Molecular determination of species boundaries in corals: Genetic analysis of the Montastraea annularis complex using amplified fragment length polymorphisms and a microsatellite marker

Analyses of DNA have not been widely used to distinguish coral sibling spec ies. The three members of the Montastraea annularis complex represent an im portant test case: they are widely studied and dominate Caribbean reefs, ye t their taxonomic status remains unclear. Analysis of amplified fragment le ngth polymorphisms (AFLPs) and a microsatellite locus, using DNA from sperm , showed that Montastraea faveolata is genetically distinct. One AFLP prime r yielded a diagnostic product (880 bp in M. faveolata, 920 bp in M, franks i and M. annularis) whose homology was established by DNA sequencing. A sec ond primer revealed a 630 bp band that was fixed in M. faveolata, and rare in M.franksi and M. annularis; in this case homologies were confirmed by So uthern hybridizations. A tetranucleotide microsatellite locus with several alleles exhibited strong frequency differences between M. faveolata and the other two taxa. We did not detect comparable differences between M, annula ris and M. franksi with either AFLPs (12 primers screened) or the microsate llite locus. Comparisons of AFLP patterns obtained from DNA from sperm, som atic tissues, and zooxanthellae suggest that the technique routinely amplif ies coral (animal) DNA. Thus analyses based on somatic tissues may be feasi ble, particularly after diagnostic differences have been established using sperm DNA.