A unifying characterization of tree-based networks and orchard networks using cherry covers

DOI10.1016/J.AAM.2021.102222MaRDI QIDQ2040997zbMATH OpenOpenAlexFDO

Authors Yanyan Li

Publication date 15 July 2021

Published in Advances in Applied Mathematics (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://arxiv.org/abs/2004.07677

zbMATH Keywords

graph theoryphylogenetic networksphylogenetics

Mathematics Subject Classification ID

Applications of graph theory (05C90) Taxonomy, cladistics, statistics in mathematical biology (92B10) Problems related to evolution (92D15)

Abstract: Phylogenetic networks are used to study evolutionary relationships between species in biology. Such networks are often categorized into classes by their topological features, which stem from both biological and computational motivations. We study two network classes in this paper: tree-based networks and orchard networks. Tree-based networks are those that can be obtained by inserting edges between the edges of an underlying tree. Orchard networks are a recently introduced generalization of the class of tree-child networks. Structural characterizations have already been discovered for tree-based networks; this is not the case for orchard networks. In this paper, we introduce cherry covers---a unifying characterization of both network classes---in which we decompose the edges of the networks into so-called cherry shapes and reticulated cherry shapes. We show that cherry covers can be used to characterize the class of tree-based networks as well as the class of orchard networks. Moreover, we also generalize these results to non-binary networks.

Recommendations

• Orchard networks are trees with additional horizontal arcs
• New characterisations of tree-based networks and proximity measures
• Tree-based unrooted phylogenetic networks
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• Tree-based networks: characterisations, metrics, and support trees

Cites work

• A class of phylogenetic networks reconstructable from ancestral profiles
• Counting phylogenetic networks
• New characterisations of tree-based networks and proximity measures
• On cherry-picking and network containment

Cited in

(7)

• Novel phylogenetic network distances based on cherry picking
• Orchard networks are trees with additional horizontal arcs
• Autopolyploidy, allopolyploidy, and phylogenetic networks with horizontal arcs
• Labellable phylogenetic networks
• Finding agreement cherry-reduced subnetworks in level-1 networks
• Phylogenetic network classes through the lens of expanding covers
• Making a network orchard by adding leaves

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