ArticleAlgorithms for molecular biology : AMB2019
NANUQ: a method for inferring species networks from gene trees under the coalescent model.
Article in Algorithms for molecular biology : AMB, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed.
- Phylogenomic evidence provides insights into the phylogeny and speciation patterns in the subgenus Caloscordum (Allium, Amaryllidaceae).Cladistics : the international journal of the Willi Hennig Society · 2026Article
- BROOQS: Spectral Methods Resolve Level-1 Hybridization Cycles without Tests of Symmetry.bioRxiv : the preprint server for biology · 2026Article
- A Genomic Perspective on Cryptic Species Reveals Complex Evolutionary Dynamics in the Gray Zone of the Speciation Continuum.Systematic biology · 2026Article
- CAMUS: scalable phylogenetic network estimation.Bioinformatics (Oxford, England) · 2026Article
- Algebraic Invariants for Inferring 4-Leaf Semi-Directed Phylogenetic Networks.Systematic biology · 2026Article
- Chloroplast genomes provide new insights into the phylogeny and evolution of the genus Hibiscus L.BMC plant biology · 2026Article
- PhyloFusion-Fast and Easy Fusion of Rooted Phylogenetic Trees into Rooted Phylogenetic Networks.Systematic biology · 2026Article
- 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
- Beyond Level-1: Identifiability of a Class of Galled Tree-Child Networks.Bulletin of mathematical biology · 2025Article
- Rapid Radiations Outweigh Reticulations During the Evolution of a 750-Million-Year-Old Lineage of Cyanobacteria.Molecular biology and evolution · 2025Article
- Phylogenetic networks empower biodiversity research.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- NANUQAlgorithms for molecular biology : AMB · 2025Article
- Phylogenomics of East Asian lineage within subgenus Anguinum (Allium, Amaryllidaceae): insights into its taxonomic puzzles and phylogenetic conflicts.BMC plant biology · 2025Article
- Phylogenomic Analyses Reveal Species Relationships and Phylogenetic Incongruence with New Member Detected inPlants (Basel, Switzerland) · 2025Article
- Squirrel: Reconstructing Semi-directed Phylogenetic Level-1 Networks from Four-Leaved Networks or Sequence Alignments.Molecular biology and evolution · 2025Article
- Deforestation-induced Hybridization in Philippine Frogs Creates a Distinct Phenotype With an Inviable Genotype.Heredity · 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
- Leveraging graphical model techniques to study evolution on phylogenetic networks.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
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Abstract
Species networks generalize the notion of species trees to allow for hybridization or other lateral gene transfer. Under the network multispecies coalescent model, individual gene trees arising from a network can have any topology, but arise with frequencies dependent on the network structure and numerical parameters. We propose a new algorithm for statistical inference of a level-1 species network under this model, from data consisting of gene tree topologies, and provide the theoretical justification for it. The algorithm is based on an analysis of quartets displayed on gene trees, combining several statistical hypothesis tests with combinatorial ideas such as a quartet-based intertaxon distance appropriate to networks, the NeighborNet algorithm for circular split systems, and the Circular Network algorithm for constructing a splits graph.
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