ArticleGenetics2010
The effects of demography and linkage on the estimation of selection and mutation parameters.
Article in Genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Tests of evolutionary and genetic rescue using flour beetles,Ecology and evolution · 2024Article
- Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection.Genetics · 2020Article
- The evolution of metabolism: How to test evolutionary hypotheses at the genomic level.Computational and structural biotechnology journal · 2020Review
- The importance of the Neutral Theory in 1968 and 50 years on: A response to Kern and Hahn 2018.Evolution; international journal of organic evolution · 2019Article
- Article
- Background selection as null hypothesis in population genomics: insights and challenges fromPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Article
- Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence.Molecular biology and evolution · 2017Article
- Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila.Genome biology and evolution · 2017Article
- Article
- The Effects of Background and Interference Selection on Patterns of Genetic Variation in Subdivided Populations.Genetics · 2015Article
- The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations.Heredity · 2015Article
- The relation between recombination rate and patterns of molecular evolution and variation in Drosophila melanogaster.Molecular biology and evolution · 2014Article
- The effects of linkage on comparative estimators of selection.BMC evolutionary biology · 2013Article
- Rates and genomic consequences of spontaneous mutational events in Drosophila melanogaster.Genetics · 2013Article
- Codon usage bias and effective population sizes on the X chromosome versus the autosomes in Drosophila melanogaster.Molecular biology and evolution · 2013Article
- Review
- The joint effects of background selection and genetic recombination on local gene genealogies.Genetics · 2011Article
- Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species.Genome biology and evolution · 2011Article
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2 authors.
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Abstract
We explore the effects of demography and linkage on a maximum-likelihood (ML) method for estimating selection and mutation parameters in a reversible mutation model. This method assumes free recombination between sites and a randomly mating population of constant size and uses information from both polymorphic and monomorphic sites in the sample. Two likelihood-ratio test statistics were constructed under this ML framework: LRTγ for detecting selection and LRTκ for detecting mutational bias. By carrying out extensive simulations, we obtain the following results. When mutations are neutral and population size is constant, LRTγ and LRTκ follow a chi-square distribution with 1 d.f. regardless of the level of linkage, as long as the mutation rate is not very high. In addition, LRTγ and LRTκ are relatively insensitive to demographic effects and selection at linked sites. We find that the ML estimators of the selection and mutation parameters are usually approximately unbiased and that LRTκ usually has good power to detect mutational bias. Finally, with a recombination rate that is typical for Drosophila, LRTγ has good power to detect weak selection acting on synonymous sites. These results suggest that the method should be useful under many different circumstances.
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