ArticleThe annals of applied statistics2014
A NOVEL SPECTRAL METHOD FOR INFERRING GENERAL DIPLOID SELECTION FROM TIME SERIES GENETIC DATA.
Article in The annals of applied statistics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed, 89 citations in OpenAlex.
- Direct estimation of genotype fitness from time series.bioRxiv : the preprint server for biology · 2026Article
- Insights into human adaptation from ancient DNA.Nature genetics · 2026Review
- The genetic architecture and spatiotemporal dynamics of adaptation across human-modified landscapes.The New phytologist · 2026Review
- Selection Estimation from Genetic Time-Series Data: Effects of Limited Sampling and Genetic Drift.Molecular biology and evolution · 2025Article
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- diplo-locus: a lightweight toolkit for inference and simulation of time-series genetic data under general diploid selection.G3 (Bethesda, Md.) · 2025Article
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- A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.PLoS genetics · 2025Article
- A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.bioRxiv : the preprint server for biology · 2025Article
- diplo-locus: A lightweight toolkit for inference and simulation of time-series genetic data under general diploid selection.bioRxiv : the preprint server for biology · 2025Article
- Article
- Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA.Molecular biology and evolution · 2024Article
- A Path Integral Approach for Allele Frequency Dynamics Under Polygenic Selection.bioRxiv : the preprint server for biology · 2024Article
- Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England.PLoS pathogens · 2024Article
- Article
- Timesweeper: accurately identifying selective sweeps using population genomic time series.Genetics · 2023Article
- Scaling the Discrete-time Wright Fisher model to biobank-scale datasets.bioRxiv : the preprint server for biology · 2023Article
- Estimating Temporally Variable Selection Intensity from Ancient DNA Data.Molecular biology and evolution · 2023Article
- Bait-ER: A Bayesian method to detect targets of selection in Evolve-and-Resequence experiments.Journal of evolutionary biology · 2023Article
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3 authors at 1 institution in 1 country.
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Abstract
The increased availability of time series genetic variation data from experimental evolution studies and ancient DNA samples has created new opportunities to identify genomic regions under selective pressure and to estimate their associated fitness parameters. However, it is a challenging problem to compute the likelihood of non-neutral models for the population allele frequency dynamics, given the observed temporal DNA data. Here, we develop a novel spectral algorithm to analytically and efficiently integrate over all possible frequency trajectories between consecutive time points. This advance circumvents the limitations of existing methods which require fine-tuning the discretization of the population allele frequency space when numerically approximating requisite integrals. Furthermore, our method is flexible enough to handle general diploid models of selection where the heterozygote and homozygote fitness parameters can take any values, while previous methods focused on only a few restricted models of selection. We demonstrate the utility of our method on simulated data and also apply it to analyze ancient DNA data from genetic loci associated with coat coloration in horses. In contrast to previous studies, our exploration of the full fitness parameter space reveals that a heterozygote-advantage form of balancing selection may have been acting on these loci.
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