Exploring the Tiers of Rooted Phylogenetic Network Space Using Tail Moves.

Remie Janssen, Mark Jones, Péter L Erdős, Leo van Iersel, Celine Scornavacca
Author Information
  1. Remie Janssen: Delft Institute of Applied Mathematics, Delft University of Technology, Postbus 5031, 2600 GA, Delft, The Netherlands. ORCID
  2. Mark Jones: Delft Institute of Applied Mathematics, Delft University of Technology, Postbus 5031, 2600 GA, Delft, The Netherlands.
  3. Péter L Erdős: MTA Rényi Institute of Mathematics, Reáltanoda u 13-15, Budapest, 1053, Hungary.
  4. Leo van Iersel: Delft Institute of Applied Mathematics, Delft University of Technology, Postbus 5031, 2600 GA, Delft, The Netherlands. l.j.j.v.iersel@gmail.com. ORCID
  5. Celine Scornavacca: Institut des Sciences de l'Evolution, CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, Montpellier, France.

Abstract

Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rooted Nearest Neighbour Interchange (rNNI) and rooted Subtree Prune and Regraft (rSPR). Recently, these moves were generalized to rooted phylogenetic networks, which are a more suitable representation of reticulate evolutionary histories, and it was shown that any two rooted phylogenetic networks of the same complexity are connected by a sequence of either rSPR or rNNI moves. Here, we show that this is possible using only tail moves, which are a restricted version of rSPR moves on networks that are more closely related to rSPR moves on trees. The connectedness still holds even when we restrict to distance-1 tail moves (a localized version of tail moves). Moreover, we give bounds on the number of (distance-1) tail moves necessary to turn one network into another, which in turn yield new bounds for rSPR, rNNI and SPR (i.e. the equivalent of rSPR on unrooted networks). The upper bounds are constructive, meaning that we can actually find a sequence with at most this length for any pair of networks. Finally, we show that finding a shortest sequence of tail or rSPR moves is NP-hard.

Keywords

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MeSH Term

Algorithms
Biological Evolution
Evolution, Molecular
Mathematical Concepts
Models, Biological
Models, Genetic
Phylogeny

Word Cloud

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