ArticlePLoS genetics2016
Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Gene tree patterns help answer: vicariance or dispersal?bioRxiv : the preprint server for biology · 2026Article
- SNaQ.jl: Improved scalability for level-1 phylogenetic network inference.Bioinformatics (Oxford, England) · 2026Article
- Estimating Waiting Distances between Genealogy Changes under a Multi-Species Extension of the Sequentially Markov Coalescent.Systematic biology · 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
- Reticulate evolutionary history underpins a revised generic circumscription of Paphiopedilum (Orchidaceae): insights from integrative phylogenomics and historical biogeography.BMC plant biology · 2025Article
- Ultrafast learning of four-node hybridization cycles in phylogenetic networks using algebraic invariants.Bioinformatics advances · 2024Article
- Estimation of species divergence times in presence of cross-species gene flow.Systematic biology · 2023Article
- Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae).Systematic biology · 2023Article
- Phylogeny ofEcology and evolution · 2023Article
- Empirical and philosophical problems with the subspecies rank.Ecology and evolution · 2022Review
- Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades.American journal of botany · 2022Article
- Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes.Systematic biology · 2022Article
- River network rearrangements promote speciation in lowland Amazonian birds.Science advances · 2022Article
- Review
- The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes.PLoS genetics · 2021Article
- On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo.PLoS computational biology · 2021Article
- Demographic History and Genomic Response to Environmental Changes in a Rapid Radiation of Wild Rats.Molecular biology and evolution · 2021Article
- Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression.eLife · 2020Article
- The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets.Systematic biology · 2020Article
- Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees.Molecular biology and evolution · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation.
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