Phylogenetic diversity and biodiversity indices on phylogenetic networks
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Abstract: 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 come to the fore as a generalization of phylogenetic trees, allowing for the representation of non-treelike evolutionary events, such as horizontal gene transfer or 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 LSA 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. Furthermore, we introduce our software package NetDiversity, which was 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 phylogentic network representing the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by widespread hybridization.
Recommendations
- Spaces of phylogenetic diversity indices: combinatorial and geometric properties
- Effects of discordance between species and gene trees on phylogenetic diversity conservation
- The equivalence of two phylogenetic biodiversity measures: the Shapley value and fair proportion index
- Combinatorial properties of phylogenetic diversity indices
- Phylogenetic networks
Cites work
- A fast algorithm for finding dominators in a flowgraph
- Comparing the rankings obtained from two biodiversity indices: the fair proportion index and the Shapley value
- Equality of Shapley value and fair proportion index in phylogenetic trees
- scientific article; zbMATH DE number 3571502 (Why is no real title available?)
- Locating a tree in a phylogenetic network
- The equivalence of two phylogenetic biodiversity measures: the Shapley value and fair proportion index
- The Shapley value of phylogenetic trees
Cited in
(17)- The fair proportion is a Shapley value on phylogenetic networks too
- Evolutionarily distinctive species often capture more phylogenetic diversity than expected
- Effects of discordance between species and gene trees on phylogenetic diversity conservation
- On the complexity of optimising variants of phylogenetic diversity on phylogenetic networks
- Revisiting Shao and Sokal's B₂ index of phylogenetic balance
- Biodiversity, Shapley value and phylogenetic trees: some remarks
- A genome evolution-based framework for measures of originality for clades
- NetDiversity
- The expected loss of feature diversity (versus phylogenetic diversity) following rapid extinction at the present
- Spaces of phylogenetic diversity indices: combinatorial and geometric properties
- Phylogenetic diversity indices from an affine and projective viewpoint
- An interchange property for the rooted phylogenetic subnet diversity on phylogenetic networks
- Phylogenetic network diversity parameterized by reticulation number and beyond
- A multivariate complexity analysis of the generalized Noah's ark problem
- How can we maximize phylogenetic diversity? Parameterized approaches for networks
- Maximizing phylogenetic diversity under ecological constraints: a parameterized complexity study
- Parameterized algorithms for diversity of networks with ecological dependencies
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