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Fig. S1 Bayesian information criterion used to select the number of clusters used in the discriminant analyses of principal components to examine the assignment of Symbiodinium C2 microsatellite alleles hosted by Acropora millepora to genetic clusters.

Fig. S2 Genetic structure of Symbiodinium C2 populations among sites, years and the bleaching status of Acropora millepora hosts at 7 sites in the Palm Islands, Great Barrier Reef using a partial data set of a subset of loci from which single alleles were recovered from Symbiodinium cultures.

Fig. S3 Population wide genetic diversity of Symbiodinium C2 among sites, years and the bleaching status of Acropora millepora hosts at the Palm Islands, Great Barrier Reef.

Table S1 Frequency of microsatellite alleles within Symbiodinium C2 populations hosted by Acropora millepora at the Palm Islands, Great Barrier Reef.

Table S2 Frequency of a subset of microsatellite alleles within Symbiodinium C2 populations hosted by Acropora millepora at the Palm Islands, Great Barrier Reef.

Table S3 (a) Analysis of variation of Symbiodinium C2 genetic diversity within individual colonies (allelic richness) and populations (% of alleles per locus) among sites, years and the bleaching status of Acropora millepora hosts at the Palm Islands, Great Barrier Reef. (b) Fishers LSD post-hoc P values for comparisons of Symbiodinium C2 genetic diversity within individual colonies among sites, years and the bleaching status of Acropora millepora hosts at the Palm Islands, Great Barrier Reef. P values in bold face indicate significance at α = 0.05. N = normally pigmented, B = bleached.

Table S4 (a) Analysis of a partial data set of microsatellite alleles at a subset of loci from which single alleles were recovered from Symbiodinium cultures. Analysis of variance was used to partition Symbiodinium C2 genetic variation among sampling years (1997, 2004 and 2009) and sites for populations hosted by Acropora millepora at the Palm Islands, Great Barrier Reef. (b) Pairwise estimates of Symbiodinium C2 genetic differentiation among sampling years and sites for populations hosted by Acropora millepora at the Palm Islands, Great Barrier Reef. Φ values (above the diagonal) indicate the magnitude of genetic differentiation between populations, and P values (below the diagonal) in bold face indicate significance after sequential Bonferroni correction at α = 0.05.

Table S5 (a) Analysis of a partial data set of microsatellite alleles at a subset of loci from which single alleles were recovered from Symbiodinium cultures. Analysis of variance was used to partition Symbiodinium C2 genetic variation among sites and the bleaching status of Acropora millepora hosts in 2009 at the Palm Islands, Great Barrier Reef. (b) Pairwise estimates of Symbiodinium C2 genetic differentiation among sites and the bleaching status of Acropora millepora hosts at the Palm Islands, Great Barrier Reef. Φ values (above the diagonal) indicate the magnitude of genetic differentiation between populations, and P values (below the diagonal) in bold face indicate significance at α = 0.05 following sequential Bonferroni correction. N = normal pigmentation, B = bleached.

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