The evolutionary history of scleractinian corals is based on knowledge of skeletal characters and their 250 million yr fossil record. However, homologies of skeletal characters are not well-understood and fossil documentation of these characters is incomplete. As a result, relationships
among families and suborders are poorly understood. We have analyzed a 225 bp segment of the nuclear 28S ribosomal RNA gene from 45 species of corals and a 566 bp segment of the mitochondrial 16S ribosomal RNA gene from 68 species. Unlike previous analyses of smaller numbers of taxa, the dataset
presented here includes both reef-building and non-reef-building taxa from 20 of 24 families and all seven suborders. Nuclear sequences analyzed under maximum parsimony and minimum evolution criteria did not resolve relationships among families and suborders. Similar analyses of mitochondrial
sequences resulted in a robust phylogenetic hypothesis. The mitochondrial hypothesis, like previous analyses of a subset of these data, did not agree with morphological hypotheses about relationships among families and suborders, and supports a polyphyletic origin of the scleractinian skeleton.
Instead of seven major monophyletic groups as hypothesized from morphological data, mitochondrial data suggest that the Scleractinia is represented by two major clades. Relationships within these major clades are not clearly differentiated but each clade is comprised of families from different
morphological suborders as defined by Veron (1995). The mitochondrial topology gives no support for the morphological suborders Archaeocoeniina, Fungiina, Caryophylliina, or Meandriina as monophyletic groups but is consistent with a monophyletic Faviina, Poritiina, and Dendrophylliina. Monophyletic
morphological families are supported with the exception of the Faviiidae, Caryophylliidae, Poritidae, and Oculinidae. The mitochondrial topology also supports the most recent taxonomic treatments of Psammocora and Fungiacyathus, genera that have been the subject of taxonomic
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