ArticlePLoS genetics2018
On the unfounded enthusiasm for soft selective sweeps II: Examining recent evidence from humans, flies, and viruses.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed.
- Allelic gene conversion softens selective sweeps.Genetics · 2026Article
- Genomic insights into natural selection in recent human history.Nature reviews. Genetics · 2026Review
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- Truncated Life History Underlies Rapid Local Adaptation in Island Rattlesnake Venom Expression.Genome biology and evolution · 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
- Ancient DNA insights into diverse pathogens and their hosts.Nature reviews. Genetics · 2026Review
- Recent Insights Into the Evolutionary Genomics of the Critically Endangered Aye-Aye (Daubentonia madagascariensis).American journal of primatology · 2025Review
- Article
- The persistence and loss of hard selective sweeps amid ancient human admixture.bioRxiv : the preprint server for biology · 2025Article
- Urban Life Shapes Genetic Diversity in the Green Anole, Anolis carolinensis.Molecular ecology · 2025Article
- Not by Selection Alone: Expanding the Scope of Gene-Culture Coevolution.Evolutionary anthropology · 2025Review
- Signatures of soft selective sweeps predominate in the yellow fever mosquitobioRxiv : the preprint server for biology · 2025Article
- A whole-genome scan for evidence of positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model.G3 (Bethesda, Md.) · 2025Article
- Compensatory Evolution Following Deleterious Episodes of GC-biased Gene Conversion in Rodents.Molecular biology and evolution · 2025Article
- An ancient origin of the naked grains of maize.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Temporal Patterns of Haplotypic and Allelic Diversity Reflect the Changing Selection Landscape of the Malaria Parasite Plasmodium falciparum.Molecular biology and evolution · 2025Article
16 more citing papers are in PubMed but not listed here.
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Since the initial description of the genomic patterns expected under models of positive selection acting on standing genetic variation and on multiple beneficial mutations-so-called soft selective sweeps-researchers have sought to identify these patterns in natural population data. Indeed, over the past two years, large-scale data analyses have argued that soft sweeps are pervasive across organisms of very different effective population size and mutation rate-humans, Drosophila, and HIV. Yet, others have evaluated the relevance of these models to natural populations, as well as the identifiability of the models relative to other known population-level processes, arguing that soft sweeps are likely to be rare. Here, we look to reconcile these opposing results by carefully evaluating three recent studies and their underlying methodologies. Using population genetic theory, as well as extensive simulation, we find that all three examples are prone to extremely high false-positive rates, incorrectly identifying soft sweeps under both hard sweep and neutral models. Furthermore, we demonstrate that well-fit demographic histories combined with rare hard sweeps serve as the more parsimonious explanation. These findings represent a necessary response to the growing tendency of invoking parameter-heavy, assumption-laden models of pervasive positive selection, and neglecting best practices regarding the construction of proper demographic null models.
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