ArticlePLoS genetics2020
VolcanoFinder: Genomic scans for adaptive introgression.
Article in PLoS genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
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- AI solutions for evolutionary genomics of nonmodel species.Evolution letters · 2026Review
- Detecting Positive Selection by Modeling Structure Within Images of Genetic Variation.Genome biology and evolution · 2026Article
- Recent advances in methods to characterize archaic introgression in modern humans.Genome research · 2026Review
- Signals of Ancestry-Specific Selection in Gentle Africanized Honey Bees.Genome biology and evolution · 2025Article
- Disentangling Complex Histories of Hybridisation: The Genomic Consequences of Ancient and Recent Introgression in Channel Island Monkeyflowers.Molecular ecology · 2025Article
- Do syngameons exist in tropical trees? Challenges to determine their existence and estimate their frequency.Biology letters · 2025Review
- Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes.Genome research · 2025Article
- Efficient Detection and Characterization of Targets of Natural Selection Using Transfer Learning.Molecular biology and evolution · 2025Article
- Efficient detection and characterization of targets of natural selection using transfer learning.bioRxiv : the preprint server for biology · 2025Article
- Human dispersal into East Eurasia: ancient genome insights and the need for research on physiological adaptations.Journal of physiological anthropology · 2025Review
- Trans-Specific Polymorphisms Between Cryptic Daphnia Species Affect Fitness and Behavior.Molecular ecology · 2025Article
- Digital Image Processing to Detect Adaptive Evolution.Molecular biology and evolution · 2024Article
- Computational Genomics and Its Applications to Anthropological Questions.American journal of biological anthropology · 2024Review
- A history of multiple Denisovan introgression events in modern humans.Nature genetics · 2024Review
- Article
- Ploidy as a leaky reproductive barrier: mechanisms, rates and evolutionary significance of interploidy gene flow.Annals of botany · 2024Review
- Widespread Adaptive Introgression of Major Histocompatibility Complex Genes across Vertebrate Hybrid Zones.Molecular biology and evolution · 2024Article
2 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method-VolcanoFinder-to detect recent events of adaptive introgression using polymorphism data from the recipient species only. VolcanoFinder detects adaptive introgression sweeps from the pattern of excess intermediate-frequency polymorphism they produce in the flanking region of the genome, a pattern which appears as a volcano-shape in pairwise genetic diversity. Using coalescent theory, we derive analytical predictions for these patterns. Based on these results, we develop a composite-likelihood test to detect signatures of adaptive introgression relative to the genomic background. Simulation results show that VolcanoFinder has high statistical power to detect these signatures, even for older sweeps and for soft sweeps initiated by multiple migrant haplotypes. Finally, we implement VolcanoFinder to detect archaic introgression in European and sub-Saharan African human populations, and uncovered interesting candidates in both populations, such as TSHR in Europeans and TCHH-RPTN in Africans. We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder.
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