ArticleMolecular biology and evolution2021
Inferring Adaptive Introgression Using Hidden Markov Models.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Weak but Repeated Patterns of Co-Introgression of Nuclear OXPHOS Genes and Mitochondrial DNA in Iberian Wall Lizards.Genome biology and evolution · 2026Article
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- Genomic signatures of rapid local selection and introgression drive adaptive phylogeography in the European river skater.BMC biology · 2026Article
- Signals of Ancestry-Specific Selection in Gentle Africanized Honey Bees.Genome biology and evolution · 2025Article
- Ploidy as a leaky reproductive barrier: mechanisms, rates and evolutionary significance of interploidy gene flow.Annals of botany · 2024Review
- Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: Crotalus and Sistrurus).Systematic biology · 2024Article
- Widespread Adaptive Introgression of Major Histocompatibility Complex Genes across Vertebrate Hybrid Zones.Molecular biology and evolution · 2024Article
- Adaptive alien genes are maintained amid a vanishing introgression footprint in a sea squirt.Evolution letters · 2024Article
- IntroUNET: Identifying introgressed alleles via semantic segmentation.PLoS genetics · 2024Article
- IntroUNET: identifying introgressed alleles via semantic segmentation.bioRxiv : the preprint server for biology · 2024Article
- Inferring multi-locus selection in admixed populations.PLoS genetics · 2023Article
- Systematic dissection of genomic features determining the vast diversity of conotoxins.BMC genomics · 2023Article
- Localizing Post-Admixture Adaptive Variants with Object Detection on Ancestry-Painted Chromosomes.Molecular biology and evolution · 2023Article
- Patterns of Population Structure and Introgression Among Recently Differentiated Drosophila melanogaster Populations.Molecular biology and evolution · 2022Article
- A need for standardized reporting of introgression: Insights from studies across eukaryotes.Evolution letters · 2022Article
- Estimating the timing of multiple admixture events using 3-locus linkage disequilibrium.PLoS genetics · 2022Article
- Human genetic admixture through the lens of population genomics.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- Estimating the time since admixture from phased and unphased molecular data.Molecular ecology resources · 2022Article
- A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population.Molecular biology and evolution · 2022Article
- Rapid adaptation to malaria facilitated by admixture in the human population of Cabo Verde.eLife · 2021Article
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5 authors.
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Abstract
Adaptive introgression-the flow of adaptive genetic variation between species or populations-has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a hidden Markov model-based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized data sets for realistic population and selection parameters. We apply Ancestry_HMM-S to a data set of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in data sets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.
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