ArticleG3 (Bethesda, Md.)2019
Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments.
Article in G3 (Bethesda, Md.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Geographic differentiation of ectoparasitic flatworms in the pelagic zone of Lake Tanganyika, Africa.Frontiers in zoology · 2026Article
- The illusion of polygenicity in pool-seq genetic mapping studies: insufficient power can mask simple genetic architectures.Genetics · 2026Article
- Rapid adaptation and extinction in synchronized outdoor evolution experiments ofScience (New York, N.Y.) · 2026Article
- Leveraging low-cost short-read sequencing: revolutionizing complex trait genetics.Molecular biology and evolution · 2026Article
- Estimating the additive genetic variance for relative fitness from changes in allele frequency.Genetics · 2026Article
- Variation in the resource environment affects patterns of seasonal adaptation at phenotypic and genomic levels inEvolution letters · 2025Article
- Beneficial reversal of dominance maintains a large-effect resistance polymorphism under fluctuating insecticide selection.Nature ecology & evolution · 2025Article
- Pervasive fitness trade-offs revealed by rapid adaptation to shifting population densities in large experimental populations ofbioRxiv : the preprint server for biology · 2025Article
- A vision of how low-coverage sequence data should contribute to genetic evaluation in the future.Journal of animal science · 2025Article
- Article
- grenedalf: population genetic statistics for the next generation of pool sequencing.Bioinformatics (Oxford, England) · 2024Article
- Induced responses contribute to rapid adaptation of Spirodela polyrhiza to herbivory by Lymnaea stagnalis.Communications biology · 2024Article
- Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data.BMC bioinformatics · 2023Article
- Article
- Adaptation in Outbred Sexual Yeast is Repeatable, Polygenic and Favors Rare Haplotypes.Molecular biology and evolution · 2022Article
- grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads.Bioinformatics (Oxford, England) · 2022Article
- Accurate recombination estimation from pooled genotyping and sequencing: a case study on barley.BMC genomics · 2022Article
- High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing.Plant methods · 2022Article
- Direct observation of adaptive tracking on ecological time scales inScience (New York, N.Y.) · 2022Article
- Powerful, efficient QTL mapping in Drosophila melanogaster using bulked phenotyping and pooled sequencing.Genetics · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Evolve-and-resequence (E+R) experiments leverage next-generation sequencing technology to track the allele frequency dynamics of populations as they evolve. While previous work has shown that adaptive alleles can be detected by comparing frequency trajectories from many replicate populations, this power comes at the expense of high-coverage (>100x) sequencing of many pooled samples, which can be cost-prohibitive. Here, we show that accurate estimates of allele frequencies can be achieved with very shallow sequencing depths (<5x) via inference of known founder haplotypes in small genomic windows. This technique can be used to efficiently estimate frequencies for any number of bi-allelic SNPs in populations of any model organism founded with sequenced homozygous strains. Using both experimentally-pooled and simulated samples 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.