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Path partitions of phylogenetic networks

Authors: Manuel Lafond; Vincent Moulton;

Path partitions of phylogenetic networks

Abstract

In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In particular, the class of forest-based networks was recently introduced to represent introgression, in which genes are swapped between between species. A network is forest-based if it can be obtained by adding arcs to a collection of trees, so that the endpoints of the new arcs are in different trees. This contrasts with so-called tree-based networks, which are formed by adding arcs within a single tree. We are interested in the computational complexity of recognizing forest-based networks, which was recently left as an open problem by Huber et al. Forest-based networks coincide with directed acyclic graphs that can be partitioned into induced paths, each ending at a leaf of the original graph. Several types of path partitions have been studied in the graph theory literature, but to our knowledge this type of leaf induced path partition has not been considered before. The study of forest-based networks in terms of these partitions allows us to establish closer relationships between phylogenetics and algorithmic graph theory, and to provide answers to problems in both fields. We show that deciding whether a network is forest-based is NP-complete, even on input networks that are tree-based, binary, and have only three leaves. This shows that partitioning a directed acyclic graph into three induced paths is NP-complete, answering a recent question of Fernau et al. We then show that the problem is polynomial-time solvable on binary networks with two leaves and on the class of orchards. Finally, for undirected graphs, we introduce unrooted forest-based networks and provide hardness results for this class as well.

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United Kingdom
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Keywords

FOS: Computer and information sciences, forest-based, Applications of graph theory, tree-based, 004, monotone NAE-3-SAT, phylogenetic networks, Problems related to evolution, Computer Science - Data Structures and Algorithms, Data Structures and Algorithms (cs.DS), path partitions

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
2
Top 10%
Average
Average
Green
hybrid