Novel methodology for construction and pruning of quasi-median networks

We address the problems inherent in construction and reduction of quasi-median networks. We describe a novel method of generating quasi-median networks that uses all characters, both binary and multistate, without imposing an arbitrary ordering of the multistate partitions. We also describe a pruning mechanism which maintains at least one shortest path between observed sequences, displaying the underlying relations between all pairs of sequences while maintaining a connected graph.Application of this approach to 5S rDNA sequence data from sea beet produced a pruned network within which genetic isolation between populations by distance was evident, demonstrating the value of this approach for exploration of evolutionary relationships.Phylogenies reconstructed from DNA data are usually depicted as hierarchical, bifurcating trees, but such trees are inappropriate when intraspecific phylogenies are studied because recombination between taxa, the persistence of ancestral alleles and the presence of multiple descendents from single ancestors give rise to a reticulated and multifurcating pattern of relationships [1]. Networks rather than hierarchical trees are therefore more suitable for studying intraspecific relationships [2]. Two main types of network have been used: true phylogenetic networks which aim to reconstruct the phylogenetic history of a set of sequences, and within which nodes represent ancestral sequences and edges represent evolutionary events; and character-display networks which display all conflict within the dataset, nodes not necessarily representing ancestral sequences and some edges not corresponding to true events [3]. To construct a true phylogenetic network the dataset must be relatively small and reticulations must be rare, and often a number of networks must be evaluated to identify the optimal one. Character-display methods are therefore more popular, especially when combined with pruning methods that reduce the number of nodes and edges, givin