ArticleMolecular biology and evolution2021
Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed.
- Untangling the effects of within-host and between-host natural selection in viruses with applications to evolution of HIV-1 co-receptor usage.Journal of the Royal Society, Interface · 2026Article
- Review
- Multiple prophage acquisition events over the course of an outbreak drive lysogenic conversion of capsular polysaccharides produced by carbapenem-resistantMicrobiology spectrum · 2026Article
- Genomic epidemiology ofMicrobial genomics · 2026Article
- Emergence of distinct Streptococcus pyogenes emm1 and emm12 lineages in China.Nature microbiology · 2026Article
- DiagnoDating: diagnostics for dated phylogenies in microbial population genetics.Molecular biology and evolution · 2026Article
- Quantifying the real-world impact of antibiotic use and genetic determinants of resistance on gonococcal dynamics.Nature microbiology · 2026Article
- Inference of Multiple Mergers while Dating a Pathogen Phylogeny.Systematic biology · 2025Article
- Genomic analysis of theMicrobial genomics · 2025Article
- Genome analysis ofMicrobial genomics · 2025Article
- Tracing SARS-CoV-2 clusters across local scales using genomic data.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Infinite Mixture Models for Improved Modeling of Across-Site Evolutionary Variation.Molecular biology and evolution · 2025Article
- A single mutation may contribute to accelerated evolution of SARS-CoV-2 toward Omicron.Nature communications · 2025Article
- Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model.PLoS computational biology · 2025Article
- Evidence for circulation of high-virulence HIV-1 subtype B variants in the United Kingdom.Virus evolution · 2025Article
- Phylogenetic meta-analysis of persistent SARS-CoV-2 infections in immunocompromised individuals highlights the challenges of robust evolutionary rate estimation caused by low genetic diversity.Virus evolution · 2025Article
- Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock.Genome biology and evolution · 2024Review
- Five centuries of genome evolution and multi-host adaptation ofMicrobial genomics · 2024Article
- Estimating geographical spread ofMicrobial genomics · 2024Article
- Detecting Episodic Evolution through Bayesian Inference of Molecular Clock Models.Molecular biology and evolution · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Phylogenetic dating is one of the most powerful and commonly used methods of drawing epidemiological interpretations from pathogen genomic data. Building such trees requires considering a molecular clock model which represents the rate at which substitutions accumulate on genomes. When the molecular clock rate is constant throughout the tree then the clock is said to be strict, but this is often not an acceptable assumption. Alternatively, relaxed clock models consider variations in the clock rate, often based on a distribution of rates for each branch. However, we show here that the distributions of rates across branches in commonly used relaxed clock models are incompatible with the biological expectation that the sum of the numbers of substitutions on two neighboring branches should be distributed as the substitution number on a single branch of equivalent length. We call this expectation the additivity property. We further show how assumptions of commonly used relaxed clock models can lead to estimates of evolutionary rates and dates with low precision and biased confidence intervals. We therefore propose a new additive relaxed clock model where the additivity property is satisfied. We illustrate the use of our new additive relaxed clock model on a range of simulated and real data sets, and we show that using this new model leads to more accurate estimates of mean evolutionary rates and ancestral dates.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.