Comparison of Tree-Child Phylogenetic Networks

TL;DR

This paper introduces and studies tree-child phylogenetic networks, providing a novel representation, a meaningful distance measure, and an alignment method, with efficient algorithms and software implementations, advancing the analysis of complex evolutionary histories.

Contribution

It presents the first true distance and alignment methods for a meaningful class of phylogenetic networks extending trees, along with polynomial algorithms and software tools.

Findings

First true distance measure for tree-child networks

Polynomial algorithms for reconstruction, distance, and alignment

Software implementations available online

Abstract

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new class of phylogenetic networks, called tree-child phylogenetic networks, where every non-extant species has some descendant through mutation. We provide an injective representation of these networks as multisets of vectors of natural numbers, their path multiplicity vectors, and we use this representation to define a distance on this class and to give an alignment method for pairs of these networks. To the best of our knowledge, they are respectively the first true distance and the first alignment method defined on a meaningful class of phylogenetic networks strictly extending the class of phylogenetic trees. Simple, polynomial algorithms for reconstructing a tree-child phylogenetic network from its path multiplicity vectors, for computing the distance between two tree-child phylogenetic networks, and for aligning a pair of tree-child phylogenetic networks, are provided, and they have been implemented as a Perl package and a Java applet, and they are available at http://bioinfo.uib.es/~recerca/phylonetworks/mudistance