ArticleMolecular biology and evolution2024
Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA.
Article in Molecular biology and evolution, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed.
- Adaptive variation in butyrylcholinesterase-influenced lipid metabolism during horse domestication.Cell reports · 2026Article
- Genomic insights into natural selection in recent human history.Nature reviews. Genetics · 2026Review
- Evolution of virulence of a plant RNA virus in developmental stage-structured host populations.Molecular biology and evolution · 2026Article
- Jomon genomics reveal cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia.Science advances · 2026Article
- ARGformer: learning on ancestral recombination graphs with transformers.Bioinformatics (Oxford, England) · 2026Article
- Selection-guided discovery in South Asians implicates the MAPT locus in insulin resistance.medRxiv : the preprint server for health sciences · 2026Article
- Article
- Fast pairwise coalescence enables gene-resolution scans for recent selection in diverse human populations.bioRxiv : the preprint server for biology · 2026Article
- Insights into human adaptation from ancient DNA.Nature genetics · 2026Review
- Using drift coefficients as a basis for inferring times, effective population sizes, and genetic adaptations.Molecular biology and evolution · 2026Article
- Optimal Reference Panel Design in Ancient DNA Imputation from Coalescent Theory, Simulation, and Real Data Application with an Ancient Reference Panel.bioRxiv : the preprint server for biology · 2026Article
- Graph transformer for ancient ancestry inference.bioRxiv : the preprint server for biology · 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
- 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
- Genetic and functional evidence implicates amedRxiv : the preprint server for health sciences · 2025Article
- Selection Estimation from Genetic Time-Series Data: Effects of Limited Sampling and Genetic Drift.Molecular biology and evolution · 2025Article
- Multiple-testing corrections in selection scans using identity-by-descent segments.American journal of human genetics · 2025Article
- Inferring Domestic Goat Demographic History Through Ancient Genome Imputation.Genome biology and evolution · 2025Article
- Evolutionary histories of functional mutations during the domestication and spread ofProceedings of the National Academy of Sciences of the United States of America · 2025Article
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2 authors.
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Abstract
We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicability and its speed. We add the ability to use ancestral recombination graphs on ancient data as emissions to the underlying hidden Markov model, which enables CLUES2 to use both temporal and linkage information to make estimates of selection coefficients. We also fully implement the ability to estimate distinct selection coefficients in different epochs, which allows for the analysis of changes in selective pressures through time, as well as selection with dominance. In addition, we greatly increase the computational efficiency of CLUES2 over CLUES using several approximations to the forward-backward algorithms and develop a new way to reconstruct historic allele frequencies by integrating over the uncertainty in the estimation of the selection coefficients. We illustrate the accuracy of CLUES2 through extensive simulations and validate the importance sampling framework for integrating over the uncertainty in the inference of gene trees. We also show that CLUES2 is well-calibrated by showing that under the null hypothesis, the distribution of log-likelihood ratios follows a χ2 distribution with the appropriate degrees of freedom. We run CLUES2 on a set of recently published ancient human data from Western Eurasia and test for evidence of changing selection coefficients through time. We find significant evidence of changing selective pressures in several genes correlated with the introduction of agriculture to Europe and the ensuing dietary and demographic shifts of that time. In particular, our analysis supports previous hypotheses of strong selection on lactase persistence during periods of ancient famines and attenuated selection in more modern periods.
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