Natural clones
Hierarchical clustering analysis of the whole dataset (Fig. 1 D) revealed six samples from a different cryptic species (Ladner and Palumbi 2012), which were removed from subsequent analyses. It also identified three pairs of natural clones, which were as genetically similar to each other as technical replicates (Fig. 1 D). All three of these pairs were from Goofnuw channel, which experiences the most wave action due to windward exposure. These clones are therefore likely to be the product of colony fragmentation by storms. Clonal replicates (natural or technical) were removed from subsequent analyses, leaving a single best-covered sample as a representative of a clonal group.