[HTML][HTML] A new codon adaptation metric predicts vertebrate body size and tendency to protein disorder
The nearly neutral theory of molecular evolution posits variation among species in the
effectiveness of selection. In an idealized model, the census population size determines …
effectiveness of selection. In an idealized model, the census population size determines …
Standard codon substitution models overestimate purifying selection for nonstationary data
BD Kaehler, VB Yap, GA Huttley - Genome biology and …, 2017 - academic.oup.com
Estimation of natural selection on protein-coding sequences is a key comparative genomics
approach for de novo prediction of lineage-specific adaptations. Selective pressure is …
approach for de novo prediction of lineage-specific adaptations. Selective pressure is …
The systematic codon usage bias has an important effect on genetic adaption in native species
AS Panja - Gene, 2024 - Elsevier
Random mutations increase genetic variety and natural selection enhances adaption over
generations. Codon usage biases (CUB) provide clues about the genome adaptation …
generations. Codon usage biases (CUB) provide clues about the genome adaptation …
Effective population size does not predict codon usage bias in mammals
MD Kessler, MD Dean - Ecology and evolution, 2014 - Wiley Online Library
Synonymous codons are not used at equal frequency throughout the genome, a
phenomenon termed codon usage bias (CUB). It is often assumed that interspecific variation …
phenomenon termed codon usage bias (CUB). It is often assumed that interspecific variation …
Codon usage bias in animals: disentangling the effects of natural selection, effective population size, and GC-biased gene conversion
Selection on codon usage bias is well documented in a number of microorganisms. Whether
codon usage is also generally shaped by natural selection in large organisms, despite their …
codon usage is also generally shaped by natural selection in large organisms, despite their …
Life history traits, protein evolution, and the nearly neutral theory in amniotes
E Figuet, B Nabholz, M Bonneau… - Molecular biology …, 2016 - academic.oup.com
The nearly neutral theory of molecular evolution predicts that small populations should
accumulate deleterious mutations at a faster rate than large populations. The analysis of …
accumulate deleterious mutations at a faster rate than large populations. The analysis of …
Phylogenetic analysis of mutational robustness based on codon usage supports that the standard genetic code does not prefer extreme environments
Á Radványi, Á Kun - Scientific Reports, 2021 - nature.com
The mutational robustness of the genetic code is rarely discussed in the context of biological
diversity, such as codon usage and related factors, often considered as independent of the …
diversity, such as codon usage and related factors, often considered as independent of the …
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 …
GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes
Background The nearly neutral theory of molecular evolution predicts that the efficacy of
natural selection increases with the effective population size. This prediction has been …
natural selection increases with the effective population size. This prediction has been …
Adaptive protein evolution in animals and the effective population size hypothesis
N Galtier - PLoS genetics, 2016 - journals.plos.org
The rate at which genomes adapt to environmental changes and the prevalence of adaptive
processes in molecular evolution are two controversial issues in current evolutionary …
processes in molecular evolution are two controversial issues in current evolutionary …