Avoiding potential biases in ses.PD estimations with the Picante software package

Faith’s phylogenetic diversity (PD) is one of the most widespread used indices of phylogenetic structure in the eco-phylogenetic literature. The metric became notably popular with the publication of the function pd as part of the Picante R package, which is nowadays a reference software for phylogenetic analyses. Because PD is not statistically independent of species richness, the routine procedure is to standardize the observed PD values for unequal richness across samples. The function ses.pd , which is also implemented in the Picante R package, is the reference function to conduct such standardization. Unfortunately, I have detected an anomaly in the function that may result in biased estimations of standardized PD values, particularly in communities with low species richness (i.e. less than four species) and unbalanced phylogenies. I conduct a simple simulation exercise to illustrate the issue and propose two alternative and easy to implement solutions to go around the problem.