I asked this question before, but without too many details. Maybe I was not clear enough. I am analyzing 40 samples with two treatments (20 samples for each treatment). I want to find out if the communities between the treatments have significantly different structures. I started with tree.shared using the Yue & Clayton theta similarity coefficient followed by a parsimony test. The results indicate that the structure is (highly) significantly different between my two treatments. Then I ran dist.shared with the same calculator followed by an amova test, which indicate that the structure is not significantly different between the two treatments (p=0.39).
There might be something that I’m missing, because I really don’t understand these results… How can they be so different?
Thank you in advance for your help!