ArticleSystematic biology2024
Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information.
Article in Systematic biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 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
- Species Diversification in the Sky Islands of Southwestern China Revealed by Genomic, Introgression, and Demographic Analyses of Asian Shrew Moles.Systematic biology · 2026Article
- Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila.Systematic biology · 2025Article
- Phylogenomic discordance is driven mainly by pervasive ancient hybridization and incomplete lineage sorting during the early divergence of major angiosperm lineages.Plant communications · 2025Article
- Disentangling Complex Histories of Hybridisation: The Genomic Consequences of Ancient and Recent Introgression in Channel Island Monkeyflowers.Molecular ecology · 2025Article
- Detecting Introgression in Shallow Phylogenies: How Minor Molecular Clock Deviations Lead to Major Inference Errors.Molecular biology and evolution · 2025Article
- Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family.Nature communications · 2025Article
- Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified.Molecular biology and evolution · 2025Article
- Phytop: a tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL.Horticulture research · 2025Article
- Reading tree leaves: inferring speciation anfd extinction processes using phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Variance ofFrontiers in genetics · 2025Article
- Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species.The Plant journal : for cell and molecular biology · 2024Article
- Detecting cryptic ghost lineage introgression in four-taxon genomic datasets.Applications in plant sciencesArticle
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2 authors.
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Abstract
In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression-the transfer of genetic material from extinct or unsampled lineages to extant species-emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving 3 species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site-pattern counts or gene-tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP uses multilocus sequence alignments directly-hence taking into account both gene-tree topologies and branch lengths, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species of Jaltomata (Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.
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