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Table S1. Localities, sampling dates and total number (n) of 25 m-long transects conducted at each site.

Table S2. PCR conditions and thermal profiles (TP) for rDNA and ORF.

Table S3. List of colonies with intragenomic polymorphisms and results of haplotype reconstructions using PHASE, fastPHASE and HAPAR (see M&M).

Table S4. Distribution of 35 rDNA haplotypes of Porites panamensis in populations in the tropical Mexican Pacific.

Table S5. Distribution of 14 ORF haplotypes of Porites panamensis in populations in the tropical Mexican Pacific.

Table S6. Estimates of effective population size (θ = 2 Ne µ) and migration rates between populations (M = m/µ). The migration rates include 95% confidence intervals. The arrows indicate the direction of gene flow and data is marked with a rectangle representing the highest values.

Figure S1. Scatter plots and regression lines of percent live coral cover against surveying effort (number of transects). ANOVA of linear regressions: total live cover F = 18.29 P = 0.004, Porites panamensis live cover F = 0.009 P = 0.926.

Figure S2. Intragenomic polymorphism due to a four base-pair indel. Variation is readily detected by observation of double peaks in some traces. (A) trace representing haplotype 1, (B) trace representing haplotype 4 and (C) trace with double signal (haplotypes 1 and 4) showing polymorphic base calls (arrows point to the “secondary” sequence).

Figure S3. Single nucleotide polymorphic position showing a double peak. (A) sequence with only one base call, and (B) sequence with double peak.

Figure S4. Correlation between percentage of live coral cover of Porites panamensis and degree latitude.

Figure S5. Frequency of alloenzymatic alleles. Five enzymatic systems (ME-1, GDH-1, GDH-2, EST-1 and LGG-1). Localities: Bahía de los Ángeles (BLA), Bahía Concepción (BC), Bahía de la Paz (LP), Punta Arenas (PA), Islas Marietas (IM) and Bahías de Huatulco (BH).

Figure S6. Frequency of alloenzymatic genotypes. Five enzymatic systems (ME-1, GDH-1, GDH-2, EST-1 and LGG-1). Localities: Bahía de los Ángeles (BLA), Bahía Concepción (BC), Bahía de la Paz (LP), Punta Arenas (PA), Islas Marietas (IM) and Bahías de Huatulco (BH).

Figure S7. Correlations between genetic diversity (Haplotype diversity – h – and standardized h(12) ; Haplotype or allelic richness – A – and standardized A(12); and expected heterozygosity – He –) and percentage live coral cover of Porites panamensis. (A, B) rDNA, (C, D) ORF and (E, F) allozymes.

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