Arboreal networks and their underlying trees

Huber, Katharina and Overman, Darren (2026) Arboreal networks and their underlying trees. Journal of Mathematical Biology. ISSN 0303-6812 (In Press)

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Abstract

Horizontal gene transfer (HGT) is an important process in bacterial evolution. Current phylogeny-based approaches to capture it cannot however appropriately account for the fact that HGT can occur between bacteria living in different ecological niches. Due to the fact that arboreal networks are a type of multiple-rooted phylogenetic network that can be thought of as a forest of rooted phylogenetic trees along with a set of additional arcs each joining two different trees in the forest, understanding the combinatorial structure of such networks might therefore pave the way to extending current phylogeny-based HGT inference methods in this direction. A central question in this context is, how can we construct an arboreal network? Answering this question is strongly informed by finding ways to encode an arboreal network, that is, breaking up the network into simpler combinatorial structures that, in a well defined sense uniquely determine the network. In the form of triplets, trinets and quarnets such encodings are known for certain types of single-rooted phylogenetic networks. By studying the underlying tree of an arboreal network, we \blue{complement} them here with an answer for arboreal networks.

Item Type:	Article
Additional Information:	Data availability: Data sharing is not applicable to this article as no datasets were generated or analysed in this study.
Uncontrolled Keywords:	arboreal network,horizontal gene transfer,enhanced quartet tree system,augmented tree,phylogenetic tree,multiple-rooted network
Faculty \ School:	Faculty of Science > School of Computing Sciences Faculty of Science
UEA Research Groups:	Faculty of Science > Research Groups > Computational Biology
Depositing User:	LivePure Connector
Date Deposited:	23 Feb 2026 11:30
Last Modified:	25 Feb 2026 00:55
URI:	https://ueaeprints.uea.ac.uk/id/eprint/102004
DOI:	issn:0303-6812

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