ArticlePLoS genetics2016
Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 179 papers.
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Who cites it
179 citing papers in PubMed.
- Genetics and genomics of hybridization.Nature reviews. Genetics · 2026Review
- The Impact of Incomplete Taxon Sampling on Inference of Gene Flow by Bayesian and Summary Methods Using Genomic Sequence Data.Systematic biology · 2026Article
- Unravelling Complex Hybrid and Polyploid Evolutionary Relationships Using Phylogenetic Placement of Homologous Gene Copies from Target Enrichment 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
- Reticulated adaptive radiation and phylogenomic diversity loss in the Hawaiian honeycreepers.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A New Challenge to Species Delimitation: Remarkable Genomic and Ecological Diversity in the Butterfly Melitaea diamina.Molecular ecology · 2026Article
- Phylogenomic conflict inPlant diversity · 2026Article
- Evidence for Cryptic Sex in Escovopsis, a Mycoparasite in the Fungus-Growing Ant Symbiosis.Genome biology and evolution · 2026Article
- CAMUS: scalable phylogenetic network estimation.Bioinformatics (Oxford, England) · 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
- Evidence of introgression amid phylogenetic conflict in Brachyotum, a plant radiation from the Tropical Andes.American journal of botany · 2026Article
- Scaling up Bayesian population phylogenomics through virtual dimension reduction.Nature communications · 2026Article
- The Genomics of Convergent Adaptation to Intertidal Gravel Beaches in Mediterranean Clingfishes.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
- Estimating Waiting Distances between Genealogy Changes under a Multi-Species Extension of the Sequentially Markov Coalescent.Systematic biology · 2026Article
- Phylogenomics, ecomorphological evolution, and historical biogeography in Deuterocohnia (Bromeliaceae: Pitcairnioideae).American journal of botany · 2026Article
- Article
- PhyloFusion-Fast and Easy Fusion of Rooted Phylogenetic Trees into Rooted Phylogenetic Networks.Systematic biology · 2026Article
119 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their genetic material. While a great deal of research has flourished into the inference of phylogenetic trees, statistical methods to infer phylogenetic networks are still limited and under development. The main disadvantage of existing methods is a lack of scalability. Here, we present a statistical method to infer phylogenetic networks from multi-locus genetic data in a pseudolikelihood framework. Our model accounts for incomplete lineage sorting through the coalescent model, and for horizontal inheritance of genes through reticulation nodes in the network. Computation of the pseudolikelihood is fast and simple, and it avoids the burdensome calculation of the full likelihood which can be intractable with many species. Moreover, estimation at the quartet-level has the added computational benefit that it is easily parallelizable. Simulation studies comparing our method to a full likelihood approach show that our pseudolikelihood approach is much faster without compromising accuracy. We applied our method to reconstruct the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), which is characterized by widespread hybridizations.
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