Systema Naturae includes representatives of every major lineage of the animal phylum Cnidaria.  However, Linnaeus did not classify the members of the phylum as is now done, and the diversity of the group is not well represented.  We contrast the Linnaean perspective on cnidarian diversity with the modern, phylogenetic perspective.  For each order, we detail diversity at the family level, providing phylogenetic context where possible.

The widespread assumption that COI and other mitochondrial genes will be ineffective DNA barcodes for anthozoan cnidarians has not been well tested for most anthozoans other than scleractinian corals. Here we examine the limitations of mitochondrial gene barcoding in the sub-class Octocorallia, a large, diverse, and ecologically important group of anthozoans. Pairwise genetic distance values (uncorrected p) were compared for three candidate barcoding regions: the Folmer region of COI; a fragment of the octocoral-specific mitochondrial protein-coding gene, msh1; and an extended barcode of msh1 plus COI with a short, adjacent intergenic region (igr1). Intraspecific variation was <0.5%, with most species exhibiting no variation in any of the three gene regions. Interspecific divergence was also low: 18.5% of congeneric morphospecies shared identical COI barcodes, and there was no discernible barcoding gap between intra- and interspecific p values. In a case study to assess regional octocoral biodiversity, COI and msh1 barcodes each identified 70% of morphospecies. In a second case study, a nucleotide character-based analysis correctly identified 70% of species in the temperate genus Alcyonium. Although interspecific genetic distances were 2× greater for msh1 than COI, each marker identified similar numbers of species in the two case studies, and the extended COI + igr1 + msh1 barcode more effectively discriminated sister taxa in Alcyonium. Although far from perfect for species identification, a COI + igr1 + msh1 barcode nonetheless represents a valuable addition to the depauperate set of characters available for octocoral taxonomy.

RAD-tag sequencing is a promising method for conducting genome-wide evolutionary studies. However, to date, only a handful of studies empirically tested its applicability above the species level. In this communication, we use RAD tags to contribute to the delimitation of species within a diverse genus of deep-sea octocorals, Chrysogorgia, for which few classical genetic markers have proved informative. Previous studies have hypothesized that single mitochondrial haplotypes can be used to delimit Chrysogorgia species. On the basis of two lanes of Illumina sequencing, we inferred phylogenetic relationships among 12 putative species that were delimited using mitochondrial data, comparing two RAD analysis pipelines (Stacks and PyRAD). The number of homologous RAD loci decreased dramatically with increasing divergence, as 470% of loci are lost when comparing specimens separated by two mutations on the 700-nt long mitochondrial phylogeny. Species delimitation hypotheses based on the mitochondrial mtMutS gene are largely supported, as six out of nine putative species represented by more than one colony were recovered as discrete, well-supported clades. Significant genetic structure (correlating with geography) was detected within one putative species, suggesting that individuals characterized by the same mtMutS haplotype may belong to distinct species. Conversely, three mtMutS haplotypes formed one well-supported clade within which no population structure was detected, also suggesting that intraspecific variation exists at mtMutS in Chrysogorgia. Despite an impressive decrease in the number of homologous loci across clades, RAD data helped us to fine-tune our interpretations of classical mitochondrial markers used in octocoral species delimitation, and discover previously undetected diversity.

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Octocorals, especially gorgonians, are conspicuous on Caribbean coral reefs, but there is no consensus regarding species relationships. Mitochondrial protein-coding genes [NADH-dehydrogenase subunits 2 (ND2) and 6 (ND6), and mutS homolog (msh1), 1633 bp] from 28 shallow-water species were sequenced to develop the first molecular phylogeny for Caribbean octocorals. The specimens were collected primarily in the Caribbean or off Brazil in 1999-2001. Morphological characters (sclerites and axial ultrastructure) were also examined in order to map them onto the molecular phylogeny. Analyses of both nucleotide and amino acid substitutions using maximum parsimony and likelihood (including maximum-likelihood and Bayesian analysis) generated very similar results, with most nodes having high levels of support. These molecular results were significantly different from the generally accepted classification. Neither Plexauridae nor Gorgoniidae were monophyletic. Plexaurella spp., nominal plexaurids, were basal to the gorgoniids, sharing many morphological characters with them. This corroborates previous findings using secondary metabolites and biosynthetic pathways. The sea fans, Gorgonia spp. and Pacifigorgia spp., as well as the pinnate gorgonians, Muriceopsis flavida and Pseudopterogorgia spp., did not have sea fan or pinnate relatives, suggesting there has been convergent evolution of colony form. Caribbean plexaurids appeared more derived and/or recently evolved according to both morphological and molecular data (e.g. Eunicea spp. and Plexaura spp.). Molecular phylogenetics is a promising approach for reconstructing phylogenetic relationships among octocorals as well as to understand their complex morphology. Electronic Supplementary Material is available if you access this article at http://dx.doi.org/10.1007/s00227-003-1018-7. On that page (frame on the left side), a link takes you directly to the supplementary material. IntroductionOctocorals, sessile cnidarians, are found in marine habitats ranging from intertidal to abyssal waters and are distributed from the Arctic to the Antarctic (Bayer 1961). Gorgonians, octocorals containing a sclero-proteinaceous axis, are ecologically important and the dominant macrofauna on many Caribbean reefs. There can be up to 40 octocoral species on a single Caribbean coral reef (Sa´nchez et al. 1997 Sa´nchez 1999), and octocoral communities produce dense and colorful gardens, which provide three-dimensional structures for many reef dwellers and scenic value for underwater activities (Fig. 1). Despite their importance, evolutionary relationships among Caribbean octocorals have received Marine Biology (2003) 142: 975-987