1. Phylogenetic methods that account for the degree of relationship between species are increasingly commonly used for cross-species comparisons of ecological data. In particular ‘phylogenetic contrasts’ are commonly used to generate data for analysis that are phylogenetically independent. The efficacy of this technique for removing phylogenetic correlations is rarely tested, however.
2. For a number of reasons, including non-Brownian modes of evolution, phylogenetic contrasts may not always be phylogenetically independent. This lack of independence defeats the object of phylogenetic analysis and effectively 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 phylogenetic 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 how the character in question evolved.