[R-sig-eco] ADONIS and pseudoreplications

[Vít Syrovátka]

Hi listers,

I am facing a problem with pseudoreplications, similar to that by  
Eduard Szöcs.
However, I want to try to explain the variation in species composition  
by some environmental variables.
I decided to use adonis() for this, as there are many zeros in the  
data-set, but don't know if it is correct, or how to do it so that it  
was correct.

The design is:
Aquatic insect larvae were collected at 17 sites three times (spring,  
summer, autumn), giving a total of 51 samples.
During each sampling campaign several chemical and substratum  
variables were measured, while others were measured only once, as they  
characterize the whole site and are not expected to change in time.

Now I want to relate the species composition to environmental  
variables. I see that the samples are not independent, so I thought  
about setting strata in the adonis model, but it didn't make me much  
sense. I am interested in the differences among sites, therefore  
strata should probably be season (?). Moreover, the effect of  
environmental variables might differ among seasons, therefore  
interaction with season should be probably included.

I ended up with this model:
adonis(log(spe+1) ~ env1 %in% season + env2 %in% season + ...,  
distance= 'bray', permut= 999, data= env)
(where season is a factor with 3 levels)

I don't feel good about this model and would greatly appreciate any  
suggestions on how to build an appropriate  model.
Is there a way to analyze such data without splitting them into 3 data- 
sets according to the season and analyze them separately?

Thanks in advance for any suggestions,
Vit Syrovatka