Phylogenetic networks: A tool to display character conflict and demographic history

Abstract

Evolutionary trees have the assumption that evolution and phylogeny can be represented in a strictly bifurcating manner. Firmly speaking, from one ancestral taxon, two descendant taxa emerge. Nevertheless, hybridization, recombination and horizontal gene transfer is in conflict with this straightforward concept. In such cases, evolutionary lines do not only separate from each other, but have the possibility of melting again and are called reticulations. Consequently, networks can represent evolutionary events more realistically than phylogenetic trees. Networks can display alternative topologies and co-existence of ancestors and descendants, which are otherwise not obvious when a comparison is done on several single trees or a consensus tree. Therefore, networks have the ability to visualize the conflicting information in a given data set. Moreover, the distribution, frequencies and arrangement of haplotypes in populations can reveal the phylogenetic histories of the taxa, regarding predictions from the coalescent theory. This review aims to: (1) give a brief comparison between phylogenetic trees and networks, (2) provide the overall concept of the coalescent theory, (3) clarify how phylogenetic networks can be used to display conflict data and evaluate phylogenetic histories, and (4) offer a useful starting point and guide for sequence analysis, with the aim to discover population dynamics.

Key words: Phylogenetic networks, reticulation, coalescent theory, population history, character conflict.