*2.5. Molecular Analyses*

Middle parts of the colonies of both species and from both depths (preserved in 100% ethanol) were cut into 8 mm fragments. The total genomic DNA of each sample was extracted using QIAGEN DNeasy Blood & Tissue Kit using the manufacturer's protocol. The concentration and quality of DNA were examined at 260 nm using a spectrophotometer (DeNovix). The internal transcribed spacer-2 (ITS2) region of the dinoflagellate ribosomal DNA (rDNA) was amplified using the primers ITS-DINO (5 GTGAATTGCAGAACTCCGTG 3 ) and ITS2-REV2 (5 CCTCCGCTTACTTATATGCTT 3 ) following conditions described in [47]. A second set of primers, SYM\_VAR\_5.8S2 (5 GAATTGCAGAACTCCGTGAACC 3 ) and SYM\_VAR\_REV (5 CGGGTTCWCTTGTYTGACTTCATGC 3 ), were used for PCR amplification of the ITS2 region, following the protocol described in [48]. This second set of primers was used in addition to the former because it has been found to perform better than other ITS2 primer sets tested on a range of Symbiodiniaceae ITS2 rDNA [48]. The presence of amplicons was checked in a 2% agarose gel in Tris-Borate-EDTA buffer. A DNA extract from a scleractinian coral of the genus *Acropora* from Toliara (Madagascar) was used as positive control.
