ReviewJournal of mathematical biology2022
Classes of explicit phylogenetic networks and their biological and mathematical significance.
Review in Journal of mathematical biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Phylogenetic Network Models as Graphical Models.Bulletin of mathematical biology · 2026Article
- SNaQ.jl: Improved scalability for level-1 phylogenetic network inference.Bioinformatics (Oxford, England) · 2026Article
- Counting Spinal Phylogenetic Networks.Bulletin of mathematical biology · 2026Article
- Counting Rankings of Tree-Child Networks.Bulletin of mathematical biology · 2026Article
- Characterizing semi-directed phylogenetic networks and their multi-rootable variants.Theory in biosciences = Theorie in den Biowissenschaften · 2025Article
- Do syngameons exist in tropical trees? Challenges to determine their existence and estimate their frequency.Biology letters · 2025Review
- Orthology and near-cographs in the context of phylogenetic networks.Algorithms for molecular biology : AMB · 2025Article
- A Dichotomy Law for Certain Classes of Phylogenetic Networks.Bulletin of mathematical biology · 2025Article
- Spaces of ranked tree-child networks.Journal of mathematical biology · 2025Article
- When are Quarnets Sufficient to Reconstruct Semi-directed Phylogenetic Networks?Bulletin of mathematical biology · 2025Article
- Phylogenetic networks empower biodiversity research.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Asymptotic Enumeration of Normal and Hybridization Networks via Tree Decoration.Bulletin of mathematical biology · 2025Article
- Mathematically tractable models of random phylogenetic networks: an overview of some recent developments.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Leveraging graphical model techniques to study evolution on phylogenetic networks.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Counting Cherry Reduction Sequences in Phylogenetic Tree-Child Networks is Counting Linear Extensions.Bulletin of mathematical biology · 2024Article
- 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
- Phylogenetic network classes through the lens of expanding covers.Journal of mathematical biology · 2024Article
- Asymmetric Cluster-Based Measures for Comparative Phylogenetics.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- Ultrafast learning of four-node hybridization cycles in phylogenetic networks using algebraic invariants.Bioinformatics advances · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately represented by a phylogenetic tree, and rooted phylogenetic networks that describe such complex processes have been introduced as a generalization of rooted phylogenetic trees. In fact, estimating rooted phylogenetic networks from genomic sequence data and analyzing their structural properties is one of the most important tasks in contemporary phylogenetics. Over the last two decades, several subclasses of rooted phylogenetic networks (characterized by certain structural constraints) have been introduced in the literature, either to model specific biological phenomena or to enable tractable mathematical and computational analyses. In the present manuscript, we provide a thorough review of these network classes, as well as provide a biological interpretation of the structural constraints underlying these networks where possible. In addition, we discuss how imposing structural constraints on the network topology can be used to address the scalability and identifiability challenges faced in the estimation of phylogenetic networks from empirical data.
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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.