorphism sequence data sets from Ciona intestinalis. Ciona is probably the best-characterized member of the fast-evolving Urochordata group (tunicates), which was recently identified as the sister group of the slow-evolving vertebrates. We introduce and validate a maximum-likelihood framework for single-nucleotide polymorphism and genotype calling, based on high-throughput short-read typing. We report that the C. intestinalis proteome is characterized by a high level of within-species diversity, efficient purifying selection, and a substantial percentage of adaptive amino acid substitutions. We conclude that the increased rate of amino acid sequence evolution in tunicates, when compared with vertebrates, is the consequence of both a 2-6 times higher per-year mutation rate and prevalent adaptive evolution.
authors: Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Montpellier, France. g.tsagkogeorga@qmul.ac.uk
authors: Georgia
authors: G
authors: Tsagkogeorga
authors: Vincent
authors: V
authors: Cahais
authors: Nicolas
authors: N
authors: Galtier
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000818:Animals; D044822:Biodiversity; D002938:Ciona intestinalis / Q000145:classification / Q000235:genetics* / Q000502:physiology; D019143:Evolution, Molecular; D023281:Genomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide