ArticleGenetics2005
A composite-likelihood approach for detecting directional selection from DNA sequence data.
Article in Genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Pervasive cryptic selection in the human noncoding genome.bioRxiv : the preprint server for biology · 2026Article
- A single mutation may contribute to accelerated evolution of SARS-CoV-2 toward Omicron.Nature communications · 2025Article
- Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2.Cell host & microbe · 2021Article
- Rapid Spread of Mutant Alleles in Worldwide SARS-CoV-2 Strains Revealed by Genome-Wide Single Nucleotide Polymorphism and Variation Analysis.Genome biology and evolution · 2021Article
- Genomic recombination events may reveal the evolution of coronavirus and the origin of SARS-CoV-2.Scientific reports · 2020Article
- Long-read bitter gourd (Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- ASFVdb: an integrative resource for genomic and proteomic analyses of African swine fever virus.Database : the journal of biological databases and curation · 2020Article
- Article
- Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence.Molecular biology and evolution · 2017Article
- Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry.BMC evolutionary biology · 2015Article
- Statistical inference of selection and divergence of the rice blast resistance gene Pi-ta.G3 (Bethesda, Md.) · 2014Article
- Robust demographic inference from genomic and SNP data.PLoS genetics · 2013Article
- Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans.Molecular biology and evolution · 2013Article
- Genome sequencing reveals complex speciation in the Drosophila simulans clade.Genome research · 2012Article
- Statistical inference of selection and divergence from a time-dependent Poisson random field model.PloS one · 2012Article
- Improved haplotype-based detection of ongoing selective sweeps towards an application in Arabidopsis thaliana.BMC research notes · 2011Article
- The effects of demography and linkage on the estimation of selection and mutation parameters.Genetics · 2010Article
- Integrating evolutionary and functional approaches to infer adaptation at specific loci.Evolution; international journal of organic evolution · 2010Article
- A population genetic hidden Markov model for detecting genomic regions under selection.Molecular biology and evolution · 2010Article
- Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We present a novel composite-likelihood-ratio test (CLRT) for detecting genes and genomic regions that are subject to recurrent natural selection (either positive or negative). The method uses the likelihood functions of Hartl et al. (1994) for inference in a Wright-Fisher genic selection model and corrects for nonindependence among sites by application of coalescent simulations with recombination. Here, we (1) characterize the distribution of the CLRT statistic (Lambda) as a function of the population recombination rate (R=4Ner); (2) explore the effects of bias in estimation of R on the size (type I error) of the CLRT; (3) explore the robustness of the model to population growth, bottlenecks, and migration; (4) explore the power of the CLRT under varying levels of mutation, selection, and recombination; (5) explore the discriminatory power of the test in distinguishing negative selection from population growth; and (6) evaluate the performance of maximum composite-likelihood estimation (MCLE) of the selection coefficient. We find that the test has excellent power to detect weak negative selection and moderate power to detect positive selection. Moreover, the test is quite robust to bias in the estimate of local recombination rate, but not to certain demographic scenarios such as population growth or a recent bottleneck. Last, we demonstrate that the MCLE of the selection parameter has little bias for weak negative selection and has downward bias for positively selected mutations.
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