ArticleBMC bioinformatics2016
In the light of deep coalescence: revisiting trees within networks.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Phylogenetic networks empower biodiversity research.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- TINNiK: inference of the tree of blobs of a species network under the coalescent model.Algorithms for molecular biology : AMB · 2024Article
- TINNiK: Inference of the Tree of Blobs of a Species Network Under the Coalescent.bioRxiv : the preprint server for biology · 2024Article
- ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE.bioRxiv : the preprint server for biology · 2023Article
- The tree of blobs of a species network: identifiability under the coalescent.Journal of mathematical biology · 2022Article
- Treewidth-based algorithms for the small parsimony problem on networks.Algorithms for molecular biology : AMB · 2022Article
- Embedding gene trees into phylogenetic networks by conflict resolution algorithms.Algorithms for molecular biology : AMB · 2022Article
- Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes.Systematic biology · 2022Article
- Identifiability of species network topologies from genomic sequences using the logDet distance.Journal of mathematical biology · 2022Article
- Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs.Systematic biology · 2022Article
- Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow.National science review · 2021Article
- Phylogenomic assessment of the role of hybridization and introgression in trait evolution.PLoS genetics · 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 divide-and-conquer method for scalable phylogenetic network inference from multilocus data.Bioinformatics (Oxford, England) · 2019Article
- Identifying Species Network Features from Gene Tree Quartets Under the Coalescent Model.Bulletin of mathematical biology · 2019Article
- NANUQ: a method for inferring species networks from gene trees under the coalescent model.Algorithms for molecular biology : AMB · 2019Article
- Modeling Hybridization Under the Network Multispecies Coalescent.Systematic biology · 2018Article
- Inferring Phylogenetic Networks Using PhyloNet.Systematic biology · 2018Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPhylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A salient concept underlying a great majority of these developments has been the notion that a network displays a set of trees and those trees can be used to infer, analyze, and study the network.
resultsIn this paper, we show that in the presence of coalescence effects, the set of displayed trees is not sufficient to capture the network. We formally define the set of parental trees of a network and make three contributions based on this definition. First, we extend the notion of anomaly zone to phylogenetic networks and report on anomaly results for different networks. Second, we demonstrate how coalescence events could negatively affect the ability to infer a species tree that could be augmented into the correct network. Third, we demonstrate how a phylogenetic network can be viewed as a mixture model that lends itself to a novel inference approach via gene tree clustering.
conclusionsOur results demonstrate the limitations of focusing on the set of trees displayed by a network when analyzing and inferring the network. Our findings can form the basis for achieving higher accuracy when inferring phylogenetic networks and open up new venues for research in this area, including new problem formulations based on the notion of a network's parental trees.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.