ArticleGenetics2016
Inferring the Frequency Spectrum of Derived Variants to Quantify Adaptive Molecular Evolution in Protein-Coding Genes of Drosophila melanogaster.
Article in Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Identification of Genetic Variation Associated With Heat Tolerance in Cowpea (Vigna unguiculata L. Walp.).Molecular ecology · 2026Article
- The distribution of fitness effects of new mutations in regulatory regions of thebioRxiv : the preprint server for biology · 2026Article
- Polarising SNPs Without Outgroup.Molecular ecology resources · 2026Article
- Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection.Molecular biology and evolution · 2024Article
- Inferring the distributions of fitness effects and proportions of strongly deleterious mutations.G3 (Bethesda, Md.) · 2023Article
- On the prospect of achieving accurate joint estimation of selection with population history.Genome biology and evolution · 2022Article
- The distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii inferred using frequency changes under experimental evolution.PLoS genetics · 2022Article
- Hunting for Beneficial Mutations: Conditioning on SIFT Scores When Estimating the Distribution of Fitness Effect of New Mutations.Genome biology and evolution · 2022Article
- Investigation of ancestral alleles in the Bovinae subfamily.BMC genomics · 2021Article
- Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice andGenome research · 2021Article
- How Good Are Predictions of the Effects of Selective Sweeps on Levels of Neutral Diversity?Genetics · 2020Article
- How Much DoesGenetics · 2020Article
- Ape Origins of Human Malaria.Annual review of microbiology · 2020Review
- Inferring Parameters of the Distribution of Fitness Effects of New Mutations When Beneficial Mutations Are Strongly Advantageous and Rare.G3 (Bethesda, Md.) · 2020Article
- Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals.PLoS genetics · 2020Article
- Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species.Molecular biology and evolution · 2020Article
- Population Genomics on the Fly: Recent Advances in Drosophila.Methods in molecular biology (Clifton, N.J.) · 2020Review
- The population genetics of structural variants in grapevine domestication.Nature plants · 2019Article
- Inferring the Nature of Missing Heritability in Human Traits Using Data from the GWAS Catalog.Genetics · 2019Article
- Understanding the Factors That Shape Patterns of Nucleotide Diversity in the House Mouse Genome.Molecular biology and evolution · 2018Article
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4 authors.
Funding
Abstract
Many approaches for inferring adaptive molecular evolution analyze the unfolded site frequency spectrum (SFS), a vector of counts of sites with different numbers of copies of derived alleles in a sample of alleles from a population. Accurate inference of the high-copy-number elements of the SFS is difficult, however, because of misassignment of alleles as derived vs. ancestral. This is a known problem with parsimony using outgroup species. Here we show that the problem is particularly serious if there is variation in the substitution rate among sites brought about by variation in selective constraint levels. We present a new method for inferring the SFS using one or two outgroups that attempts to overcome the problem of misassignment. We show that two outgroups are required for accurate estimation of the SFS if there is substantial variation in selective constraints, which is expected to be the case for nonsynonymous sites in protein-coding genes. We apply the method to estimate unfolded SFSs for synonymous and nonsynonymous sites in a population of Drosophila melanogaster from phase 2 of the Drosophila Population Genomics Project. We use the unfolded spectra to estimate the frequency and strength of advantageous and deleterious mutations and estimate that ∼50% of amino acid substitutions are positively selected but that <0.5% of new amino acid mutations are beneficial, with a scaled selection strength of Nes ≈ 12.
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