Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
Open accessAbstract
A stringent branch-site codon model was used to detect positive selection in vertebrate evolution. We show that the test is robust to the large evolutionary distances involved. Positive selection was detected in 77% of 884 genes studied. Most positive selection concerns a few sites on a single branch of the phylogenetic tree: Between 0.9% and 4.7% of sites are affected by positive selection depending on the branches. No functional category was overrepresented among genes under positive selection. Surprisingly, whole genome duplication had no effect on the prevalence of positive selection, whether the fish-specific genome duplication or the two rounds at the origin of vertebrates. Thus positive selection has not been limited to a few gene classes, or to specific evolutionary events such as duplication, but has been pervasive during vertebrate evolution.
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Branch-site tests were shown to be robust to the large evolutionary distances of the vertebrate phylogeny.
“This was achieved by using branch-site tests, which were shown to be robust to the large evolutionary distances of the vertebrate phylogeny59.”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [59]
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- Authors
- Studer, R. A., Penel, S., Duret, L., & Robinson-Rechavi, M.
- Affiliations
- SIB Swiss Institute of Bioinformatics (CH)
- Centre National de la Recherche Scientifique (FR)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2008-06-18
- Volume
- 18
- Issue
- 9
- Pages
- 1393-1402
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2527703
- OpenAlex
- W2052743506
- Cited by
- 84
- References
- 90
- Citations by year
- 2025: 1 · 2023: 2 · 2022: 3 · 2020: 7 · 2019: 4 · 2017: 4 · 2016: 4 · 2015: 1 · 2014: 5 · 2013: 10 · 2012: 8
- Type
- posted content
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- other-oa
- Locations
- Genome Research (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- IRIS (submittedVersion)
- SERVAL (Université de Lausanne) (submittedVersion)
- Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, cc-by)
- Funders
- National Science Foundation
- Agence Nationale de la Recherche
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (116798)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- positive selection, vertebrate evolution, gene duplication, whole-genome duplication, protein-coding genes, vertebrate origin
- MeSH terms
- Animals, Codon, Selection, Genetic, Vertebrates, Computational Biology, Gene Duplication
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