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PLoS Comput Biol. 2017 Aug 1;13(8):e1005611. doi: 10.1371/journal.pcbi.1005611. eCollection 2017 Aug.

Rearrangement moves on rooted phylogenetic networks.

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Laboratoire d'Informatique Gaspard-Monge (LIGM), Université Paris-Est, CNRS, ENPC, ESIEE Paris, UPEM, F-77454, Marne-la-Vallée, France.
Delft Institute of Applied Mathematics, Delft University of Technology, Postbus 5031, 2628 CD Delft, The Netherlands.
Department of Mathematics and Statistics, University of Ottawa, K1N 6N5 Ottawa, Canada.
Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier, CNRS, 34095 Montpellier Cedex 5, France.
Institut de Biologie Computationnelle (IBC), 34095 Montpellier, France.
Institut des Sciences de l'Evolution (ISE-M), Université de Montpellier, CNRS, IRD, EPHE, 34095 Montpellier Cedex 5, France.


Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network-that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose "horizontal" moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and "vertical" moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves-named rNNI and rSPR-reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results-separating the contributions of horizontal and vertical moves-we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide a solid basis for practical phylogenetic network reconstruction.

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