ArticlePLoS computational biology2014
An HMM-based comparative genomic framework for detecting introgression in eukaryotes.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 58 citations in OpenAlex.
- Genetics and genomics of hybridization.Nature reviews. Genetics · 2026Review
- Recent advances in methods to characterize archaic introgression in modern humans.Genome research · 2026Review
- Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC.Systematic biology · 2026Article
- Recurrent evolution of small body size and loss of the sword ornament in Northern swordtail fish.Evolution; international journal of organic evolution · 2024Article
- Selection Shapes the Genomic Landscape of Introgressed Ancestry in a Pair of Sympatric Sea Urchin Species.Genome biology and evolution · 2024Article
- Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks.Molecular ecology resources · 2021Article
- The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes.PLoS genetics · 2021Article
- The Genetic Architecture of Variation in the Sexually Selected Sword Ornament and Its Evolution in Hybrid Populations.Current biology : CB · 2021Article
- Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression.eLife · 2020Article
- Disentangling Population History and Character Evolution among Hybridizing Lineages.Molecular biology and evolution · 2020Article
- Divergence-Based Introgression Polarization.Genome biology and evolution · 2020Article
- Article
- Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data.Cell systems · 2018Article
- The genomic impact of historical hybridization with massive mitochondrial DNA introgression.Genome biology · 2018Article
- IntroMap: a signal analysis based method for the detection of genomic introgressions.BMC genetics · 2017Article
- Genomic insights into adaptive divergence and speciation among malaria vectors of theEvolutionary applications · 2017Article
- Inferring Local Genealogies on Closely Related Genomes.Comparative genomics : RECOMB ... International Workshop, RCG ... : revised selected papers. RECOMB-CG (Conference) · 2017Article
- A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation.BMC bioinformatics · 2016Article
- Phylogenetic incongruence and the evolutionary origins of cardenolide-resistant forms of Na(+) ,K(+) -ATPase in Danaus butterflies.Evolution; international journal of organic evolution · 2016Article
- Powerful methods for detecting introgressed regions from population genomic data.Molecular ecology · 2016Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on PhyloNet-HMM-a new comparative genomic framework for detecting introgression in genomes. PhyloNet-HMM combines phylogenetic networks with hidden Markov models (HMMs) to simultaneously capture the (potentially reticulate) evolutionary history of the genomes and dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus) genome detected a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgressed genomic regions. Based on our analysis, it is estimated that about 9% of all sites within chromosome 7 are of introgressive origin (these cover about 13 Mbp of chromosome 7, and over 300 genes). Further, our model detected no introgression in a negative control data set. We also found that our model accurately detected introgression and other evolutionary processes from synthetic data sets simulated under the coalescent model with recombination, isolation, and migration. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism.
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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.