Treffer: Molecular Evolution in Small Steps under Prevailing Negative Selection: A Nearly Universal Rule of Codon Substitution.

Title:
Molecular Evolution in Small Steps under Prevailing Negative Selection: A Nearly Universal Rule of Codon Substitution.
Authors:
Chen Q; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China., Lan A; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China., Shen X; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China., Wu CI; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.; Department of Ecology and Evolution, University of Chicago.
Source:
Genome biology and evolution [Genome Biol Evol] 2019 Oct 01; Vol. 11 (10), pp. 2702-2712.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 101509707 Publication Model: Print Cited Medium: Internet ISSN: 1759-6653 (Electronic) Linking ISSN: 17596653 NLM ISO Abbreviation: Genome Biol Evol Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford, UK : Oxford University Press
MeSH Terms:
Codon* , Evolution, Molecular*, Amino Acids/genetics ; Models, Genetic ; Selection, Genetic
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Contributed Indexing:
Keywords: Fisher’s Geometric Model; amino acid distance; codon evolution; negative selection
Substance Nomenclature:
0 (Amino Acids)
0 (Codon)
Entry Date(s):
Date Created: 20190911 Date Completed: 20200327 Latest Revision: 20200327
Update Code:
20250114
PubMed Central ID:
PMC6777424
DOI:
10.1093/gbe/evz192
PMID:
31504473
Database:
MEDLINE

Weitere Informationen

The widely accepted view that evolution proceeds in small steps is based on two premises: 1) negative selection acts strongly against large differences and 2) positive selection favors small-step changes. The two premises are not biologically connected and should be evaluated separately. We now extend a previous approach to studying codon evolution in the entire genome. Codon substitution rate is a function of the physicochemical distance between amino acids (AAs), equated with the step size of evolution. Between nine pairs of closely related species of plants, invertebrates, and vertebrates, the evolutionary rate is strongly and negatively correlated with a set of AA distances (ΔU, scaled to [0, 1]). ΔU, a composite measure of evolutionary rates across diverse taxa, is influenced by almost all of the 48 physicochemical properties used here. The new analyses reveal a crucial trend hidden from previous studies: ΔU is strongly correlated with the evolutionary rate (R2 > 0.8) only when the genes are predominantly under negative selection. Because most genes in most taxa are strongly constrained by negative selection, ΔU has indeed appeared to be a nearly universal measure of codon evolution. In conclusion, molecular evolution at the codon level generally takes small steps due to the prevailing negative selection. Whether positive selection may, or may not, follow the small-step rule is addressed in a companion study.
(© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)