ArticleGenetics2008
The polymorphism frequency spectrum of finitely many sites under selection.
Article in Genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Ecological and evolutionary dynamics of the oral microbiome across childhood.bioRxiv : the preprint server for biology · 2026Article
- Estimation of demography and mutation rates from one million haploid genomes.American journal of human genetics · 2025Article
- Eco-evolutionary robustness of wild bacterial communities to experimental perturbation.The ISME journal · 2025Article
- Recurrent mutation in the ancestry of a rare variant.Genetics · 2023Article
- Effects ofFrontiers in public health · 2022Article
- Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence.Molecular biology and evolution · 2017Article
- Article
- PReFerSim: fast simulation of demography and selection under the Poisson Random Field model.Bioinformatics (Oxford, England) · 2016Article
- Triallelic Population Genomics for Inferring Correlated Fitness Effects of Same Site Nonsynonymous Mutations.Genetics · 2016Article
- Purifying selection, drift, and reversible mutation with arbitrarily high mutation rates.Genetics · 2014Article
- The equilibrium allele frequency distribution for a population with reproductive skew.Genetics · 2014Article
- Identifying signatures of selection in genetic time series.Genetics · 2014Article
- General triallelic frequency spectrum under demographic models with variable population size.Genetics · 2014Article
- Why to account for finite sites in population genetic studies and how to do this with Jaatha 2.0.Ecology and evolution · 2013Article
- Evolution of the human gastrokine locus and confounding factors regarding the pseudogenicity of GKN3.Physiological genomics · 2013Article
- Molecular hyperdiversity defines populations of the nematode Caenorhabditis brenneri.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Molecular hyperdiversity and evolution in very large populations.Molecular ecology · 2013Article
- Article
- The allele-frequency spectrum in a decoupled Moran model with mutation, drift, and directional selection, assuming small mutation rates.Theoretical population biology · 2012Article
- A population genetics-phylogenetics approach to inferring natural selection in coding sequences.PLoS genetics · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The distribution of genetic polymorphisms in a population contains information about evolutionary processes. The Poisson random field (PRF) model uses the polymorphism frequency spectrum to infer the mutation rate and the strength of directional selection. The PRF model relies on an infinite-sites approximation that is reasonable for most eukaryotic populations, but that becomes problematic when is large ( greater, similar 0.05). Here, we show that at large mutation rates characteristic of microbes and viruses the infinite-sites approximation of the PRF model induces systematic biases that lead it to underestimate negative selection pressures and mutation rates and erroneously infer positive selection. We introduce two new methods that extend our ability to infer selection pressures and mutation rates at large : a finite-site modification of the PRF model and a new technique based on diffusion theory. Our methods can be used to infer not only a "weighted average" of selection pressures acting on a gene sequence, but also the distribution of selection pressures across sites. We evaluate the accuracy of our methods, as well that of the original PRF approach, by comparison with Wright-Fisher simulations.
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