Molecular and morphological supertree of stony corals (Anthozoa: Scleractinia) using matrix representation parsimony

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Abstract
The supertree algorithm matrix representation with parsimony was used to combine existing hypotheses of coral relationships and provide the most comprehensive species‐level estimate of scleractinian phylogeny, comprised of 353 species (27% of extant species), 141 genera (63%) and 23 families (92%) from all seven suborders. The resulting supertree offers a guide for future studies in coral systematics by highlighting regions of concordance and conflict in existing source phylogenies. It should also prove useful in formal comparative studies of character evolution. Phylogenetic effort within Scleractinia has been taxonomically uneven, with a third of studies focussing on the Acroporidae or its most diverse genera. Sampling has also been geographically non‐uniform, as tropical, reef‐forming taxa have been considered twice as often as non‐reef species. The supertree indicated that source trees concur on numerous aspects of coral relationships, such as the division between robust versus complex corals and the distant relationship between families in Archaeocoeniina. The supertree also supported the existence of a large, taxonomically diverse and monophyletic group of corals with many Atlantic representatives having exsert corallites. Another large, unanticipated clade consisted entirely of solitary deep‐water species from three families. Important areas of ambiguity include the relationship of Astrocoeniidae to Pocilloporidae and the relative positions of several, mostly deep‐water genera of Caryophylliidae. Conservative grafting of species at the base of congeneric groups with uncontroversial monophyletic status resulted in a more comprehensive, though less resolved tree of 1016 taxa.