ArticlePLoS genetics2012
The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection.
Article in PLoS genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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Who cites it
96 citing papers in PubMed.
- Genetics and genomics of hybridization.Nature reviews. Genetics · 2026Review
- BROOQS: Spectral Methods Resolve Level-1 Hybridization Cycles without Tests of Symmetry.bioRxiv : the preprint server for biology · 2026Article
- Phylogenetic Network Models as Graphical Models.Bulletin of mathematical biology · 2026Article
- Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting.Plant diversity · 2026Article
- Evidence of introgression amid phylogenetic conflict in Brachyotum, a plant radiation from the Tropical Andes.American journal of botany · 2026Article
- SNaQ.jl: Improved scalability for level-1 phylogenetic network inference.Bioinformatics (Oxford, England) · 2026Article
- Impact of Data Error on Phylogenetic Network Inference from Gene Trees Under the Multispecies Network Coalescent.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A Multi-Evidence Approach to the Systematics of the GenusInternational journal of molecular sciences · 2025Article
- Phylogenomics of Marine Angelfishes: Diagnosing Sources of Systematic Discordance for an Iconic Reef Fish Family (F: Pomacanthidae).Systematic biology · 2025Article
- Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila.Systematic biology · 2025Article
- Beyond Level-1: Identifiability of a Class of Galled Tree-Child Networks.Bulletin of mathematical biology · 2025Article
- Phylogenetic networks empower biodiversity research.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified.Molecular biology and evolution · 2025Article
- Are Ophiolitic Substrates Drivers for Reticulate Evolution inEcology and evolution · 2025Article
- Reading tree leaves: inferring speciation anfd extinction processes using phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Rapid Radiation of a Plant Lineage Sheds Light on the Assembly of Dry Valley Biomes.Molecular biology and evolution · 2025Article
- TINNiK: inference of the tree of blobs of a species network under the coalescent model.Algorithms for molecular biology : AMB · 2024Article
- Phylogenomics, reticulation, and biogeographical history of Elaeagnaceae.Plant diversity · 2024Article
- Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information.Systematic biology · 2024Article
- TINNiK: Inference of the Tree of Blobs of a Species Network Under the Coalescent.bioRxiv : the preprint server for biology · 2024Article
36 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa.
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