Supplement 1. Source code and directions for computing, displaying, and testing the decomposition of trait diversity along a phylogenetic tree, with example data sets provided.

File List supfileA.R supfileB.pdf Description The file subfileA.R provides the source code for three functions in the R environment. The functions depend on the ade4 package of R. The function decdiv decomposes trait diversity across the nodes of a phylogenetic tree. It depends on the phylogenetic tree, a data frame (or alternatively a vector) containing the abundances of the species in communities, and trait distances between species. The trait distances might have been computed in R, for instance with the ade4 package where several functions are available (e.g., ‘dist.ktab’, ‘dist.binary’, ‘dist.quant’, ‘dist.prop’). The function plot.decdiv opens a graphics device and displays the phylogeny. It includes an argument that allows the display of circles at nodes whose diameter reflects the contributions of nodes to trait diversity. The function rtest.decdiv computes the “single-node skewness test”, “few-nodes skewness test” and “tips/root node skewness test” (or alternatively tips skewness test and root skewness tests separately by specifying options). The file subfileB.pdf contains directions for using the functions. It also provides examples with data sets contained in the package ade4 of the R environment.