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Mathematical Biosciences
Article . 2018 . Peer-reviewed
License: Elsevier TDM
Data sources: Crossref
https://dx.doi.org/10.48550/ar...
Article . 2017
License: arXiv Non-Exclusive Distribution
Data sources: Datacite
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Phylogenetic diversity and biodiversity indices on phylogenetic networks

Authors: Kristina Wicke; Mareike Fischer;

Phylogenetic diversity and biodiversity indices on phylogenetic networks

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.

Keywords

Probability (math.PR), Populations and Evolution (q-bio.PE), Biodiversity, Models, Biological, FOS: Biological sciences, FOS: Mathematics, Mathematics - Combinatorics, Combinatorics (math.CO), Quantitative Biology - Populations and Evolution, Mathematics - Probability, Phylogeny

  • BIP!
    Impact byBIP!
    citations
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    9
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
9
Top 10%
Average
Average
Green
bronze
Related to Research communities
Italian National Biodiversity Future Center