ArticleMolecular biology and evolution2018
Bayesian Inference of Species Networks from Multilocus Sequence Data.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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82 citing papers in PubMed, 224 citations in OpenAlex.
- The Impact of Incomplete Taxon Sampling on Inference of Gene Flow by Bayesian and Summary Methods Using Genomic Sequence Data.Systematic biology · 2026Article
- Algebraic Invariants for Inferring 4-Leaf Semi-Directed Phylogenetic Networks.Systematic biology · 2026Article
- SNaQ.jl: Improved scalability for level-1 phylogenetic network inference.Bioinformatics (Oxford, England) · 2026Article
- Scaling up Bayesian population phylogenomics through virtual dimension reduction.Nature communications · 2026Article
- Phylogenetic Resolution and Conflict in the Species-Rich Flowering Plant Family Leguminosae.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
- Do syngameons exist in tropical trees? Challenges to determine their existence and estimate their frequency.Biology letters · 2025Review
- Distinguishing Phylogenetic Level-2 Networks with Quartets and Inter-Taxon Quartet Distances.Bulletin of mathematical biology · 2025Article
- The power of coalescent methods for inferring recent and ancient gene flow in endangered Bactrian camels.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model.Molecular biology and evolution · 2025Article
- NANUQAlgorithms for molecular biology : AMB · 2025Article
- Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified.Molecular biology and evolution · 2025Article
- Squirrel: Reconstructing Semi-directed Phylogenetic Level-1 Networks from Four-Leaved Networks or Sequence Alignments.Molecular biology and evolution · 2025Article
- Misspecification Strikes: ASTRAL can Mislead in the Presence of Hybridization, even for Nonanomalous Scenarios.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
- Mathematically tractable models of random phylogenetic networks: an overview of some recent developments.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Hierarchical Heuristic Species Delimitation Under the Multispecies Coalescent Model with Migration.Systematic biology · 2024Article
- TINNiK: inference of the tree of blobs of a species network under the coalescent model.Algorithms for molecular biology : AMB · 2024Article
- The Meaning and Measure of Concordance Factors in Phylogenomics.Molecular biology and evolution · 2024Review
- Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation.Systematic biology · 2024Article
22 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 3 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reticulate species evolution, such as hybridization or introgression, is relatively common in nature. In the presence of reticulation, species relationships can be captured by a rooted phylogenetic network, and orthologous gene evolution can be modeled as bifurcating gene trees embedded in the species network. We present a Bayesian approach to jointly infer species networks and gene trees from multilocus sequence data. A novel birth-hybridization process is used as the prior for the species network, and we assume a multispecies network coalescent prior for the embedded gene trees. We verify the ability of our method to correctly sample from the posterior distribution, and thus to infer a species network, through simulations. To quantify the power of our method, we reanalyze two large data sets of genes from spruces and yeasts. For the three closely related spruces, we verify the previously suggested homoploid hybridization event in this clade; for the yeast data, we find extensive hybridization events. Our method is available within the BEAST 2 add-on SpeciesNetwork, and thus provides an extensible framework for Bayesian inference of reticulate evolution.
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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.