An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees

Abstract

A phylogenetic network is a model for reticulate evolution. A hybridization network is one type of phylogenetic network for a set of discordant gene trees and ''displays'' each gene tree. A central computational problem on hybridization networks is: given a set of gene trees, reconstruct the minimum (i.e., most parsimonious) hybridization network that displays each given gene tree. This problem is known to be NP-hard, and existing approaches for this problem are either heuristics or making simplifying assumptions (e.g., work with only two input trees or assume some topological properties).In this article, we develop an exact algorithm (called PIRN C ) for inferring the minimum hybridization networks from multiple gene trees. The PIRN C algorithm does not rely on structural assumptions (e.g., the so-called galled networks). To the best of our knowledge, PIRN C is the first exact algorithm implemented for this formulation. When the number of reticulation events is relatively small (say, four or fewer), PIRN C runs reasonably efficient even for moderately large datasets. For building more complex networks, we also develop a heuristic version of PIRN C called PIRN CH . Simulation shows that PIRN CH usually produces networks with fewer reticulation events than those by an existing method.PIRN C and PIRN CH have been implemented as part of the software package called PIRN and is available online.

Computational approaches to species phylogeny inference and gene tree reconciliation

“…Introducing the notion of a phylogenetic network, the parsimony version of the inference problem under HGT becomes: find a phylogenetic network with the minimum number of reticulation nodes needed to display all of the gene trees. Several methods have been proposed recently for solving versions of this problem [29, 30, 31, 32, 33, 34, 35]. The progress on likelihood approaches for dealing with gene tree incongruence has been much greater for ILS than the other evolutionary processes, owing mainly to the mature theoretical foundations of the coalescent model that deal with ILS naturally.…”

Mechanistic insights into the evolution of DUF26-containing proteins in land plants

“…Gene tree reconciliation was carried out using DLCpar (version 1.0) 89 downloaded from https://www.cs.hmc.edu/~yjw/software/dlcpar/. NCBI taxonomy was used as the species tree, downloaded in newick format from PhyloT website, http://phylot.biobyte.de/.…”

Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization

“…This problem is NP-hard [116] and methods were developed for solving it and variations thereof, some of which are heuristics [115,123,89,124]. Furthermore, the view of a phylogenetic network in terms of the set of trees it displays was used for pursuing other questions in this domain.…”