On Computing the Maximum Parsimony Score of a Phylogenetic Network

TL;DR

This paper analyzes the computational complexity of maximum parsimony scores in phylogenetic networks, providing algorithms, complexity results, and software tools for different definitions and conditions.

Contribution

It introduces complexity results for hardwired and softwired maximum parsimony, including polynomial algorithms, NP-hardness proofs, and fixed-parameter tractability analyses.

Findings

Hardwired parsimony for 2-state characters is polynomial-time solvable.

Hardwired parsimony with more states is NP-hard but approximable.

Softwired parsimony is computationally hard, with fixed-parameter tractability in network level.

Abstract

Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods such as Maximum Parsimony need to be modified in order to be applicable to networks. In this paper, we discuss two different definitions of Maximum Parsimony on networks, "hardwired" and "softwired", and examine the complexity of computing them given a network topology and a character. By exploiting a link with the problem Multicut, we show that computing the hardwired parsimony score for 2-state characters is polynomial-time solvable, while for characters with more states this problem becomes NP-hard but is still approximable and fixed parameter tractable in the parsimony score. On the other hand we show that, for the softwired definition, obtaining even weak approximation guarantees is already difficult for binary characters and restricted network topologies, and fixed-parameter tractable algorithms in the parsimony score are unlikely. On the positive side we show that computing the softwired parsimony score is fixed-parameter tractable in the level of the network, a natural parameter describing how tangled reticulate activity is in the network. Finally, we show that both the hardwired and softwired parsimony score can be computed efficiently using Integer Linear Programming. The software has been made freely available.