ArticleGenome biology2019
Benchmarking software tools for detecting and quantifying selection in evolve and resequencing studies.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci.eLife · 2026Article
- Haplotype structure: an overlooked key factor shaping the genomic selection response.Genetics · 2026Article
- PolyAdapt: Characterizing Polygenic Adaptive Architectures in the Presence of Strong Linkage Disequilibrium.Genome biology and evolution · 2026Article
- Genomic responses to increased temperature and pollinator selection in Brassica rapa L.The New phytologist · 2026Article
- The Genetic Architecture of Venom Resistance: A Novel Approach to Target Identification and Coevolutionary Discovery.Molecular biology and evolution · 2026Article
- Low-Coverage Whole-Genome Analysis of Population Structure, Bottlenecks, and Selection in Indiana Bats Before and After White-Nose Syndrome.Molecular ecology · 2025Article
- 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
- Article
- Biotic interactions promote local adaptation to soil in plants.Nature communications · 2024Article
- A Path Integral Approach for Allele Frequency Dynamics Under Polygenic Selection.bioRxiv : the preprint server for biology · 2024Article
- Genomewide architecture of adaptation in experimentally evolvedJournal of genetics · 2024Article
- Haplotype based testing for a better understanding of the selective architecture.BMC bioinformatics · 2023Article
- 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
- Bait-ER: A Bayesian method to detect targets of selection in Evolve-and-Resequence experiments.Journal of evolutionary biology · 2023Article
- Experimental evolution reveals the synergistic genomic mechanisms of adaptation to ocean warming and acidification in a marine copepod.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Pollinator loss causes rapid adaptive evolution of selfing and dramatically reduces genome-wide genetic variability.Evolution; international journal of organic evolution · 2022Article
- The molecular architecture of Drosophila melanogaster defense against Beauveria bassiana explored through evolve and resequence and quantitative trait locus mapping.G3 (Bethesda, Md.) · 2021Article
- Highly Parallel Genomic Selection Response in Replicated Drosophila melanogaster Populations with Reduced Genetic Variation.Genome biology and evolution · 2021Article
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Authors and funding
7 authors.
Funding
Abstract
backgroundThe combination of experimental evolution with whole-genome resequencing of pooled individuals, also called evolve and resequence (E&R) is a powerful approach to study the selection processes and to infer the architecture of adaptive variation. Given the large potential of this method, a range of software tools were developed to identify selected SNPs and to measure their selection coefficients.
resultsIn this benchmarking study, we compare 15 test statistics implemented in 10 software tools using three different scenarios. We demonstrate that the power of the methods differs among the scenarios, but some consistently outperform others. LRT-1, CLEAR, and the CMH test perform best despite LRT-1 and the CMH test not requiring time series data. CLEAR provides the most accurate estimates of selection coefficients.
conclusionThis benchmark study will not only facilitate the analysis of already existing data, but also affect the design of future data collections.
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