ArticleGenetics2017
Clear: Composition of Likelihoods for Evolve and Resequence Experiments.
Article in Genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Direct estimation of genotype fitness from time series.bioRxiv : the preprint server for biology · 2026Article
- Linkage-aware inference of fitness from short-read time-series genomic data.bioRxiv : the preprint server for biology · 2026Article
- Linkage-aware inference of fitness from short-read time-series genomic data.Virus evolution · 2026Article
- Selection Estimation from Genetic Time-Series Data: Effects of Limited Sampling and Genetic Drift.Molecular biology and evolution · 2025Article
- Aphid herbivory on macrophytes drives adaptive evolution in an aquatic community via indirect effects.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A single mutation may contribute to accelerated evolution of SARS-CoV-2 toward Omicron.Nature communications · 2025Article
- A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.PLoS genetics · 2025Article
- Repeatability of evolution and genomic predictions of temperature adaptation in seed beetles.Nature ecology & evolution · 2025Article
- A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.bioRxiv : the preprint server for biology · 2025Article
- Article
- Timesweeper: accurately identifying selective sweeps using population genomic time series.Genetics · 2023Article
- Embracing Complexity: Yeast Evolution Experiments Featuring Standing Genetic Variation.Journal of molecular evolution · 2023Review
- Bézier interpolation improves the inference of dynamical models from data.Physical review. E · 2023Article
- Bait-ER: A Bayesian method to detect targets of selection in Evolve-and-Resequence experiments.Journal of evolutionary biology · 2023Article
- Inferring Epistasis from Genetic Time-series Data.Molecular biology and evolution · 2022Article
- Contemporary NMolecular ecology resources · 2021Article
- MPL resolves genetic linkage in fitness inference from complex evolutionary histories.Nature biotechnology · 2021Article
- Multiple mechanisms drive genomic adaptation to extreme ONature communications · 2021Article
- The Effects of Quantitative Trait Architecture on Detection Power in Short-Term Artificial Selection Experiments.G3 (Bethesda, Md.) · 2020Article
- Inference of Selection from Genetic Time Series Using Various Parametric Approximations to the Wright-Fisher Model.G3 (Bethesda, Md.) · 2019Article
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4 authors.
Funding
Abstract
The advent of next generation sequencing technologies has made whole-genome and whole-population sampling possible, even for eukaryotes with large genomes. With this development, experimental evolution studies can be designed to observe molecular evolution "in action" via evolve-and-resequence (E&R) experiments. Among other applications, E&R studies can be used to locate the genes and variants responsible for genetic adaptation. Most existing literature on time-series data analysis often assumes large population size, accurate allele frequency estimates, or wide time spans. These assumptions do not hold in many E&R studies. In this article, we propose a method-composition of likelihoods for evolve-and-resequence experiments (Clear)-to identify signatures of selection in small population E&R experiments. Clear takes whole-genome sequences of pools of individuals as input, and properly addresses heterogeneous ascertainment bias resulting from uneven coverage. Clear also provides unbiased estimates of model parameters, including population size, selection strength, and dominance, while being computationally efficient. Extensive simulations show that Clear achieves higher power in detecting and localizing selection over a wide range of parameters, and is robust to variation of coverage. We applied the Clear statistic to multiple E&R experiments, including data from a study of adaptation of
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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.