ArticleMolecular biology and evolution2012
Detecting selective sweeps from pooled next-generation sequencing samples.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- The Evolution and Role of Molecular Tools in Measuring Diversity and Genomic Selection in Livestock Populations (Traditional and Up-to-Date Insights): A Comprehensive Exploration.Veterinary sciences · 2024Review
- Selection of Genome-Wide SNPs for Pooled Allelotyping Assays Useful for Population Monitoring.Genome biology and evolution · 2022Article
- Neutral and adaptive drivers of genomic change in introduced brook trout (Ecology and evolution · 2022Article
- Detecting Genetic Variation of ColonizingFrontiers in bioinformatics · 2022Article
- Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits.BMC genomics · 2021Review
- Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping.BMC genomics · 2021Article
- Museomics Dissects the Genetic Basis for Adaptive Seasonal Coloration in the Least Weasel.Molecular biology and evolution · 2021Article
- Population genomics of invasive rodents on islands: Genetic consequences of colonization and prospects for localized synthetic gene drive.Evolutionary applications · 2021Article
- Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds.Frontiers in genetics · 2021Article
- Genomic Uniqueness of Local Sheep Breeds From Morocco.Frontiers in genetics · 2021Article
- Within-population sperm competition intensity does not predict asymmetry in conpopulation sperm precedence.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses.Molecular biology and evolution · 2020Article
- Analysis of genome-wide SNPs based on 2b-RAD sequencing of pooled samples reveals signature of selection in different populations ofJournal of biosciences · 2019Article
- A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes.Molecular ecology resources · 2019Article
- Patterns of genomic differentiation between two Lake Victoria cichlid species, Haplochromis pyrrhocephalus and H. sp. 'macula'.BMC evolutionary biology · 2019Article
- Supervised Machine Learning for Population Genetics: A New Paradigm.Trends in genetics : TIG · 2018Review
- Genomic selection signatures in sheep from the Western Pyrenees.Genetics, selection, evolution : GSE · 2018Article
- Identifying consistent allele frequency differences in studies of stratified populations.Methods in ecology and evolution · 2017Article
- Evolutionary toxicology in an omics world.Evolutionary applications · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Due to its cost effectiveness, next-generation sequencing of pools of individuals (Pool-Seq) is becoming a popular strategy for characterizing variation in population samples. Because Pool-Seq provides genome-wide SNP frequency data, it is possible to use them for demographic inference and/or the identification of selective sweeps. Here, we introduce a statistical method that is designed to detect selective sweeps from pooled data by accounting for statistical challenges associated with Pool-Seq, namely sequencing errors and random sampling among chromosomes. This allows for an efficient use of the information: all base calls are included in the analysis, but the higher credibility of regions with higher coverage and base calls with better quality scores is accounted for. Computer simulations show that our method efficiently detects sweeps even at very low coverage (0.5× per chromosome). Indeed, the power of detecting sweeps is similar to what we could expect from sequences of individual chromosomes. Since the inference of selective sweeps is based on the allele frequency spectrum (AFS), we also provide a method to accurately estimate the AFS provided that the quality scores for the sequence reads are reliable. Applying our approach to Pool-Seq data from Drosophila melanogaster, we identify several selective sweep signatures on chromosome X that include some previously well-characterized sweeps like the wapl region.
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Registered trials
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.