ArticleMicrobial genomics2016
Genome-scale rates of evolutionary change in bacteria.
Article in Microbial genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 183 papers, 1 of them a synthesis that pooled it.
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Who cites it
183 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- The Limits of Bayesian Estimates of Divergence Times in Measurably Evolving Populations.Genome biology and evolution · 2026Article
- Investigating pathways of vancomycin-resistantmedRxiv : the preprint server for health sciences · 2026Article
- Article
- Genomic surveillance reveals long-term endemicity and outbreak potential ofMicrobial genomics · 2026Article
- The Phylodynamic Threshold of Measurably Evolving Populations.Molecular biology and evolution · 2026Article
- The island biology of the host microbiome.Trends in microbiology · 2026Review
- Insights into infectious diseases through ancient pathogen genomics.Nature reviews. Microbiology · 2026Review
- Reconstructing the Network of Horizontal Gene Exchange in Bacteria to Differentiate Direct and Indirect Transfers.Genome biology and evolution · 2026Article
- Genomic signatures of dominant clones and evolutionary divergence ofMicrobial genomics · 2026Article
- Genomic and patient epidemiology ofMicrobiology spectrum · 2026Article
- A bacterial ecocline in Klebsiella pneumoniae may explain its backboned phylogeny.PLoS biology · 2026Article
- Multicountry genomic analysis underscores regional cholera spread in Africa.Nature communications · 2026Article
- Pathogenic potential and phylogenomic analysis ofMicrobial genomics · 2026Article
- Tick-associated microorganisms (Current research in parasitology & vector-borne diseases · 2026Article
- A Novel Bioinformatics Pipeline and a Machine-Learning Approach for Antimicrobial Resistance Phenotypic Prediction.Bioinformatics and biology insights · 2026Article
- Genomic and ecological systems-thinking framework for pathogenicFrontiers in public health · 2026Article
- Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.Nature communications · 2025Article
- Reliable estimates of Japanese encephalitis virus evolutionary rate supported by a formal test of temporal signal.Molecular genetics and genomics : MGG · 2025Article
- Community-associated Carbapenem-Resistant Organism Case Investigations in New York City.Open forum infectious diseases · 2025Article
123 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with 'ancient DNA' data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from approximately 10
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.