arleyc/areapd

The package areaPD contains functions for calculating phylogenetic diversity (PD) for a set of geographic areas, calculating complementarity PD given a selected area, and drawing a Venn's diagram of PD within and between areas, given a phylogenetic tree and an assignment of samples (e.g., alleles, species, etc.) to areas.

areaPD

The functions in areaPD can calculate phylogenetic diversity (PD) and endemism PD for a set of geographic areas, the complementarity PD given a selected area, and constructing a Venn’s diagram of PD within and between areas, given one or more phylogenetic trees and an assignment of samples (e.g., alleles, species, etc.) to areas.

Installation

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("arleyc/areaPD")

Example

library(areaPD)
#PD calculation for a set of areas and a given phylogeny
data("homodata")
data("homotree")
homoPD<-multiareaPD(homodata[1:5,],homotree)

limnoPD<-multiareaPD(limnodata[1:5,],limnotree)

contoPD<-multiareaPD(contodata[1:5,],contotree)

latiPD<-multiareaPD(latidata[1:5,],latitree)

#complementarity PD calculation for a set of areas given a phylogeny
#(in red) and a selected area (LCL, in green)
homoPDcomp<-compareaPD(homodata[1:5,],homotree,LCL)

#endemism PD calculation for a set of areas given a phylogeny
homoPDend<-endemismPD(homodata[1:5,],homotree)

#drawing a Venn's diagram for a set of five areas given four
#different phylogenetic trees
vennout<-makeVennPD(list(homoPD,limnoPD,contoPD,latiPD))

References

Faith, P. D. (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.

Faith, P. D. (2016) The PD phylogenetic diversity framework: linking evolutionary history to feature diversity for biodiversity conservation. In: Biodiversity Conservation and Phylogenetic Systematics, Topics in Biodiversity and Conservation, 14, DOI 10.1007/978-3-319-22461-9_3.

Faith, P. D., Reid, C. A. M., and Hunter, J. (2004) Integrating phylogenetic diversity, complementarity, and endemism for conservation assessment. Conservation Biology, 18, 255-261.

Moritz, C., and Faith, D. P. (1998) Comparative phylogeography and the identification of genetically divergent areas for conservation. Molecular Ecology, 7, 419-429.

Citation

Camargo, A., Elgue, E., Fernandez, F., Lima, L., and Maneyro, R. (2023) Conservation prioritization of the northern hills of Uruguay based on the intra-specific phylogenetic diversity of frogs and lizards. Journal for Nature Conservation, 75, 126468. doi: 10.1016/j.jnc.2023.126468