An advice needed on paper statistical analysis description

Dear list members,


I in the final stages of writing a paper which summarized some of my PhD 
aspects. I did a lot of mixed effects modelling. I have started with the 
lme function (I prefer it on `lmer` becuase it is more documented and 
more flexible in terms of weight and correlation structures). I came out 
with non-convincing p-values (As Zuur's 2009 book describes it - between 
0.001 to 0.1) on most models so I decided to run the models with MCMC 
simulations using BUGS with the JAGS software in order to make 
statistical inferences from the confidence intervals. Some models are 
simple ANOVAs with random effects and sometimes a variance structure and 
some models are ANCOVA models. I also used a GLMM with negative binomial 
distribution model with dispersion parameter structure using JAGS. This 
latter kind of model is not yet implemented in R as well as I know.


Now I wonder what to write on the paper. I guess I should explain why I 
used the somehow more complex approach (writing the models myself in 
JAGS) and I hope the reviewers will not reject the paper... I want to 
submit the paper to Ecology and most papers in this journal with BUGS 
analysis are much more complex and unique to a specific problem.


I will be thankful to hear your advices.


Thanks,

Ofir.