ArticlePLoS genetics2016
Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 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
49 citing papers in PubMed, 92 citations in OpenAlex.
- Inference of elevated mutation rates and variant effects using 700k exomes.bioRxiv : the preprint server for biology · 2026Article
- Causal inference clarifies the roles of background selection and mutation rate variation in shaping human genetic diversity.bioRxiv : the preprint server for biology · 2026Article
- Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.PLoS genetics · 2026Article
- Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.bioRxiv : the preprint server for biology · 2026Article
- Mutation-selection-drift balance models of complex diseases.Genetics · 2025Article
- Article
- Estimation of demography and mutation rates from one million haploid genomes.American journal of human genetics · 2025Article
- Mutation-selection-drift balance models of complex diseases.bioRxiv : the preprint server for biology · 2025Article
- Article
- Diverse genetic conflicts mediated by molecular mimicry and computational approaches to detect them.Seminars in cell & developmental biology · 2025Review
- Benchmarking of variant pathogenicity prediction methods using a population genetics approach.Bioinformatics advances · 2025Article
- Digital Image Processing to Detect Adaptive Evolution.Molecular biology and evolution · 2024Article
- Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation.Science (New York, N.Y.) · 2024Article
- Context-adjusted proportion of singletons (CAPS): a novel metric for assessing negative selection in the human genome.NAR genomics and bioinformatics · 2024Article
- Conditional frequency spectra as a tool for studying selection on complex traits in biobanks.bioRxiv : the preprint server for biology · 2024Article
- Bayesian estimation of gene constraint from an evolutionary model with gene features.bioRxiv : the preprint server for biology · 2024Article
- The Promise of Inferring the Past Using the Ancestral Recombination Graph.Genome biology and evolution · 2024Article
- Quantifying negative selection in human 3' UTRs uncovers constrained targets of RNA-binding proteins.Nature communications · 2024Article
- A mutation rate model at the basepair resolution identifies the mutagenic effect of polymerase III transcription.Nature genetics · 2023Article
- Article
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 at 2 institutions in 1 country.
Funding
Abstract
The site frequency spectrum (SFS) has long been used to study demographic history and natural selection. Here, we extend this summary by examining the SFS conditional on the alleles found at the same site in other species. We refer to this extension as the "phylogenetically-conditioned SFS" or cSFS. Using recent large-sample data from the Exome Aggregation Consortium (ExAC), combined with primate genome sequences, we find that human variants that occurred independently in closely related primate lineages are at higher frequencies in humans than variants with parallel substitutions in more distant primates. We show that this effect is largely due to sites with elevated mutation rates causing significant departures from the widely-used infinite sites mutation model. Our analysis also suggests substantial variation in mutation rates even among mutations involving the same nucleotide changes. In summary, we show that variable mutation rates are key determinants of the SFS in humans.
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.