I am making comparisons of epiphytes on freshwater algae. After viewing rarefaction plots, I had to eliminate a few of my replicates. For one comparison, I have one species from three different streams. The first stream has one replicate (n=1), the second stream is n=2 and the third stream is n=3. With this limited sampling, am I able to use the shannon diversity metric? I’m not sure if this metric would be valid considering I do not have equal replicates across the three streams.
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Hello Anna,
Yes, you could calculate the Shannon diversity for each of your samples! This diversity measure is calculated on a per-sample basis.
But, like you said...
you don't have enough statistical power to run a test test to compare groups. And that's the case for any alpha diversity metric, not just Shannon's. 
Once you get some more samples, you will be good to go!
Colin
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