ArticleSystematic biology2017
Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent.
Article in Systematic biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Reading tree leaves: inferring speciation anfd extinction processes using phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information.Systematic biology · 2024Article
- Classes of explicit phylogenetic networks and their biological and mathematical significance.Journal of mathematical biology · 2022Review
- Estimation of Cross-Species Introgression Rates Using Genomic Data Despite Model Unidentifiability.Molecular biology and evolution · 2022Article
- Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow.National science review · 2021Article
- On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo.PLoS computational biology · 2021Article
- Of Traits and Trees: Probabilistic Distances under Continuous Trait Models for Dissecting the Interplay among Phylogeny, Model, and Data.Systematic biology · 2021Article
- The rigid hybrid number for two phylogenetic trees.Journal of mathematical biology · 2021Article
- Probabilities of Unranked and Ranked Anomaly Zones under Birth-Death Models.Molecular biology and evolution · 2020Article
- Integrated likelihood for phylogenomics under a no-common-mechanism model.BMC genomics · 2020Article
- A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis.Molecular biology and evolution · 2020Article
- Pervasive hybridizations in the history of wheat relatives.Science advances · 2019Article
- Article
- Identifying Species Network Features from Gene Tree Quartets Under the Coalescent Model.Bulletin of mathematical biology · 2019Article
- Modeling Hybridization Under the Network Multispecies Coalescent.Systematic biology · 2018Article
- Bayesian Inference of Species Networks from Multilocus Sequence Data.Molecular biology and evolution · 2018Article
- Rearrangement moves on rooted phylogenetic networks.PLoS computational biology · 2017Article
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Authors and funding
2 authors.
Funding
Abstract
Recent work in estimating species relationships from gene trees has included inferring networks assuming that past hybridization has occurred between species. Probabilistic models using the multispecies coalescent can be used in this framework for likelihood-based inference of both network topologies and parameters, including branch lengths and hybridization parameters. A difficulty for such methods is that it is not always clear whether, or to what extent, networks are identifiable-that is whether there could be two distinct networks that lead to the same distribution of gene trees. For cases in which incomplete lineage sorting occurs in addition to hybridization, we demonstrate a new representation of the species network likelihood that expresses the probability distribution of the gene tree topologies as a linear combination of gene tree distributions given a set of species trees. This representation makes it clear that in some cases in which two distinct networks give the same distribution of gene trees when sampling one allele per species, the two networks can be distinguished theoretically when multiple individuals are sampled per species. This result means that network identifiability is not only a function of the trees displayed by the networks but also depends on allele sampling within species. We additionally give an example in which two networks that display exactly the same trees can be distinguished from their gene trees even when there is only one lineage sampled per species. [gene tree, hybridization, identifiability, maximum likelihood, species tree, phylogeny.].
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