| Summary: | <p>Abstract</p> <p>Background</p> <p>Morphological data suggest that, unlike most other groups of marine organisms, scleractinian corals of the genus <it>Stylophora </it>are more diverse in the western Indian Ocean and in the Red Sea than in the central Indo-Pacific. However, the morphology of corals is often a poor predictor of their actual biodiversity: hence, we conducted a genetic survey of <it>Stylophora </it>corals collected in Madagascar, Okinawa, the Philippines and New Caledonia in an attempt to find out the true number of species in these various locations.</p> <p>Results</p> <p>A molecular phylogenetic analysis of the mitochondrial ORF and putative control region concurs with a haploweb analysis of nuclear ITS2 sequences in delimiting three species among our dataset: species A and B are found in Madagascar whereas species C occurs in Okinawa, the Philippines and New Caledonia. Comparison of ITS1 sequences from these three species with data available online suggests that species C is also found on the Great Barrier Reef, in Malaysia, in the South China Sea and in Taiwan, and that a distinct species D occurs in the Red Sea. Shallow-water morphs of species A correspond to the morphological description of <it>Stylophora madagascarensis</it>, species B presents the morphology of <it>Stylophora mordax</it>, whereas species C comprises various morphotypes including <it>Stylophora pistillata </it>and <it>Stylophora mordax</it>.</p> <p>Conclusions</p> <p>Genetic analysis of the coral genus <it>Stylophora </it>reveals species boundaries that are not congruent with morphological traits. Of the four hypotheses that may explain such discrepancy (phenotypic plasticity, morphological stasis, morphological convergence, and interspecific hybridization), the first two appear likely to play a role but the fourth one is rejected since mitochondrial and nuclear markers yield congruent species delimitations. The position of the root in our molecular phylogenies suggests that the center of origin of <it>Stylophora</it> is located in the western Indian Ocean, which probably explains why this genus presents a higher biodiversity in the westernmost part of its area of distribution than in the "Coral Triangle".</p>
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