Sea anemones (order Actiniaria) are among the most diverse and successful members of the anthozoan subclass Hexacorallia, occupying benthic marine habitats across all depths and latitudes. Actiniaria comprises approximately 1,200 species of solitary and skeleton-less polyps and lacks any anatomical synapomorphy. Although monophyly is anticipated based on higher-level molecular phylogenies of Cnidaria, to date, monophyly has not been explicitly tested and at least some hypotheses on the diversification of Hexacorallia have suggested that actiniarians are para- or poly-phyletic. Published phylogenies have demonstrated the inadequacy of existing morphological-based classifications within Actiniaria. Superfamilial groups and most families and genera that have been rigorously studied are not monophyletic, indicating conflict with the current hierarchical classification. We test the monophyly of Actiniaria using two nuclear and three mitochondrial genes with multiple analytical methods. These analyses are the first to include representatives of all three currently-recognized suborders within Actiniaria. We do not recover Actiniaria as a monophyletic clade: the deep-sea anemone Boloceroides daphneae, previously included within the infraorder Boloceroidaria, is resolved outside of Actiniaria in several of the analyses. We erect a new genus and family for B. daphneae, and rank this taxon incerti ordinis. Based on our comprehensive phylogeny, we propose a new formal higher-level classification for Actiniaria composed of only two suborders, Anenthemonae and Enthemonae. Suborder Anenthemonae includes actiniarians with a unique arrangement of mesenteries (members of Edwardsiidae and former suborder Endocoelantheae). Suborder Enthemonae includes actiniarians with the typical arrangement of mesenteries for actiniarians (members of former suborders Protantheae, Ptychodacteae, and Nynantheae and subgroups therein). We also erect subgroups within these two newly-erected suborders. Although some relationships among these newly-defined groups are still ambiguous, morphological and molecular results are consistent enough to proceed with a new higher-level classification and to discuss the putative functional and evolutionary significance of several morphological attributes within Actiniaria.

The combination of coloniality and symbiosis in Scleractinia is thought to confer competitive advantage over other benthic invertebrates, and it is likely the key factor for the dominance of corals in tropical reefs. However, the extant Scleractinia are evenly split between zooxanthellate and azooxanthellate species. Most azooxanthellate species are solitary and nearly absent from reefs, but have much wider geographic and bathymetric distributions than reef corals. Molecular phylogenetic analyses have repeatedly recovered clades formed by colonial/zooxanthellate and solitary/azooxanthellate taxa, suggesting that coloniality and symbiosis were repeatedly acquired and/or lost throughout the history of the Scleractinia. Using Bayesian ancestral state reconstruction, we found that symbiosis was lost at least three times and coloniality lost at least six times, and at least two instances in which both characters were lost. All of the azooxanthellate lineages originated from ancestors that were reconstructed as symbiotic, corroborating the onshore-offshore diversification trend recorded in marine taxa. Symbiotic sister taxa of two of these descendant lineages are extant in Caribbean reefs but disappeared from the Mediterranean before the end of the Miocene, whereas extant azooxanthellate lineages have trans-Atlantic distributions. Thus, the phyletic link between reef and nonreef communities may have played an important role in the dynamics of extinction and recovery that marks the evolutionary history of scleractinians, and some reef lineages may have escaped local extinction by diversifying into offshore environments. However, this macroevolutionary mechanism offers no hope of mitigating the effects of climate change on coral reefs in the next century.coral reefs | Bayes Traits | zooxanthellae | ancestral state reconstruction | phylogeny I n most marine organisms, coloniality is thought to have evolved from solitary ancestors and proceeded through progressive weakening of zooidal individuality in favor of increased individualization of the colony (1). In Scleractinia, colonial species are thought to have originated from solitary ancestors, most likely via incomplete asexual budding (2). This notion is almost intuitive, since all sexually produced coral colonies start as a larva that metamorphoses into a single polyp. Colonial integration supposedly increased in evolutionary time through dissolution of skeletal barriers among polyps (2-4). This range of morphological variability is in full display in extant Scleractinia, from the exclusively solitary species within the genus Anthemiphyllia, to the "quasicolonial" Anomocora carinata, in which "the daughter corallites [break] free of the parent before a third generation bud appears" (5), to the loosely integrated colonies of Rhizosmilia maculata in which partial colonial mortality may yield solitary daughter polyps and finally the highly integrated colonies of Favia favus, in which polyp damage invariably results in a colony-wide regenerative response (6). Although most...

Acontia-nematocyst-dense, thread-like extensions of the mesenterial filaments-are the characteristic feature of the actiniarian group Acontiaria. Phylogenetic analyses have shown that acontiate taxa form a clade that also includes some taxa without acontia. We analyse five molecular markers from 85 actiniarians to explore the phylogenetic relationships among families in Acontiaria, including acontiate species assigned to other higher taxa and species without acontia that have been allied to Acontiaria. Based on our results, we redefine the group to accommodate those lineages that have lost acontia, and formalize it as superfamily Metridioidea. Based on stable and well supported clades, we resurrect Phelliidae and Amphianthidae, redefine Kadosactinidae and Actinoscyphiidae, and move two species to new genera: that previously termed Sagartiogeton erythraios belongs in Jasonactis gen. nov.; and that previously termed Anthosactis pearseae belongs in Ostiactis gen. nov., type genus of Ostiactinidae fam. nov. We also synonymized Halcampoididae and Halcampidae (as Halcampidae) and Andvakiidae and Isophelliidae (as Andvakiidae). The results of our phylogenetic analyses indicate that the diagnostic morphological characters used in the family-level taxonomy of acontiate actiniarians such as the nematocysts of the acontia, the marginal sphincter muscle, and mesenteries divisible into macro-and microcnemes, have to be revisited, as these features are highly homoplasious.

Scleractinian corals, which include the architects of coral reefs, are found throughout the world's oceans and have left a rich fossil record over their 240 million year history. Their classification has been marked by confusion but recently developed molecular and morphological tools are now leading to a better understanding of the evolutionary history of this important group. Although morphological characters have been the basis of traditional classification in the group, they are relatively few in number. In addition, our current understanding of skeletal growth and homology is limited, and homoplasy is rampant, limiting the usefulness of morphological phylogenetics. Molecular phylogenetic hypotheses for the order, which have been primarily focused on reef-building corals, differ significantly from traditional classification. They suggest that the group is represented by two major lineages and do not support the monophyly of traditional suborders and most traditional families. It appears that once a substantial number of azooxanthellate taxa are included in molecular phylogenetic analyses, basal relationships within the group will be clearly defined. Understanding of relationships at lower taxonomic levels will be best clarified by combined analyses of morphological and molecular characters. Molecular phylogenies are being used to inform our understanding of the evolution of morphological characters in the Scleractinia. Better understanding of the evolution of these characters will help to integrate the systematics of fossil and extant taxa. We demonstrate how the combined use of morphological and molecular tools holds great promise for ending confusion in scleractinian systematics.

Leptothecata are hydrozoans whose hydranths are covered by perisarc and gonophores and whose medusae bear gonads on their radial canals. They develop complex polypoid colonies and exhibit considerable morphological variation among species with respect to growth, defensive structures and mode of development. For instance, several lineages within this order have lost the medusa stage. Depending on the author, traditional taxonomy in hydrozoans may be either polyp- or medusa-oriented. Therefore, the absence of the latter stage in some lineages may lead to very different classification schemes. Molecular data have proved useful in elucidating this taxonomic challenge. We analyzed a super matrix of new and published rRNA gene sequences (16S, 18S and 28S), employing newly proposed methods to measure branch support and improve phylogenetic signal. Our analysis recovered new clades not recognized by traditional taxonomy and corroborated some recently proposed taxa. We offer a thorough taxonomic revision of the Leptothecata, erecting new orders, suborders, infraorders and families. We also discuss the origination and diversification dynamics of the group from a macroevolutionary perspective.

Myxozoans are a diverse group of microscopic endoparasites that have been the focus of much controversy regarding their phylogenetic position. Two dramatically different hypotheses have been put forward regarding the placement of Myxozoa within Metazoa. One hypothesis, supported by ribosomal DNA (rDNA) data, place Myxozoa as a sister taxon to Bilateria. The alternative hypothesis, supported by phylogenomic data and morphology, place Myxozoa within Cnidaria. Here, we investigate these conflicting hypotheses and explore the effects of missing data, model choice, and inference methods, all of which can have an effect in placing highly divergent taxa. In addition, we identify subsets of the data that most influence the placement of Myxozoa and explore their effects by removing them from the data sets. Assembling the largest taxonomic sampling of myxozoans and cnidarians to date, with a comprehensive sampling of other metazoans for 18S and 28S nuclear rDNA sequences, we recover a well-supported placement of Myxozoa as an early diverging clade of Bilateria. By conducting parametric bootstrapping, we find that the bilaterian placement of Buddenbrockia could not alone be explained by long-branch attraction. After trimming a published phylogenomic data set, to circumvent problems of missing data, we recover the myxozoan Buddenbrockia plumatellae as a medusozoan cnidarian. In further explorations of these data sets, we find that removal of just a few identified sites under a maximum likelihood criterion employing the Whelan and Goldman amino acid substitution model changes the placement of Buddenbrockia from within Cnidaria to the alternative hypothesis at the base of Bilateria. Under a Bayesian criterion employing the CAT model, the cnidarian placement is more resilient to data removal, but under one test, a well-supported early diverging bilaterian position for Buddenbrockia is recovered. Our results confirm the existence of two relatively stable placements for myxozoans and demonstrate that conflicting signal exists not only between the two types of data but also within the phylogenomic data set. These analyses underscore the importance of careful model selection, taxon and data sampling, and in-depth data exploration when investigating the phylogenetic placement of highly divergent taxa.

A stable phylogenetic hypothesis for families within jellyfish class Scyphozoa has been elusive. Reasons for the lack of resolution of scyphozoan familial relationships include a dearth of morphological characters that reliably distinguish taxa and incomplete taxonomic sampling in molecular studies. Here, we address the latter issue by using maximum likelihood and Bayesian methods to reconstruct the phylogenetic relationships among all 19 currently valid scyphozoan families, using sequence data from two nuclear genes: 18S and 28S rDNA. Consistent with prior morphological hypotheses, we find strong evidence for monophyly of subclass Discomedusae, order Coronatae, rhizostome suborder Kolpophorae and superfamilies Actinomyariae, Kampylomyariae, Krikomyariae, and Scapulatae. Eleven of the 19 currently recognized scyphozoan families are robustly monophyletic, and we suggest recognition of two new families pending further analyses. In contrast to long-standing morphological hypotheses, the phylogeny shows coronate family Nausithoidae, semaeostome family Cyaneidae, and rhizostome suborder Daktyliophorae to be nonmonophyletic. Our analyses neither strongly support nor strongly refute monophyly of order Rhizostomeae, superfamily Inscapulatae, and families Ulmaridae, Catostylidae, Lychnorhizidae, and Rhizostomatidae. These taxa, as well as familial relationships within Coronatae and within rhizostome superfamily Inscapulatae, remain unclear and may be resolved by additional genomic and taxonomic sampling. In addition to clarifying some historically difficult taxonomic questions and highlighting nodes in particular need of further attention, the molecular phylogeny presented here will facilitate more robust study of phenotypic evolution in the Scyphozoa, including the evolution characters associated with mass occurrences of jellyfish.

Higher order chromatin organization in concert with epigenetic regulation is a key process that determines gene expression at the global level. The organization of dynamic chromatin domains and their associated protein factors is intertwined with nuclear function to create higher levels of functional zones within the cell nucleus. As a step towards elucidating the organization and dynamics of these functional zones, we have investigated the spatial proximities among a constellation of functionally related sites that are found within euchromatic regions of the cell nucleus including: HP1g, nascent transcript sites (TS), active DNA replicating sites in early S-phase (PCNA) and RNA polymerase II sites. We report close associations among these different sites with proximity values specific for each combination. Analysis of matrin 3 and SAF-A sites demonstrates that these nuclear matrix proteins are highly proximal with the functionally related sites as well as to each other and display closely aligned and overlapping regions following application of the minimal spanning tree (MST) algorithm to visualize higher order network-like patterns. Our findings suggest that multiple factors within the nuclear microenvironment collectively form higher order combinatorial arrays of function. We propose a model for the organization of these functional neighborhoods which takes into account the proximity values of the individual sites and their spatial organization within the nuclear architecture. J. Cell. Biochem. 105: 391-403, 2008. ß 2008 KEY WORDS: RNA POLYMERASE II SITES; HP1g SITES; REPLICATION SITES; TRANSCRIPTION SITES; CELL NUCLEUS; PROLIFERATING CELL NUCLEAR ANTIGEN; NUCLEAR MATRIX; MATRIN 3; SAF-A; COMPUTER IMAGE SEGMENTATION; PROXIMITY ANALYSIS; PATTERN RECOGNITION IMAGE ANALYSIS; MINIMAL SPANNING TREE NETWORKS D espite significant advances in molecular biology and biochemistry, our understanding of the nucleus is at its infancy. The genome is more than a linear sequence of DNA [Misteli, 2007] and is segmented into chromosomes which occupy distinct territories in the interphase cell nucleus [Cremer et al., 2001]. Chromatin within these chromosomes is arranged into multiple levels of hierarchical organization from the nucleosomal 10 nm arrays to the 30 nm fibers to chromatin loops and higher order domains [Berezney, 2002;Cremer et al., 2006;Razin et al., 2007]. Although the eukaryotic nucleus is devoid of any internal membranes, it introduces an incredible level of complexity and several layers of control, which regulate the genomic functions and increase the efficiency of processivity and enzyme regulatory mechanisms. Moreover, the compartmentalization of genomic functions and factors that mediate these functions suggests a high level of structural organization [Berezney et al., 1996;Strouboulis Journal of Cellular Biochemistry ARTICLE Journal of Cellular Biochemistry 105: 391-403 (2008) 391Abbreviations used: DAPI, 4 0 ,6-diamidino-2-phenylindole; HP1g, heterochromatin protein 1, gamma; MST, minimal span...