[R] Pairwise comparisons, adonis (Vegan)

Hazel Knipe hazel_knipe at hotmail.co.uk
Thu Sep 3 23:09:39 CEST 2015

Hello all, 
I am an undergraduate, so bare with me if I don't make complete sense! 
I have performed a permanova using the function Adonis (vegan), to test for significant difference in OTU datasets from different species (n=5) at different sites (n=6) with a total of 20 libraries (unbalanced). I have got a significant result, but I would like to know which species/ sites are causing this result.
adonis(formula = vegdist(comm, method = "bray") ~ Species, data = metadata, strata = Site) 
I have heard you can run multiple adonis tests, and then adjust the P value (which correction?), although I am not sure my reduced datasets meet the assumptions, or if the permutations produce a meaningful result at such a low number.  
Does anyone know how to get around this, or if I should be using a different test for this data? 
Thank you in advance, 
Hazel Knipe
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