ArticleProceedings of the National Academy of Sciences of the United States of America2013
Frequent adaptation and the McDonald-Kreitman test.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers.
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140 citing papers in PubMed.
- Diversity and divergence of two sympatric, sibling octopus species.Molecular biology and evolution · 2026Article
- MKado: a toolkit for McDonald-Kreitman tests of natural selection.G3 (Bethesda, Md.) · 2026Article
- Epistasis among clustered lineage-specific amino acid substitutions in the Drosophila Trio protein.PLoS genetics · 2026Article
- The distribution of fitness effects of new mutations in regulatory regions of thebioRxiv : the preprint server for biology · 2026Article
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- Comparative population genomics reveals convergent adaptation across independent origins of avian obligate brood parasitism.Nature ecology & evolution · 2026Article
- Protein structure shapes natural genetic variation andbioRxiv : the preprint server for biology · 2025Article
- The impact of non-neutral synonymous mutations when inferring selection on nonsynonymous mutations.Genetics · 2025Article
- Epistasis among clustered lineage-specific adaptive amino acid substitutions in the Drosophila Trio protein.bioRxiv : the preprint server for biology · 2025Article
- Article
- The Evolutionary History and Modern Diversity of Triterpenoid Cyclases.Molecular biology and evolution · 2025Article
- The evolutionary history and modern diversity of triterpenoid cyclases.bioRxiv : the preprint server for biology · 2025Article
- Faster adaptation but slower divergence of X chromosomes under paternal genome elimination.Nature communications · 2025Article
- Inferring demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data.G3 (Bethesda, Md.) · 2025Article
- Article
- The population genetics of convergent adaptation in maize and teosinte is not locally restricted.eLife · 2025Article
- Evolutionary signatures of the erosion of sexual reproduction genes in domesticated cassava (Manihot esculenta).G3 (Bethesda, Md.) · 2025Article
- Applying the Classic Test dN/dS to Detect Selection in Archaea.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Detection of domestication signals through the analysis of the full distribution of fitness effects.Peer community journal · 2025Article
- Adaptation in human immune cells residing in tissues at the frontline of infections.Nature communications · 2024Article
80 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Population genomic studies have shown that genetic draft and background selection can profoundly affect the genome-wide patterns of molecular variation. We performed forward simulations under realistic gene-structure and selection scenarios to investigate whether such linkage effects impinge on the ability of the McDonald-Kreitman (MK) test to infer the rate of positive selection (α) from polymorphism and divergence data. We find that in the presence of slightly deleterious mutations, MK estimates of α severely underestimate the true rate of adaptation even if all polymorphisms with population frequencies under 50% are excluded. Furthermore, already under intermediate rates of adaptation, genetic draft substantially distorts the site frequency spectra at neutral and functional sites from the expectations under mutation-selection-drift balance. MK-type approaches that first infer demography from synonymous sites and then use the inferred demography to correct the estimation of α obtain almost the correct α in our simulations. However, these approaches typically infer a severe past population expansion although there was no such expansion in the simulations, casting doubt on the accuracy of methods that infer demography from synonymous polymorphism data. We propose a simple asymptotic extension of the MK test that yields accurate estimates of α in our simulations and should provide a fruitful direction for future studies.
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