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Table S1 Morpho-species diversity in the genus Pocillopora from the Eastern Pacific, as reported by regional diversity inventories and coral atlases.

Table S2 Characteristics and amplification conditions of the microsatellite loci used to analyze the population structure of eastern Pacific Pocillopora spp (n, number of alleles; He, expected; and Ho, observed heterozygosity; F, frequency; and Ta, annealing temperature).

Table S3 Allelic frequencies per locus for Pocillopora types I, II, and III and across types (Overall). Samples size, number of unique genotypes and number private alleles (bold) are shown by type and overall.

Table S4 (a) Pairwise Population Fst Values (below diagonal) and corresponding probability values (above diagonal). Tests of significance with (α = 0.5) are in bold-faced numerals. No significance in population differentiation was detected following bonforroni corrections. (b) Pairwise Population Rst Values (below diagonal) and corresponding probability values (above diagonal). Tests of significance with (α = 0.5) are in bold-faced numerals. No significance in population differentiation was detected following bonforroni corrections.

Figure S1 Estimated population structure of type 1 colonies sampled throughout the far Tropical Eastern Pacific depicting limited population subdivision over a latitudinal gradient. The plot figure shown for a given K is based on the composite probabilities of five independent statistical runs at that K. Groupings with the high statistical support (black arrowhead) K = 2 appear to distinguishes ‘high latitude’ and ‘low latitude’ populations of type 1.

Figure S2 (a) Principal coordinate analysis (PCoA) and (b) Structurama analyses of the multilocus genotypes (n = 342) obtained from samples collected in the EP. Colors correspond to three genetic groupings (blue, type 1; green, type 2; yellow, type 3). The branches of three putative ‘F-2 hybrids’ are in black.

Figure S3 Genetic structure of Pocillopora populations containing (a) types 1 and 2 from the Clipperton Atoll and (b) types 1 and 3 from the Gulf of Panama. Despite being sympatric, each population exhibited strong genetic differentiation corresponding to the mitochondrial ORF and nuclear ITS2 lineages present. There was no evidence of mixed genotypes to indicate hybridization.

Figure S4 Phylogenetic similarity based on maximum parsimony of ITS2 sequences originating from bacterial cloning of PCR amplifications published by Combosch et al. (2008) in their analysis of TEP Pocillopora with sequences generated by direct sequencing reported by this study (see Fig. 2b). The sequences corresponding to ITS2 clade III (Combosch et al. 2008) are encompassed within the dashed box.

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