I'm running a comparison of fish species communities between 6 sites at 3 locations (North, East and West) where the sites either have a reef at them (Yes, No). I found a significant effect through an ANOSIM and PERMANOVA so I did a follow up analysis via a two-way crossed analysis in SIMPER to try to determine which species were contributing to the differences. My SIMPER analysis identified 6 species which explained >70% of the variation between the sites with a reef versus the sites without a reef. The number one species (F0301) contributed 19.55% to the dissimilarity between the two groups. To illustrate this point visually I tried to build some simple bar graphs showing the average number of F0301 at the reef sites versus the non-reef sites but these values were almost identical (mean = 4.15, and 4.16; SE = 0.9, 1.1).
What is happening here? I have tried controlling for location, and running a paired T-test but there's still no difference between the raw values. However the SIMPER analyses appear legitimate-- an NMDS plot appears to show a higher concentration of species F0301 in the no reef group, and F0301 is the only species that has a correlation factor > 0.6.
All tests were run in PRIMER V7