Dr. Courtney Duchardt explains how prairie dogs are ecosystem engineers, the ecological implications of Sylvatic plague, and the complex ways that livestock and wildlife coexist.

https://youtu.be/R2LX5ntuVyw?si=8l7cy7Br2lQu_rJa

I have a natural and degraded site and at each site I sample (core sample for macrofauna), I sample 4 habitats each 5 times for a total of 40 samples.

When performing permanova to compare these two sites should I use the replicates (40 samples) or the 8 site+habitat combinations? Im assuming that because of the experimental design the samples are dependent and thus I should use the site+habitat in my analysis.

Am I wrong?

In this experimental design I'm not certain about the independence of the variables so I'd love some feedback!!

Thank you so much!