Appendix S1 Detailed methods descriptions for ploidy modeling and preparation of ITS2 samples for 454 sequencing.

Fig. S1 (a) Mean temperature (±one standard deviation) in each treatment tank for the duration of the 6-week experiment. (b) Continuous temperature data (measurements taken every 8 min) for the one control and the one heat tank equipped with HOBO (Onset) data loggers for the duration of the 6-week experiment.

Fig. S2 (a) Histogram of high-frequency 100% identity sequence clusters indicating size of the cluster, for example the ‘>25’ bar indicates the number of clusters that were assigned at least 25 individual sequence reads. (b) The proportion of total read data represented in the high-frequency clusters.

Fig. S3 Correlations of frequencies of haplotypes 3 and 6 for inshore and offshore populations.

Fig. S4 Pairwise correlations between frequencies of dominant haplotypes (1, 2, 4 and 7) among individual colonies across all populations and experimental treatments.

Fig. S5 Mean parameter ± 95% profile likelihood confidence intervals for individual subpopulations and the entire dataset.

Table S1 Summary of eight polymorphic Porites astreoides SSR markers assessed across 21 individuals from the offshore site of Sugarloaf Key, Florida.

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