The anthozoan sub-class Octocorallia includes over 3500 nominal species of soft corals and gorgonian sea fans, many of which serve as critical foundation species in benthic marine ecosystems in shallow waters to the deep sea. Despite their familiarity and ecological impor-tance, the diversity and taxonomy of octocorals remain poorly known. All of the orders, subordinal groups, and a majority of families have been recognized to be poly- or paraphyletic, but poor resolution of the deeper nodes in mitochondrial or single-locus nuclear gene trees have hindered formal revision of the higher-level taxonomy of the group. We used sequence data from target-capture of 739 ultraconserved and exon loci to reconstruct a fully resolved phylogeny for 185 octocoral taxa represent-ing 55 of 63 currently recognized families. We use this phylogeny, sup-plemented with a gene tree for mitochondrial mtMutS for an additional 107 taxa, to guide a revision of the families and orders of Octocorallia. We (1) elevate the anthozoan sub-classes Octocorallia and Hexacorallia to the rank of Class; (2) replace the three currently recognized orders of Octocorallia (Alcyonacea, Pennatulacea, Helioporacea) with two new orders reflecting reciprocally monophyletic major clades; and (3) revise all families with the exception of the 15 recognized families of sea pens, which we accommodate within a new superfamily. The revised classifi-cation of Octocorallia thus comprises 79 families, including 18 that are newly described and three that have been reinstated or elevated in rank. In addition, two new genera are described and another three reinstated. We leave the family assignment of 46 of 413 genera as incertae sedis until further molecular or morphological data can be obtained to confirm their phylogenetic affinities.

Our ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species of corals has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia. Species delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications. When mtMutS and 28S were concatenated, a 0.3% genetic distance threshold delimited the majority of morphospecies. In contrast, 12 of the 15 examined morphospecies formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of > 6000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia. A genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating coral diversity. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.