[PDF][PDF] Strong purifying selection on codon usage bias
Codon usage bias (CUB), where certain codons are used more frequently than expected by
chance, is a ubiquitous phenomenon and occurs across the tree of life. The dominant …
chance, is a ubiquitous phenomenon and occurs across the tree of life. The dominant …
Molecular evolution in small steps under prevailing negative selection: a nearly universal rule of codon substitution
Q Chen, A Lan, X Shen, CI Wu - Genome biology and evolution, 2019 - academic.oup.com
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 …
1) negative selection acts strongly against large differences and 2) positive selection favors …
Inferring adaptive codon preference to understand sources of selection shaping codon usage bias
Alternative synonymous codons are often used at unequal frequencies. Classically, studies
of such codon usage bias (CUB) attempted to separate the impact of neutral from selective …
of such codon usage bias (CUB) attempted to separate the impact of neutral from selective …
Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles
M Botzman, H Margalit - Genome biology, 2011 - Springer
Background It is widely acknowledged that synonymous codons are used unevenly among
genes in a genome. In organisms under translational selection, genes encoding highly …
genes in a genome. In organisms under translational selection, genes encoding highly …
Genetic robustness and selection at the protein level for synonymous codons
M Archetti - Journal of Evolutionary Biology, 2006 - academic.oup.com
Synonymous codons are neutral at the protein level, therefore natural selection at the
protein level should have no effect on their frequencies. Synonymous codons, however …
protein level should have no effect on their frequencies. Synonymous codons, however …
Genome-wide patterns of codon usage in the Pacific oyster genome
K Song - Journal of Ocean University of China, 2021 - Springer
The use of synonymous codons with varying frequencies has been observed in many
species, and the magnitude varies among closely related species and genes within the …
species, and the magnitude varies among closely related species and genes within the …
The codon statistics database: a database of codon usage bias
K Subramanian, B Payne, F Feyertag… - Molecular Biology …, 2022 - academic.oup.com
Abstract We present the Codon Statistics Database, an online database that contains codon
usage statistics for all the species with reference or representative genomes in RefSeq (over …
usage statistics for all the species with reference or representative genomes in RefSeq (over …
Gene duplication, gene conversion and codon bias
DA Hickey, S Wang, C Magoulas - Non-Neutral Evolution: Theories and …, 1994 - Springer
Within many genes, synonymous codons are found in very unequal frequencies. This
observation of codon bias is often interpreted as a reflection of natural selection acting to …
observation of codon bias is often interpreted as a reflection of natural selection acting to …
Accounting for background nucleotide composition when measuring codon usage bias
JA Novembre - Molecular biology and evolution, 2002 - academic.oup.com
The phenomenon of codon usage bias has been important in the study of evolution because
it provides examples of weak selection working at the molecular level. During the last two …
it provides examples of weak selection working at the molecular level. During the last two …
Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale
Adaptation in protein-coding sequences can be detected from multiple sequence alignments
across species or alternatively by leveraging polymorphism data within a population. Across …
across species or alternatively by leveraging polymorphism data within a population. Across …