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The following supplementary material is available for this article:

Figure S1 Putative PCR-chimeras detected in the bacterial cloned dataset of Symbiodinium ‘type’ C1 (culture 152) and ‘type’ E2 (culture CCMP 421).

Figure S2 Unrooted maximum parsimony phylogenies of ITS2 region sequence variants generated via PCR and bacterial cloning from two clonal Symbiodinium cultures: (A) culture 77 (‘type’ A3; GenBank Accession Numbers EU074925–EU074938), (B) culture 152 (‘type’ C1; GenBank Accession Numbers EU074939–EU074961).

Figure S3 Secondary structural analyses and alignments of ITS2 sequences from clonal isolates of Symbiodinium ‘type’ A3 (culture 77).

Figure S4 Secondary structural analyses and alignments of ITS2 sequences from clonal isolates of Symbiodinium ‘type’ B1 (culture 13).

Figure S5 Secondary structural analyses and alignments of ITS2 sequences from clonal isolates of Symbiodinium ‘type’ C1 (culture 152).

Figure S6 Secondary structural analyses and alignments of ITS2 sequences from clonal isolates of Symbiodinium ‘type’ E2 (culture CCMP 421).

Figure S7 Putative PCR-chimeras detected in the bacterial cloned dataset of Symbiodinium populations of Hawaiian Porites spp. corals (data from Apprill & Gates 2007). Suspected chimeric sequences include clones: A) KB102C_5B, B) KB135_63, C) KB179B_7.

Table S1 Summary of clones obtained from estimates of Taq polymerase/bacterial cloning error in Symbiodinium ‘type’ A3 (culture 77).

Table S2 Summary of clones obtained from estimates of Taq polymerase/bacterial cloning error in Symbiodinium ‘type’ C1 (culture 152).

Table S3 Summary of secondary structural disruptions and PCR-chimeras identified within the 5.8S-rDNA and ITS2 of bacterial clones originating from Symbiodinium ‘type’ A3 (culture 77).

Table S4 Summary of secondary structural disruptions and PCR-chimeras identified within the 5.8S-rDNA and ITS2 of bacterial clones originating from Symbiodinium ‘type’ B1 (culture 13).

Table S5 Summary of secondary structural disruptions and PCR-chimeras identified within the 5.8S-rDNA and ITS2 of bacterial clones originating from Symbiodinium ‘type’ C1 (culture 152).

Table S6 Summary of secondary structural disruptions and PCR-chimeras identified within the 5.8S-rDNA and ITS2 of bacterial clones originating from Symbiodinium ‘type’ D1a (culture A001).

Table S7 Summary of secondary structural disruptions and PCR-chimeras identified within the 5.8S-rDNA and ITS2 of bacterial clones originating from Symbiodinium ‘type’ E2 (culture CCMP 421).

Table S8 Summary of secondary structural/processing site disruptions and PCR-chimeras identified within the 5.8S-rDNA and ITS2 of bacterial clones originating from Symbiodinium populations of Hawaiian Porites spp. corals (data from Apprill & Gates 2007).

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