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

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dc.contributor.author Bordewich, Magnus en
dc.contributor.author Linz, Simone en
dc.contributor.author Semple, Charles en
dc.date.accessioned 2018-10-14T22:28:34Z en
dc.date.issued 2017-06 en
dc.identifier.citation Journal of Theoretical Biology 423:1-12 21 Jun 2017 en
dc.identifier.issn 0022-5193 en
dc.identifier.uri http://hdl.handle.net/2292/41370 en
dc.description.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. en
dc.format.medium Print-Electronic en
dc.language eng en
dc.relation.ispartofseries Journal of theoretical biology en
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. en
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm en
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/ en
dc.subject Hybridization, Genetic en
dc.subject Computational Biology en
dc.subject Phylogeny en
dc.subject Gene Transfer, Horizontal en
dc.subject Algorithms en
dc.subject Gene Regulatory Networks en
dc.subject Spatial Analysis en
dc.title Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks. en
dc.type Journal Article en
dc.identifier.doi 10.1016/j.jtbi.2017.03.032 en
pubs.begin-page 1 en
pubs.volume 423 en
dc.rights.holder Copyright: Elsevier Ltd. en
dc.identifier.pmid 28414085 en
pubs.end-page 12 en
pubs.publication-status Published en
dc.rights.accessrights http://purl.org/eprint/accessRights/OpenAccess en
pubs.subtype Research Support, Non-U.S. Gov't en
pubs.subtype Journal Article en
pubs.elements-id 623397 en
pubs.org-id Science en
pubs.org-id School of Computer Science en
dc.identifier.eissn 1095-8541 en
pubs.record-created-at-source-date 2017-04-18 en
pubs.dimensions-id 28414085 en

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