ArticleMolecular biology and evolution2014
A guide for the design of evolve and resequencing studies.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers, 1 of them a synthesis that pooled it.
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Who cites it
89 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis suggests the microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster.BMC microbiology · 2021Pooled it
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- Beyond Mendel: a call to revisit the genotype-phenotype map through new experimental paradigms.Genetics · 2026Article
- The Genetic Architecture of Venom Resistance: A Novel Approach to Target Identification and Coevolutionary Discovery.Molecular biology and evolution · 2026Article
- Parallel adaptive responses to postponed reproduction increase lifespan and immune defense.bioRxiv : the preprint server for biology · 2026Article
- Leveraging low-cost short-read sequencing: revolutionizing complex trait genetics.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
- Ecological stoichiometry and life history theory, not the identity of genomic variants, predict rapid adaptation.bioRxiv : the preprint server for biology · 2025Article
- Imputef: imputation of polyploid genotype classes and allele frequencies.BMC genomics · 2025Article
- Expression Divergence in Response to Sex-biased Selection.Molecular biology and evolution · 2025Article
- High Gene Expression Predicts Extremely Low Segregation of Deleterious Mutations in Large Penguin Populations.Molecular biology and evolution · 2025Article
- Ultra-sensitive detection of transposon insertions across multiple families by transposable element display sequencing.Genome biology · 2025Article
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- A Path Integral Approach for Allele Frequency Dynamics Under Polygenic Selection.bioRxiv : the preprint server for biology · 2024Article
- Genomics for monitoring and understanding species responses to global climate change.Nature reviews. Genetics · 2024Review
- Experimental evolution of hybrid populations to identify Dobzhansky-Muller incompatibility loci.Ecology and evolution · 2024Article
- Rapid genomic evolution in Brassica rapa with bumblebee selection in experimental evolution.BMC ecology and evolution · 2024Article
29 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
Standing genetic variation provides a rich reservoir of potentially useful mutations facilitating the adaptation to novel environments. Experimental evolution studies have demonstrated that rapid and strong phenotypic responses to selection can also be obtained in the laboratory. When combined with the next-generation sequencing technology, these experiments promise to identify the individual loci contributing to adaption. Nevertheless, until now, very little is known about the design of such evolve & resequencing (E&R) studies. Here, we use forward simulations of entire genomes to evaluate different experimental designs that aim to maximize the power to detect selected variants. We show that low linkage disequilibrium in the starting population, population size, duration of the experiment, and the number of replicates are the key factors in determining the power and accuracy of E&R studies. Furthermore, replication of E&R is more important for detecting the targets of selection than increasing the population size. Using an optimized design, beneficial loci with a selective advantage as low as s = 0.005 can be identified at the nucleotide level. Even when a large number of loci are selected simultaneously, up to 56% can be reliably detected without incurring large numbers of false positives. Our computer simulations suggest that, with an adequate experimental design, E&R studies are a powerful tool to identify adaptive mutations from standing genetic variation and thereby provide an excellent means to analyze the trajectories of selected alleles in evolving populations.
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