Hi, I wanted to thank everyone for their responses and recommendations. Some of them were quite helpful and have got me thinking in new ways.
With respect to the use of the Rao index, I didn't express my question very well. What I was really trying to discern was whether it was appropriate to use the Rao index values as a distance matrix of functional dissimilarity between estuaries that could then be evaluated using standard multivariate methods (i.e. clustering). I have not seen Shannon entropy used this way either, but it is understood that pairwise beta diversity calculated by either of these approaches is a measure of dissimilarity between sites. So, on that basis, it doesn't seem too much of a stretch. Also, the index values are used as dissimilarities in Mantel tests or other matrix calculations. I am not sure whether the reason these indices have not been used this way is because it would be inappropriate statistically or mathematically, or whether there is some ecological reason for not doing it. Thanks again. - Katharine
