ArticlePLoS genetics2021
Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data.
Article in PLoS genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A cosmopolitan inversion facilitates seasonal adaptation in overwintering Drosophila.Genetics · 2024Pooled it
- Allelic gene conversion softens selective sweeps.Genetics · 2026Article
- Multiple genomic approaches reveal geographic structure and local selection signals in invasive Anopheles stephensi from the Horn of Africa and Yemen.BMC genomics · 2026Article
- Haplotype-Based Models Improve Sweep Detection in Ancient Populations with Complex Demography.bioRxiv : the preprint server for biology · 2026Article
- Pseudogene revival drives repeated adaptation in fission yeast.Molecular biology and evolution · 2026Article
- The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Across Urban, Rural, and Forested Environments in Gabon.Molecular ecology · 2026Article
- Soft Selective Sweeps Predominate in the Yellow Fever Mosquito Aedes aegypti.Molecular biology and evolution · 2026Article
- Article
- The persistence and loss of hard selective sweeps amid ancient human admixture.bioRxiv : the preprint server for biology · 2025Article
- Continent-wide differentiation of fitness traits and patterns of climate adaptation among European populations ofEvolution letters · 2025Article
- Signatures of soft selective sweeps predominate in the yellow fever mosquitobioRxiv : the preprint server for biology · 2025Article
- An ancient origin of the naked grains of maize.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- New perspectives on Drosophila melanogaster de novo gene origination revealed by investigation of ancient African genetic variation.Genetics · 2025Article
- A highland-adaptation variant near MCUR1 reduces its transcription and attenuates erythrogenesis in Tibetans.Cell genomics · 2025Article
- Genomic Islands of Divergence Between Drosophila yakuba Subspecies are Predominantly Driven by Chromosomal Inversions and the Recombination Landscape.Molecular ecology · 2025Article
- Linkage equilibrium between rare mutations.Genetics · 2024Article
- From sub-Saharan Africa to China: Evolutionary history and adaptation ofScience advances · 2024Article
- Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species.Genetics · 2024Article
- A Novel Approach Utilizing Domain Adversarial Neural Networks for the Detection and Classification of Selective Sweeps.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
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3 authors.
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Abstract
Whether hard sweeps or soft sweeps dominate adaptation has been a matter of much debate. Recently, we developed haplotype homozygosity statistics that (i) can detect both hard and soft sweeps with similar power and (ii) can classify the detected sweeps as hard or soft. The application of our method to population genomic data from a natural population of Drosophila melanogaster (DGRP) allowed us to rediscover three known cases of adaptation at the loci Ace, Cyp6g1, and CHKov1 known to be driven by soft sweeps, and detected additional candidate loci for recent and strong sweeps. Surprisingly, all of the top 50 candidates showed patterns much more consistent with soft rather than hard sweeps. Recently, Harris et al. 2018 criticized this work, suggesting that all the candidate loci detected by our haplotype statistics, including the positive controls, are unlikely to be sweeps at all and that instead these haplotype patterns can be more easily explained by complex neutral demographic models. They also claim that these neutral non-sweeps are likely to be hard instead of soft sweeps. Here, we reanalyze the DGRP data using a range of complex admixture demographic models and reconfirm our original published results suggesting that the majority of recent and strong sweeps in D. melanogaster are first likely to be true sweeps, and second, that they do appear to be soft. Furthermore, we discuss ways to take this work forward given that most demographic models employed in such analyses are necessarily too simple to capture the full demographic complexity, while more realistic models are unlikely to be inferred correctly because they require a large number of free parameters.
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