Folding and unfolding phylogenetic trees and networks

Huber, Katharina, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Steel, Mike and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2016) Folding and unfolding phylogenetic trees and networks. Journal of Mathematical Biology, 73 (6). 1761–1780. ISSN 0303-6812

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Abstract

Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network $N$ can be "unfolded" to obtain a MUL-tree $U(N)$ and, conversely, a MUL-tree $T$ can in certain circumstances be "folded" to obtain a phylogenetic network $F(T)$ that exhibits $T$. In this paper, we study properties of the operations $U$ and $F$ in more detail. In particular, we introduce the class of stable networks, phylogenetic networks $N$ for which $F(U(N))$ is isomorphic to $N$, characterise such networks, and show that they are related to the well-known class of tree-sibling networks.We also explore how the concept of displaying a tree in a network $N$ can be related to displaying the tree in the MUL-tree $U(N)$. To do this, we develop a phylogenetic analogue of graph fibrations. This allows us to view $U(N)$ as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in $U(N)$ and reconcilingphylogenetic trees with networks.

Item Type:	Article
Additional Information:	The paper is published open access under the CC BY license.
Uncontrolled Keywords:	phylogenetic networks,multi-labelled trees, graph fibrations,tree and network reconciliation,universal cover of a digraph
Faculty \ School:	Faculty of Science > School of Computing Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Data Science and AI
Depositing User:	Pure Connector
Date Deposited:	01 Apr 2016 10:11
Last Modified:	10 Dec 2024 01:27
URI:	https://ueaeprints.uea.ac.uk/id/eprint/58034
DOI:	10.1007/s00285-016-0993-5

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