What I have been doing of late is trying to work on a revision of a paper I wrote on the subterranean probe. One of the reviewers suggested I use a program called ANOSIM, which is an analysis of similarity which gives you a significance value. Money is always a problem in our lab and apparently the best place to get this program is through a very expensive software package called PRIMER, but we eventually found a free package called PAST that includes it. Great. The thing about ANOSIM is that you can choose which distance measure you want to use -- Bray-Curtis, Jaccard's, Raup-Crick, etc. etc. But we are having trouble finding any sort of discussion about how you choose the distance measure. The one thing we were able to find says that Bray-Curtis should be used for abundance data, not presence-absence data (which is what we have). Bray-Curtis seems to be the default, and most of the published papers we have been able to find use it (including some with presence-absence data), but none of them seem to include an explanation of why they chose it. And the distance measures which appear to be more appropriate for presence-absence data seem to give wildly different results. So we're kind of at a loss. Does anybody out there understand this stuff?