Journal Article

The Population Genomics of a Fast Evolver: High Levels of Diversity, Functional Constraint, and Molecular Adaptation in the Tunicate <i>Ciona intestinalis</i>

Georgia Tsagkogeorga, Vincent Cahais and Nicolas Galtier

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 4, issue 8, pages 740-749
Published in print January 2012 |
Published online June 2012 | e-ISSN: 1759-6653 | DOI: http://dx.doi.org/10.1093/gbe/evs054

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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.

Keywords: substitution rate; population size; mutation rate; next-generation sequencing; transcriptome

Journal Article.  6981 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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