Discover Community Create You

Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Article

Weak selection on synonymous codons substantially inflates dN/dS estimates in bacteria.

Proceedings of the National Academy of Sciences of the United States of America - 18 May 2021

Rahman Shakibur, Kosakovsky Pond Sergei L, Webb Andrew, Hey Jody

Abstract excerpt

Synonymous codon substitutions are not always selectively neutral as revealed by several types of analyses, including studies of codon usage patterns among genes. We analyzed codon usage in 13 bacterial genomes sampled from across a large order of bacteria, Enterobacterales, and identified presumptively neutral and selected classes of synonymous substitutions. To estimate substitution rates, given a...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Bacterial Load
Share to Biological Evolution

Methodology Data sources Editorial policy Privacy Delete account & data About Contact Helena Bioinformatics

Share to Enterobacteriaceae

Share to Genome, Bacterial

Share to Models, Statistical

Share to Selection, Genetic

Share to Silent Mutation

Source

Open in PubMed Open full text

Identifiers

PMID: 33972434
DOI: 10.1073/pnas.2023575118
PMCID: PMC8157954

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 7 Sept 2026. Manifest publication-graph-cohort-2026-09-08.1.

Source receipt: pubmed, retrieved 7 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence. Graph snapshot: 2026-09-29.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

Weak selection on synonymous codons substantially inflates dN/dS estimates in bacteria.PMID 33972434Read ↗

Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation.Semantic proximity Read ↗

Estimating the evolutionary fitness of specific synonymous codon changes.Semantic proximity Read ↗

Selection on codon bias.Semantic proximity Read ↗

Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage.Semantic proximity Read ↗

Adjusting for selection on synonymous sites in estimates of evolutionary distance.Semantic proximity Read ↗

Codon usage and selection on proteins.Semantic proximity Read ↗

Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage.Semantic proximity Read ↗

Significance and roles of synonymous codon usage in the evolutionary process of Proteus.Semantic proximity Read ↗

The relationship between dN/dS and scaled selection coefficients.Semantic proximity Read ↗

Effects of Synonymous Mutations beyond Codon Bias: The Evidence for Adaptive Synonymous Substitutions from Microbial Evolution Experiments.Semantic proximity Read ↗

No Evidence that Selection on Synonymous Codon Usage Affects Patterns of Protein Evolution in Bacteria.Semantic proximity Read ↗

A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes.Semantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.