ArticleGenetics2013
Learning natural selection from the site frequency spectrum.
Article in Genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers, 1 of them a synthesis that pooled it.
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Who cites it
70 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection.Nature genetics · 2018Pooled it
- Genomic insights into natural selection in recent human history.Nature reviews. Genetics · 2026Review
- Why there are so many definitions of fitness in models.Genetics · 2026Review
- Neural posterior estimation for population genetics.Genetics · 2026Article
- Article
- Machine learning for evolutionary genetics and molecular evolution.Trends in genetics : TIG · 2026Review
- Soft Selective Sweeps Predominate in the Yellow Fever Mosquito Aedes aegypti.Molecular biology and evolution · 2026Article
- Neural posterior estimation for population genetics.bioRxiv : the preprint server for biology · 2026Article
- Coalescent theory of the ψ directionality index.G3 (Bethesda, Md.) · 2025Article
- Signatures of soft selective sweeps predominate in the yellow fever mosquitobioRxiv : the preprint server for biology · 2025Article
- Single-cell mutational burden distributions in birth-death processes.PLoS computational biology · 2025Article
- Population size rescaling significantly biases outcomes of forward-in-time population genetic simulations.Genetics · 2025Article
- Digital Image Processing to Detect Adaptive Evolution.Molecular biology and evolution · 2024Article
- Tree Sequences as a General-Purpose Tool for Population Genetic Inference.Molecular biology and evolution · 2024Article
- Tree sequences as a general-purpose tool for population genetic inference.bioRxiv : the preprint server for biology · 2024Article
- Population size rescaling significantly biases outcomes of forward-in-time population genetic simulations.bioRxiv : the preprint server for biology · 2024Article
- Exploring Adaptive Phenotypes for the Human Calcium-Sensing Receptor Polymorphism R990G.Molecular biology and evolution · 2024Article
- IntroUNET: Identifying introgressed alleles via semantic segmentation.PLoS genetics · 2024Article
- IntroUNET: identifying introgressed alleles via semantic segmentation.bioRxiv : the preprint server for biology · 2024Article
- Power of neutrality tests for detecting natural selection.G3 (Bethesda, Md.) · 2023Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Genetic adaptation to external stimuli occurs through the combined action of mutation and selection. A central problem in genetics is to identify loci responsive to specific selective constraints. Many tests have been proposed to identify the genomic signatures of natural selection by quantifying the skew in the site frequency spectrum (SFS) under selection relative to neutrality. We build upon recent work that connects many of these tests under a common framework, by describing how selective sweeps affect the scaled SFS. We show that the specific skew depends on many attributes of the sweep, including the selection coefficient and the time under selection. Using supervised learning on extensive simulated data, we characterize the features of the scaled SFS that best separate different types of selective sweeps from neutrality. We develop a test, SFselect, that consistently outperforms many existing tests over a wide range of selective sweeps. We apply SFselect to polymorphism data from a laboratory evolution experiment of Drosophila melanogaster adapted to hypoxia and identify loci that strengthen the role of the Notch pathway in hypoxia tolerance, but were missed by previous approaches. We further apply our test to human data and identify regions that are in agreement with earlier studies, as well as many novel regions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.