Assessing the match between OTUs and known AM fungal species.

We visualized the OTUs from each of the four sequence clustering methods by color-coding points (sequences) in the MDS visualization according to their OTU membership for OTUs containing at least 10 sequences, and OTUs were colored according to their size (the number of sequences that they contained). We evaluated how well the OTUs produced by each clustering method matched the known species composition by calculating the adjusted Rand index (54, 55) using the phyclust package in R with the null model assumption that all sequences from each species would be assigned to the same OTU. Rand index values can range from 0 to 1, with a value of 1 indicating a perfect match between OTUs and species.