Interpreting and estimating measures of community phylogenetic structuring

1. To characterize the spatial phylogenetic structure of communities, Hardy & Senterre (2007) (J. Ecol., 95, 493-506) partition Gini-Simpson diversity and its generalization, Rao's entropy, defining I(ST) and P(ST) as the proportion of diversity expressed among sites. 2. Interpreting I(ST) as a measure of 'differentiation' between sites is inadequate because low values are actually compatible with high differentiation (low species sharing) in species rich communities. To avoid an inadequate use of I(ST), for example in conservation biology, we offer a more literal interpretation: I(ST) expresses the 'local species identity excess'. Similarly, P(ST) expresses the 'local phylogenetic similarity excess'. 3. Villeger & Mouillot (2008) (J. Ecol., 96, 845-848, this issue) argue that the equations of Hardy & Senterre (2007) to compute diversity are inadequate when sites differ in size, and they provide new expressions weighting sites by their sizes. We argue that whether sites must be weighted equally or not depends on the question being asked. Moreover, actual size and sample size must be distinguished, the latter being important for defining estimators. 4. Synthesis. The formulations given by Hardy & Senterre (2007) and by Villeger & Mouillot (2008)are both correct in the specific contexts we detail.