Phylogenetic tests of ecological and evolutionary hypotheses: checking forphylogenetic independence

1. Phylogenetic methods that account for the degree of relationship between species are increasingly commonly used for cross-species comparisons of ec ological data. In particular 'phylogenetic contrasts' are commonly used to generate data for analysis that are phylogenetically independent. The effic acy of this technique for removing phylogenetic correlations is rarely test ed, however. 2. For a number of reasons, including non-Brownian modes of evolution, phyl ogenetic contrasts may not always be phylogenetically independent. This lac k of independence defeats the object of phylogenetic analysis and effective ly invalidates the results of such analyses. Typically such problems may be overcome using simple data transformations but it is necessary to identify the correct transformation for each analysis variable. 3. Examples are presented for which contrasts have failed to control for ph ylogenetic correlation. This was because the correct transformation of the data was not identified prior to analysis. It is highlighted that the very act of transformation of data increases our understanding of the ecological variables being studied because the choice of transformation depends on ho w the character in question evolved.