ArticleBMC genomics2015
A maximum pseudo-likelihood approach for phylogenetic networks.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
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94 citing papers in PubMed.
- The Impact of Incomplete Taxon Sampling on Inference of Gene Flow by Bayesian and Summary Methods Using Genomic Sequence Data.Systematic biology · 2026Article
- BROOQS: Spectral Methods Resolve Level-1 Hybridization Cycles without Tests of Symmetry.bioRxiv : the preprint server for biology · 2026Article
- Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys).Genome biology and evolution · 2026Article
- Atlantic forest origins and Amazon connections: the evolutionary history of Adenocalymma.Annals of botany · 2026Article
- Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting.Plant diversity · 2026Article
- CAMUS: scalable phylogenetic network estimation.Bioinformatics (Oxford, England) · 2026Article
- Evidence for Cryptic Sex in Escovopsis, a Mycoparasite in the Fungus-Growing Ant Symbiosis.Genome biology and evolution · 2026Article
- SNaQ.jl: Improved scalability for level-1 phylogenetic network inference.Bioinformatics (Oxford, England) · 2026Article
- The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompanied by Pervasive Hybridization.Systematic biology · 2026Article
- Phylogenomics of Marine Angelfishes: Diagnosing Sources of Systematic Discordance for an Iconic Reef Fish Family (F: Pomacanthidae).Systematic biology · 2025Article
- Distinguishing Phylogenetic Level-2 Networks with Quartets and Inter-Taxon Quartet Distances.Bulletin of mathematical biology · 2025Article
- Building a robust backbone for Astragalus using a clade-specific target enrichment bait set.American journal of botany · 2025Article
- NANUQAlgorithms for molecular biology : AMB · 2025Article
- Phylogenomic Analyses Reveal Species Relationships and Phylogenetic Incongruence with New Member Detected inPlants (Basel, Switzerland) · 2025Article
- Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified.Molecular biology and evolution · 2025Article
- Incomplete lineage sorting and introgression among genera and species of Liliaceae tribe Tulipeae: insights from phylogenomics.BMC biology · 2025Article
- Squirrel: Reconstructing Semi-directed Phylogenetic Level-1 Networks from Four-Leaved Networks or Sequence Alignments.Molecular biology and evolution · 2025Article
- Phylogenomics resolves key relationships inEvolution letters · 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
34 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
backgroundSeveral phylogenomic analyses have recently demonstrated the need to account simultaneously for incomplete lineage sorting (ILS) and hybridization when inferring a species phylogeny. A maximum likelihood approach was introduced recently for inferring species phylogenies in the presence of both processes, and showed very good results. However, computing the likelihood of a model in this case is computationally infeasible except for very small data sets.
resultsInspired by recent work on the pseudo-likelihood of species trees based on rooted triples, we introduce the pseudo-likelihood of a phylogenetic network, which, when combined with a search heuristic, provides a statistical method for phylogenetic network inference in the presence of ILS. Unlike trees, networks are not always uniquely encoded by a set of rooted triples. Therefore, even when given sufficient data, the method might converge to a network that is equivalent under rooted triples to the true one, but not the true one itself. The method is computationally efficient and has produced very good results on the data sets we analyzed. The method is implemented in PhyloNet, which is publicly available in open source.
conclusionsMaximum pseudo-likelihood allows for inferring species phylogenies in the presence of hybridization and ILS, while scaling to much larger data sets than is currently feasible under full maximum likelihood. The nonuniqueness of phylogenetic networks encoded by a system of rooted triples notwithstanding, the proposed method infers the correct network under certain scenarios, and provides candidates for further exploration under other criteria and/or data in other scenarios.
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