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

Bordewich, Magnus and Linz, Simone and Semple, Charles (2017) 'Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks.', Journal of theoretical biology., 423 . pp. 1-12.

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.

Item Type:Article
Full text:(AM) Accepted Manuscript
Available under License - Creative Commons Attribution Non-commercial No Derivatives.
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Status:Peer-reviewed
Publisher Web site:https://doi.org/10.1016/j.jtbi.2017.03.032
Publisher statement:© 2017 This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/
Date accepted:20 March 2017
Date deposited:27 April 2017
Date of first online publication:13 April 2017
Date first made open access:13 April 2018

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