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Fig. S1. Comparison of the clusters or populations predicted by BAPS and AdaptML respectively. Clusters predicted by BAPS are displayed in the outer circle in different colours according to the legend. Significant AdaptML populations are shown in the inner circle in different colours in according to the legend.

Fig. S2. Comparison of phylogenetic relationships of V. splendidus-like populations #18–25 from Hunt and colleagues (2008a) and population #16 from this study demonstrating that these are interleaved and indistinguishable based on maximum likelihood estimation of the hsp60 sequence. The assignment of each strain to a population is indicated by the colours on the outer circle. Population numbers in the legend correspond to populations from this study 16 (I) or in Hunt and colleagues (2008a) (F). Clones were removed for analysis. Scale bar is in units of nucleotide substitutions per site.

Fig. S3. Comparison of number of strains per sequence type (ST) for each sample of crab and mussel compartments, aggregate zooplankton and seawater. Crab and mussel samples were from eight single specimens, while the eight zooplankton samples contained ∼50 live or dead specimens, and seawater samples represented subsamples (5 µl to 5 ml) from eight 4 l samples. Colours indicate isolates per ST: grey = 1–3, pink = 4–9 and red = > 10.

Fig. S4. Kullback–Leibler (K–L) divergences for all pairs of habitats predicted in Hunt and colleagues (2008a) represented as a heatmap. K–L divergences are not symmetric so will be slightly different above and below diagonal.

Fig. S5. Kullback–Leibler (K–L) divergences for all pairs of habitats predicted in this study represented as a heatmap. K–L divergences are not symmetric so will be slightly different above and below diagonal.

Table S1. Calculated Shannon diversity indices for each population as a measure of generalized distribution across all sampling categories.

Table S2. Shannon diversity index (H) for each host demonstrates lowest diversity across zooplankton host categories.

Table S3. Comparison of the likelihood values and number of matching habitats for trees using different substitution models as compared with the GTR substitution model (use in all further analyses).

Table S4. Reproducibility of the total number of habitats resulting from 100 independent trials, which predicted three to six total habitats with the per cent distribution across those trials as listed above.

Table S5. Reproducibility of inferred habitats.

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