The evolutionary history of scleractinian corals, based on morphological taxonomy and inferences from the fossil record, has been poorly understood. Molecular techniques developed over the past ten years are now being used to gain a new perspective on scleractinian phylogeny. DNA sequences, mitochondrial genome structure, and morphological characters support a basal position for the Anthozoa in the phylum Cnidaria. Mitochondrial and nuclear DNA sequences suggest a relatively derived position of the order Scleractinia within the class Anthozoa. Mitochondrial and nuclear DNA sequences have provided a new hypothesis for evolution within the Scleractinia that is different from hypotheses based on morphological characters of extant and fossil taxa. Groupings within the two major lineages defined by molecular data do not correspond to morphological suborder groupings although groupings of genera within families do correspond to traditional taxonomy. This new molecular hypothesis suggests that the Scleractinia are represented by two major lineages that diverged from each other before the appearance of the scleractinian skeleton in the fossil record. This divergence time supports the hypotheses that the Scleractinia are not related to the Rugosa of the Paleozoic and that the scleractinian skeleton has evolved more than once. These two major lineages may represent two architectural strategies within the Scleractinia that have led to their great morphological diversity.
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