ArticlePLoS genetics2019
An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data.
Article in PLoS genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
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115 citing papers in PubMed.
- Ancient DNA and Human Physiology.Physiology (Bethesda, Md.) · 2026Review
- Genomic insights into natural selection in recent human history.Nature reviews. Genetics · 2026Review
- Jomon genomics reveal cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia.Science advances · 2026Article
- A VIM2/4 deletion, and premature truncations of CMT2 and FBX5, drive DNA methylation changes after colonization of a novel habitat.Nature plants · 2026Article
- Selection-guided discovery in South Asians implicates the MAPT locus in insulin resistance.medRxiv : the preprint server for health sciences · 2026Article
- A global map for introgressed structural variation and selection in humans.Science (New York, N.Y.) · 2026Article
- Fast pairwise coalescence enables gene-resolution scans for recent selection in diverse human populations.bioRxiv : the preprint server for biology · 2026Article
- Rapid adaptive increase of amylase gene copy number in Indigenous Andeans.Nature communications · 2026Article
- Using drift coefficients as a basis for inferring times, effective population sizes, and genetic adaptations.Molecular biology and evolution · 2026Article
- Polygenic and single-locus selection on BMI during Polynesian expansion.Journal of human genetics · 2026Article
- Graph transformer for ancient ancestry inference.bioRxiv : the preprint server for biology · 2026Article
- Article
- Summary statistics and approximate bayesian computation are comparable to convolutional neural networks for inferring times to fixation.bioRxiv : the preprint server for biology · 2026Article
- Polarising SNPs Without Outgroup.Molecular ecology resources · 2026Article
- Sudan's complex genetic admixture history drives adaptation to malaria in Sudanese Copts.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Likelihoods for a general class of ARGs under the SMC.Genetics · 2026Article
- Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies.Genome biology and evolution · 2026Review
- Selection scans and downstream analysis with selscan.Human population genetics and genomics · 2026Article
- The origin of the double-muscle mutation in theFrontiers in veterinary science · 2026Article
- Multiple-testing corrections in selection scans using identity-by-descent segments.American journal of human genetics · 2025Article
55 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Most current methods for detecting natural selection from DNA sequence data are limited in that they are either based on summary statistics or a composite likelihood, and as a consequence, do not make full use of the information available in DNA sequence data. We here present a new importance sampling approach for approximating the full likelihood function for the selection coefficient. Our method CLUES treats the ancestral recombination graph (ARG) as a latent variable that is integrated out using previously published Markov Chain Monte Carlo (MCMC) methods. The method can be used for detecting selection, estimating selection coefficients, testing models of changes in the strength of selection, estimating the time of the start of a selective sweep, and for inferring the allele frequency trajectory of a selected or neutral allele. We perform extensive simulations to evaluate the method and show that it uniformly improves power to detect selection compared to current popular methods such as nSL and SDS, and can provide reliable inferences of allele frequency trajectories under many conditions. We also explore the potential of our method to detect extremely recent changes in the strength of selection. We use the method to infer the past allele frequency trajectory for a lactase persistence SNP (MCM6) in Europeans. We also infer the trajectory of a SNP (EDAR) in Han Chinese, finding evidence that this allele's age is much older than previously claimed. We also study a set of 11 pigmentation-associated variants. Several genes show evidence of strong selection particularly within the last 5,000 years, including ASIP, KITLG, and TYR. However, selection on OCA2/HERC2 seems to be much older and, in contrast to previous claims, we find no evidence of selection on TYRP1.
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