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Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks

Bordewich, Magnus; Linz, Simone; Semple, Charles

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Authors

Simone Linz

Charles Semple



Abstract

Over the last fifteen years, phylogenetic networks have become a popular tool to analyse relationships between species whose past includes reticulation events such as hybridisation or horizontal gene transfer. However, the space of phylogenetic networks is significantly larger than that of phylogenetic trees, and how to analyse and search this enlarged space remains a poorly understood problem. Inspired by the widely-used rooted subtree prune and regraft (rSPR) operation on rooted phylogenetic trees, we propose a new operation—called subnet prune and regraft (SNPR)—that induces a metric on the space of all rooted phylogenetic networks on a fixed set of leaves. We show that the spaces of several popular classes of rooted phylogenetic networks (e.g. tree child, reticulation visible, and tree based) are connected under SNPR and that connectedness remains for the subclasses of these networks with a fixed number of reticulations. Lastly, we bound the distance between two rooted phylogenetic networks under the SNPR operation, show that it is computationally hard to compute this distance exactly, and analyse how the SNPR-distance between two such networks relates to the rSPR-distance between rooted phylogenetic trees that are embedded in these networks.

Citation

Bordewich, M., Linz, S., & Semple, C. (2017). Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks. Journal of Theoretical Biology, 423, 1-12. https://doi.org/10.1016/j.jtbi.2017.03.032

Journal Article Type Article
Acceptance Date Mar 20, 2017
Online Publication Date Apr 13, 2017
Publication Date Jun 21, 2017
Deposit Date Apr 27, 2017
Publicly Available Date Apr 13, 2018
Journal Journal of Theoretical Biology
Print ISSN 0022-5193
Publisher Elsevier
Peer Reviewed Peer Reviewed
Volume 423
Pages 1-12
DOI https://doi.org/10.1016/j.jtbi.2017.03.032
Public URL https://durham-repository.worktribe.com/output/1359281

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