Chameleon performance evaluation
We performed all Chameleon analyses on pairwise Bray-Curtis compositional similarities between samples (Clarke, 1993) using the scluster function in CLUTO software version 2.1.2 (Karypis, 1999). First, since we found little information in the literature to guide parameter-setting, we assessed solutions of 15 clusters over a range of neighbourhood sizes (15 – 1000 neighbours), degrees of sub-partitioning (up to 500 sub-partitions or agglomerative phase omitted) and linkage functions (single or complete) (Table 1). We focused carried out our initial trials using the cluster-weighted single-link criterion function in the agglomerative phase, as recommended for non-spherical clusters (Karypis, 1999). For each solution we calculated average pairwise within-cluster association (homogeneity) and the proportion of samples located in clusters other than that of their nearest neighbour (misclassification rate). We found using the single linkage function caused chaining (sensu Peet & Roberts 2013) when the number of sub-partitions specified was larger than 30. We repeated the relevant trials using an option forcing Chameleon to prioritise large clusters over small in the partitioning phase. On the basis of the preliminary results, we undertook subsequent analyses using the complete linkage function and assessed performance over a range of thematic scales (15 – 250 clusters) and degrees of sub-partitioning (30 – 500 sub-partitions) with neighbourhood size fixed at either 30 or 1000 (Table 1).