ArticleNature ecology & evolution2019
Exploiting selection at linked sites to infer the rate and strength of adaptation.
Article in Nature ecology & evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- Pervasive relaxed selection on spermatogenesis genes coincident with the evolution of polygyny in gorillas.eLife · 2026Article
- Article
- The impact of non-neutral synonymous mutations when inferring selection on nonsynonymous mutations.Genetics · 2025Article
- Article
- The population genetics of convergent adaptation in maize and teosinte is not locally restricted.eLife · 2025Article
- Local genetic adaptation to habitat in wild chimpanzees.Science (New York, N.Y.) · 2025Article
- Applying the Classic Test dN/dS to Detect Selection in Archaea.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Adaptation in human immune cells residing in tissues at the frontline of infections.Nature communications · 2024Article
- Local genetic adaptation to habitat in wild chimpanzees.bioRxiv : the preprint server for biology · 2024Article
- Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection.Molecular biology and evolution · 2024Article
- An efficient and robust ABC approach to infer the rate and strength of adaptation.G3 (Bethesda, Md.) · 2024Article
- A quantitative genetic model of background selection in humans.PLoS genetics · 2024Article
- CEGA: a method for inferring natural selection by comparative population genomic analysis across species.Genome biology · 2023Article
- impMKT: the imputed McDonald and Kreitman test, a straightforward correction that significantly increases the evidence of positive selection of the McDonald and Kreitman test at the gene level.G3 (Bethesda, Md.) · 2022Review
- Globally Relaxed Selection and Local Adaptation in Boechera stricta.Genome biology and evolution · 2022Article
- The relative fitness of the de novo variants in general Lithuanian population vs. in individuals with intellectual disability.European journal of human genetics : EJHG · 2022Article
- Intermolecular Interactions Drive Protein Adaptive and Coadaptive Evolution at Both Species and Population Levels.Molecular biology and evolution · 2022Article
- Dissecting Genomic Determinants of Positive Selection with an Evolution-Guided Regression Model.Molecular biology and evolution · 2022Article
- Article
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3 authors.
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Abstract
Genomic data encode past evolutionary events and have the potential to reveal the strength, rate and biological drivers of adaptation. However, joint estimation of adaptation rate (α) and adaptation strength remains challenging because evolutionary processes such as demography, linkage and non-neutral polymorphism can confound inference. Here, we exploit the influence of background selection to reduce the fixation rate of weakly beneficial alleles to jointly infer the strength and rate of adaptation. We develop a McDonald-Kreitman-based method to infer adaptation rate and strength, and estimate α = 0.135 in human protein-coding sequences, 72% of which is contributed by weakly adaptive variants. We show that, in this adaptation regime, α is reduced ~25% by linkage genome-wide. Moreover, we show that virus-interacting proteins undergo adaptation that is both stronger and nearly twice as frequent as the genome average (α = 0.224, 56% due to strongly beneficial alleles). Our results suggest that, while most adaptation in human proteins is weakly beneficial, adaptation to viruses is often strongly beneficial. Our method provides a robust framework for estimation of adaptation rate and strength across species.
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