phylo.betapart.core {betapart}

Core calculations of phylogenetic dissimilarities metrics

Description

Computes the basic quantities needed for computing the multiple-site phylogenetic beta diversity measures and pairwise phylogenetic dissimilarity matrices.

Usage

phylo.betapart.core(x, tree)

Arguments

x

a community matrix or data frame, where rows are sites and columns are species.

tree

a phylogenetic tree of class phylo with tips names identic to species names from the community matrix.

Value

The function returns a list with:

sumSi

the sum of the phylogenetic diversity values of all sites

St

the total phylogenetic diversity in the dataset

shared

a matrix containing the phylogenetic diversity shared between pairs of sites

sum.not.shared

a matrix containing the total phylogenetic diversity not shared between pairs of sites: b+c

max.not.shared

a matrix containing the total maximum phylogenetic diversity not shared between pairs of sites: max(b,c)

min.not.shared

a matrix containing the total minimum phylogenetic diversity not shared between pairs of sites: min(b,c)

Author(s)

Julien De Bortoli ([e-mail]), Fabien Leprieur([e-mail]), Andrés Baselga and David Orme

References

Baselga A. (2012) The relationship between species replacement, dissimilarity derived from nestedness, and nestedness. Global Ecology and Biogeography 21, 1223-1232

Bryant JA, Lamanna C, Morlon H, Kerkhoff AJ, Enquist BJ, et al. (2008) Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences of the United States of America 105: 11505-11511.

Faith DP, Lozupone CA, Nipperess D, Knight R (2009) The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology's "Phylogenetic Beta Diversity" Framework. Int J Mol Sci 10: 4723-4741. doi: 10.3390/ijms10114723.

Leprieur F, Albouy C, De Bortoli J, Cowman PF, Bellwood DR, et al. (2012) Quantifying Phylogenetic Beta Diversity: Distinguishing between "True" Turnover of Lineages and Phylogenetic Diversity Gradients. PLoS ONE 7(8): e42760. doi:10.1371/journal.pone.0042760

Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71: 8228-8235.

See Also

phylo.beta.pair, phylo.beta.multi

Examples

# toy tree for 6 species (sp1 to sp6)
require(ape)
toy.tree<-read.tree(text="(((sp1:1,sp2:1):5,(sp3:3,sp4:3):3):2,(sp5:7,sp6:7):1);")
plot(toy.tree)

# toy community table with 6 assemblages (A to F) with 6 species (sp1 to sp6)
toy.comm<-matrix(nrow=6, ncol=6)
rownames(toy.comm)<-c("A","B","C","D","E","F")
colnames(toy.comm)<-c("sp1","sp2","sp3","sp4","sp5","sp6")
toy.comm[1,]<-c(1,1,1,0,0,0)
toy.comm[2,]<-c(0,1,1,1,0,0)
toy.comm[3,]<-c(0,0,1,1,1,0)
toy.comm[4,]<-c(0,0,1,1,1,1)
toy.comm[5,]<-c(0,0,0,1,1,1)
toy.comm[6,]<-c(1,0,0,1,1,1)

toy.phylocore<-phylo.betapart.core(toy.comm, toy.tree)