Phylogenetic diversity and biodiversity indices on phylogenetic networks

• Published in: Mathematical biosciences 2018-04, Vol.298, p.80-90
• Main Authors: Wicke, Kristina, Fischer, Mareike
• Format: Article
• Language: English
• Subjects: Biodiversity; Biological evolution; Conservation; Diversity indices; Evolution; Fair proportion index; Genetic diversity; Heredity; Hybridization; Models, Biological; Networks; Perl; Phylogenetic diversity; Phylogenetic networks; Phylogenetics; Phylogeny; Plant diversity; Shapley value; Species; Species diversity; Trees; Wildlife conservation; Xiphophorus
• ISSN: 0025-5564; 1879-3134
• DOI: 10.1016/j.mbs.2018.02.005

•First introduction of phylogenetic diversity concepts in the presence of reticulation events like hybridization or horizontal gene transfer.•First introduction of biodiversity prioritization indices for phylogenetic networks.•Comparison of all introduced concepts theoretically and practically (the latter concerning a platyfish dataset).•Free software package concerning an implementation of the proposed concepts. In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species according to their contribution to overall phylogenetic diversity. However, in many cases evolution is not treelike and thus, phylogenetic networks have been developed as a generalization of phylogenetic trees, allowing for the representation of non-treelike evolutionary events, such as hybridization. Here, we extend the concepts of phylogenetic diversity and phylogenetic diversity indices from phylogenetic trees to phylogenetic networks. On the one hand, we consider the treelike content of a phylogenetic network, e.g. the (multi)set of phylogenetic trees displayed by a network and the so-called lowest stable ancestor tree associated with it. On the other hand, we derive the phylogenetic diversity of subsets of taxa and biodiversity indices directly from the internal structure of the network. We consider both approaches that are independent of so-called inheritance probabilities as well as approaches that explicitly incorporate these probabilities. Furthermore, we introduce our software package NetDiversity, which is implemented in Perl and allows for the calculation of all generalized measures of phylogenetic diversity and generalized phylogenetic diversity indices established in this note that are independent of inheritance probabilities. We apply our methods to a phylogenetic network representing the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by widespread hybridization.