The agreement distance of unrooted phylogenetic networks

A rearrangement operation makes a small graph-theoretical change to a phylogenetic network to transform it into another one. For unrooted phylogenetic trees and networks, popular rearrangement operations are tree bisection and reconnection (TBR) and prune and regraft (PR) (called subtree prune and regraft (SPR) on trees). Each of these operations induces a metric on the sets of phylogenetic trees and networks. The TBR-distance between two unrooted phylogenetic trees $T$ and $T'$ can be characterised by a maximum agreement forest, that is, a forest with a minimum number of components that covers both $T$ and $T'$ in a certain way. This characterisation has facilitated the development of fixed-parameter tractable algorithms and approximation algorithms. Here, we introduce maximum agreement graphs as a generalisations of maximum agreement forests for phylogenetic networks. While the agreement distance -- the metric induced by maximum agreement graphs -- does not characterise the TBR-distance of two networks, we show that it still provides constant-factor bounds on the TBR-distance. We find similar results for PR in terms of maximum endpoint agreement graphs.Comment: 23 pages, 13 figures, final journal versio

Rearrangement operations on unrooted phylogenetic networks

Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree prune and regraft), and TBR (tree bisection and reconnection). Recently, these operations have been extended to unrooted phylogenetic networks, which are generalisations of phylogenetic trees that can model reticulated evolutionary relationships. Here, we study global and local properties of spaces of phylogenetic networks under these three operations. In particular, we prove connectedness and asymptotic bounds on the diameters of spaces of different classes of phylogenetic networks, including tree-based and level-k networks. We also examine the behaviour of shortest TBR-sequence between two phylogenetic networks in a class, and whether the TBR-distance changes if intermediate networks from other classes are allowed: for example, the space of phylogenetic trees is an isometric subgraph of the space of phylogenetic networks under TBR. Lastly, we show that computing the TBR-distance and the PR-distance of two phylogenetic networks is NP-hard

Rooted NNI moves on tree-based phylogenetic networks

We show that the space of rooted tree-based phylogenetic networks is connected under rooted nearest-neighbour interchange (rNNI) moves.Comment: Fixed typos and references to labels in the last subsectio

On Patchworks and Hierarchies

Motivated by questions in biological classification, we discuss some elementary combinatorial and computational properties of certain set systems that generalize hierarchies, namely, 'patchworks', 'weak patchworks', 'ample patchworks' and 'saturated patchworks' and also outline how these concepts relate to an apparently new 'duality theory' for cluster systems that is based on the fundamental concept of 'compatibility' of clusters.Comment: 17 pages, 2 figure