I am analyzing taxa community composition in relation to explanatory variables by distance-based redundancy analysis (db-RDA), based on Bray-Curtis dissimilarities on untransformed abundances, with R. I have a stratified design (3 stream reaches) and initially I had the same number of replicates per site. As predictors, I'm using, among other variables, treatments 1, 2, and 3. At the end of the study, I lost all replicates from, say, treatment 1 at a given site, and a couple of replicates per site for, say, treatment 2. I ran the db-RDA model for sites combined (but with permutations stratified within sites), and then ran a separate model per site. What are the consequences of an unbalanced design when using db-RDA?