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Summary of the PERMANOVA analysis

A summary of the essential commands associated with performing this PERMANOVA analysis of the holdfast data according to the 3-factor hierarchical experimental design is given in the table below:

Step
 To implement in PRIMER:
1. Select variable subset From the original data sheet: click Select > Variables... > ($\bullet$Indicator levels > Indicator name: Phylum), click Levels...> (Selection > Include: Mollusca), click OK.
2. Jaccard resemblance From the subset-selected data sheet: click Analyse > Resemblance > (Measure $\bullet$Other > S7 Jaccard) & (Analyse between $\bullet$Samples), click OK.
3. Specify the design
  • From the resemblance matrix: click PERMANOVA+ > Create PERMANOVA design... > (Title: Three-way nested design) & (Number of factors: 3), click OK.
  • Fill in the appropriate details of the design in the design file.
4. Run PERMANOVA From the resemblance matrix: click PERMANOVA+ > PERMANOVA... > (Design Worksheet: Design1) & (Num. permutations: 9999) & (default settings for the rest), click OK.
5. Ordination of centroids
  • From the resemblance matrix: click PERMANOVA+ > Distance Among Centroids... > Centroids > (Grouping factor: Area).
  • From the resulting resemblance matrix among area centroids: click Analyse > MDS > Non-metric MDS..., take all the defaults and click OK.
  • To specify labels and symbols: click Graph > Sample Labels & Symbols....
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