Hello everybody and sorry if my english was not good enough to resume the question within the requested characters.

The problem is that we want to see differences between samples taken among two consecutive gradients of benthic marine communities (in fact, a "single" gradient divided by a landform). At each gradient, samples were taken randomly in groups of 4 each 5m along two different transects (randomly stratified sampling method with two different dependence degrees: first within samples belonging to each 4-samples group and second between samples of different groups). I think that there is no problem because dependence is the same within the samples of each factor level, but I want to see your recommendations. We want to analyze by Primer-e + PERMANOVA:

Differences between transects belonging to the same gradient at the same and different times.

Differences between the "two" gradients

Thank you all and good thoughts

Hello Juan Sempere-Valverde, regarding non-independence, the Permanova analysis may be a good option.

In the Permanova + for Primer guide (Anderson et al., 2008) we can read the following: ".....it must be admitted that the correlation structure among samples through time, if any, will be effectively ignored under permutation. Thus, differences in correlation structure through time among treatments (i. e. lack of sphericity) may, therefore, produce a statistically significant result. However, we consider that differences in correlation structure through time are indicative of (at least one type of) a treatment effect, so should warrant closer inspection by the investigator in any event ".

Enrique, i am very grateful for your answer, we finally used PERMANOVA and included Anderson et al. 2008 as follows: " Possible correlation structure among samples, derived from the stratified-random sampling methodology, would be ignored by PERMANOVA under permutation (Anderson et al. 2008).". Yet I found that PERMANOVA is unaffected by differences in correlation structure for balanced designs in Anderson & Walsh (2013) - http://coralreefdiagnostics.com/s/Anderson_et_al-2013-ANOSIM-vs-PERMANOVA.pdf

Thus i interpreted that differences found by PERMANOVA reflect changes in community structure and carried out SIMPER to detect the variables that contributed the most.

Best regards