I was hoping some of the uers would chime in on this. I’d be interested to see what steps they would take. By the way, I have another case study (eco data) to be released with v3.04.
The most important outcome from PATN is to name the groups. Box and Whisker plots are most helpful for this. I’d consider using two-step association on your species (and name the resulting groups).
I’d then use a two-way table to help confirm your suspicions. Enough or too many groups?
I usually find that I have to iterate through sites and more likely species to reduce noise. B&W and species classification is basic for this.
What about environment data and correlates? What’s driving the variation between the groups? This is basic.
These are just a few ideas for you to kick around.