The cryptochrome family of photoreceptors

CRY1, the primary photoreceptor responsible for blue light-mediated inhibition of hypocotyl elongation in Arabidopsis thaliana, has been characterized. The properties of CRY1, and those of the related protein CRY2, and their relationship to the photolyase family of flavoproteins are discussed.     

Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria

Background

Microsatellite loci have high mutation rates and thus are indicative of mutational processes within the genome. By concentrating on the symbiotic and aposymbiotic cnidarians, we investigated if microsatellite abundances follow a phylogenetic or ecological pattern. Individuals from eight species were shotgun sequenced using 454 GS-FLX Titanium technology. Sequences from the three available cnidarian genomes (Nematostella vectensis, Hydra magnipapillata and Acropora digitifera) were added to the analysis for a total of eleven species representing two classes, three subclasses and eight orders within the phylum Cnidaria.

Results

Trinucleotide and tetranucleotide repeats were the most abundant motifs, followed by hexa- and dinucleotides. Pentanucleotides were the least abundant motif in the data set. Hierarchical clustering and log likelihood ratio tests revealed a weak relationship between phylogeny and microsatellite content. Further, comparisons between cnidaria harboring intracellular dinoflagellates and those that do not, show microsatellite coverage is higher in the latter group.

Conclusions

Our results support previous studies that found tri- and tetranucleotides to be the most abundant motifs in invertebrates. Differences in microsatellite coverage and composition between symbiotic and non-symbiotic cnidaria suggest the presence/absence of dinoflagellates might place restrictions on the host genome.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-939) contains supplementary material, which is available to authorized users.     

Generation of bilateral symmetry in Anthozoa: a model

Polyps of Anthozoa usually display bilateral symmetry with respect to their mouth opening, to their pharynx, and in particular to the arrangement of their mesenteries. Mesenteries, which are endodermal folds running from the apical to the basal end of the body, subdivide the gastric cavity into pouches. They form in a bilateral symmetric sequence. In this article I propose that early in polyp development the endoderm subdivides successively into three different types of compartments. A mesentery forms at the border between compartments. Two of the compartments are homologous to those of Scyphozoa. They form by mutual activation of cell states that locally exclude each other. The third compartment leads to siphonoglyph formation and is an evolutionary innovation of the Anthozoa. The mechanism that controls the number and spatial arrangement of the third type of compartment changes the radial symmetry into a bilateral one and occasionally into a different one. The dynamics of its formation indicate an activator-inhibitor mechanism. Computer models are provided that reproduce decision steps in the generation of the mesenteries.     

A simple test: evaluating explanations for the relative simplicity of the Edwardsiidae (Cnidaria: Anthozoa)

Many members of the cnidarian subclass Zoantharia (sea anemones, corals, and their allies) pass through a larval stage with eight complete mesenteries and without posterior musculature. This larva is usually transient, developing into an adult with 12 or more mesenteries. The adults of one family of sea anemones, the Edwardsiidae, bear the larval number and arrangement of mesenteries and lack the pedal disc seen in other sea anemones. The morphology of the Edwardsiidae has been interpreted in a number of ways: (1) the Edwardsiidae are the most basal extant zoantharian, having diverged before the evolution of additional mesenteries and basal musculature; (2) they are relatively advanced sea anemones that have secondarily simplified because they burrow in sand or mud rather than attaching to a hard substrate; or (3) edwardsiids are derived anemones that have retained a juvenile morphology through paedomorphosis. Phylogenetic analyses of small subunit ribosomal gene sequences reveal that the Edwardsiidae are derived zoantharians, nested within sea anemones. None of the proposed explanations fully explain the edwardsiid's body plan; edwardsiid anatomy is a mosaic of retained primitive and derived features. The results of the present study provide insight into zoantharian phylogeny and illustrate how phylogenetic tests can be used to study the evolution of cnidarian body plans.     

Origin and early diversification of the phylum Cnidaria Verrill: major developments in the analysis of the taxon's Proterozoic–Cambrian history

Diploblastic eumetazoans of the phylum Cnidaria originated during the Neoproterozoic Era, possibly during the Cryogenian Period. The oldest known fossil cnidarians occur in strata of Ediacaran age and consist of polypoid forms that were either nonbiomineralizing or weakly so. The oldest possible anthozoans, including the genus Ramitubus, may be related to tabulate corals and occur in the Doushantuo Lagerstätte (upper Doushantuo Formation, South China), the age of which is poorly constrained (approximately 585 Ma?). Conulariid scyphozoans may first appear as early as 635–577 Ma (Lantian Formation, South China). A definite conulariid, most similar to Palaeozoic species assigned to the genus Paraconularia, occurs in association with the possible scyphozoan, Corumbella werneri, in the latest Ediacaran (c. 543 Ma) Tamengo Formation of Brazil. Basal Cambrian (c. 540 Ma) phosphorites in the upper Kuanchuanpu Formation (South China) yield solitary polyps of the oldest probable anthozoan (Eolympia pediculata), which appears to have been a stem hexacorallian. This same formation contains fossils interpreted by some authors as pentaradial cubozoan polyps; however, both the oldest known cubozoans and the oldest hydrozoans, all medusae, may actually occur in the Cambrian (Series 3, c. 505 Ma) Marjum Formation (Utah, USA). Although these recently published palaeontological data tend to corroborate the hypothesis that Cnidaria has a relatively deep Neoproterozoic history, the timing of major internal branching events remains poorly constrained, with, for example, the results of some molecular clock analyses indicating that the two cnidarian subphyla (Anthozoaria and Medusozoa) may have originated as many as one billion years ago. Further progress towards elucidating the evolution and early fossil record of cnidarians may accrue from: (1) an intensive search for phosphatized soft parts in possible anthozoans from the Ediacaran Doushantuo Formation; (2) an expanded search for Ediacaran conulariids; and (3) additional detailed analyses of the taphonomy and preservation of Ediacaran and Cambrian cnidarians, including possible pentaradial cubozoan polyps from the Fortunian upper Kuanchuanpu Formation.     

Ultrastructure of nematocyst discharge in catch tentacles of the sea anemone Haliplanella luciae (Cnidaria: Anthozoa)

The mature nematocyst lies just beneath the cnidodyte plasma membrane. A microtubule array surrounds the nematocyst capsule just beneath the capsule tip. We propose that the array helps to hold the capsule at the cnidocyte cell surface until discharge. The undischarged capsule tip is sealed by three apical flaps, joined together along complex radial seams. The seams are filled with subunits that appear to bind the flaps together. Upon discharge, the flaps separate along the radial seams to permit thread eversion. The everted thread is lined on both sides by subunits that are stained by antimonate, indicating that they bind calcium. We suggest that, together, the subunits hold the uneverted thread in its folded and coiled configuration. Thread eversion would follow subunit uncoupling. The capsule and thread interiors of partially discharged nematocysts are stained by antimonate. In contrast, the capsule and thread interiors of fully discharged nematocysts are not stained by antimonate. Thus, nematocyst calcium might be injected into the target tissue where it is presumed to act in conjunction with nematocyst venom to promote cell death.     

Sperm ultrastructure of a member of the black coral family Aphanipathidae: Rhipidipathes reticulata (Anthozoa, Antipatharia)

Fertile male polyps of three colonies of the black coral Rhipidipathes reticulata (Aphanipathidae) from Togian Islands (Indonesia) have been the source of the sperm investigated at ultrastructural level, in order to compare their organization with that of other members belonging to the family Antipathidae and Myriopathidae. The extension of the studies to a representative of the family Aphanipathidae stresses once more the structural similarity of the male gametes in antipatharians. A sketch of the sperm model reports the similarity and differences in the examined taxa. Among the micro-characters, the cup-like body linked to the pericentriolar apparatus, is exclusive of the antipatharians. Other inclusions concern the more common pro-acrosomal vesicles or the acrosomelike structure observed only in Antipathella subpinnata and Myriopathes japonica. Lipid vesicles are occasionally present. A typical inclusion, the electron-dense content of which has a C-shaped configuration, is restricted to Rhipidipathes reticulata and is associated to the cup-like body or to the mitochondrion.     

Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia)

Molecular analyses are transforming our understanding of the evolution of scleractinian corals and conflict with traditional classification, which is based on skeletal morphology. A new classification system, which integrates molecular and morphological data, is essential for documenting patterns of biodiversity and establishing priorities for marine conservation, as well as providing the morphological characters needed for linking present‐day corals with fossil species. The present monograph is the first in a series whose goal is to develop such an integrated system. It addresses the taxonomic relationships of 55 Recent zooxanthellate genera (one new) in seven families (one new), which were previously assigned to the suborder Faviina (eight genera are transferred to incertae sedis). The present monograph has two objectives. First, we introduce the higher‐level classification system for the 46 genera whose relationships are clear. Second, we formally revise the taxonomy of those corals belonging to the newly discovered family‐level clade (restricted today to the western Atlantic and Caribbean regions); this revised family Mussidae consists of ten genera (one of which is new) and 26 species that were previously assigned to the ‘traditional’ families Faviidae and Mussidae. To guide in discovering morphologic characters diagnostic of higher‐level taxa, we mapped a total of 38 morphologic characters [19 macromorphology, eight micromorphology, 11 microstructure] onto a molecular tree consisting of 67 species [22 Indo‐Pacific and seven Atlantic species in the traditional family Faviidae; 13 Indo‐Pacific and ten Atlantic species in the traditional family Mussidae; 13 species in the traditional families Merulinidae (5), Pectiniidae (7), and Trachyphylliidae (1); two Atlantic species of traditional Montastraea], and trace character histories using parsimony. To evaluate the overall effectiveness of morphological data in phylogeny reconstruction, we performed morphology‐based phylogenetic analyses using 27 (80 states) of the 38 characters, and compared morphological trees with molecular trees. The results of the ancestral state reconstructions revealed extensive homoplasy in almost all morphological characters. Family‐ and subfamily‐level molecular clades [previously identified as XVII?XXI] are best distinguished on the basis of the shapes of septal teeth and corresponding microstructure. The newly revised family Mussidae (XXI) has septal teeth with regular pointed tips (a symplesiomorphy) and a stout blocky appearance. It has two subfamilies, Mussinae and Faviinae. The subfamily Mussinae is distinguished by spine‐shaped teeth and widely spaced costoseptal clusters of calcification centres. The subfamily Faviinae is distinguished by blocky, pointed tricorne or paddle‐shaped teeth with elliptical bases, transverse structures such as carinae that cross the septal plane, and well‐developed aligned granules. Defining diagnostic characters for the broader data set is more challenging. In analyses of taxonomic subsets of the data set that were defined by clade, morphological phylogenetic analyses clearly distinguished the families Mussidae (XXI) and Lobophylliidae (XIX), as well as the two subfamilies of Mussidae (Mussinae, Faviinae), with one exception (Homophyllia australis). However, analyses of the entire 67‐species data set distinguished the family Lobophylliidae (XIX), but not the Merulinidae (XVII) and not the newly defined Mussidae (XXI), although the subfamily Mussinae was recovered as monophyletic. Some lower‐level relationships within the Merulinidae (XVII) agree with molecular results, but this particular family is especially problematic and requires additional molecular and morphological study. Future work including fossils will not only allow estimation of divergence times but also facilitate examination of the relationship between these divergences and changes in the environment and biogeography. Published 2012. This article is a U.S. Government work and is in the public domain in the USA. Zoological Journal of the Linnean Society, 2012, 166 , 465–529.     

Gametogenic cycles and reproduction in the beadlet sea anemone Actinia equina (Cnidaria: Anthozoa)

Sexual Actinia equina have been maintained in the laboratory. Monthly biopsies show that these animals have annual gametogenic cycles. Regular samples from several natural populations suggest that animals in the wild show similar gametogenic periodicity. In the laboratory, males release sperm, but females brood young, at least for a few weeks. Members of these broods are released sporadically, usually after a water change. Males and non-sexual adults kept in isolation for over a year release a few juveniles during and at the end of that time. These young are likely to be asexually reproduced. There appears to be geographical variation of anemone size and in the frequency of sexual individuals in populations round the British Coast, so that modes of reproduction may vary.     

Evolution of vertebrate retinal photoreception

Recent findings shed light on the steps underlying the evolution of vertebrate photoreceptors and retina. Vertebrate ciliary photoreceptors are not as wholly distinct from invertebrate rhabdomeric photoreceptors as is sometimes thought. Recent information on the phylogenies of ciliary and rhabdomeric opsins has helped in constructing the likely routes followed during evolution. Clues to the factors that led the early vertebrate retina to become invaginated can be obtained by combining recent knowledge about the origin of the pathway for dark re-isomerization of retinoids with knowledge of the inability of ciliary opsins to undergo photoreversal, along with consideration of the constraints imposed under the very low light levels in the deep ocean. Investigation of the origin of cell classes in the vertebrate retina provides support for the notion that cones, rods and bipolar cells all originated from a primordial ciliary photoreceptor, whereas ganglion cells, amacrine cells and horizontal cells all originated from rhabdomeric photoreceptors. Knowledge of the molecular differences between cones and rods, together with knowledge of the scotopic signalling pathway, provides an understanding of the evolution of rods and of the rods'' retinal circuitry. Accordingly, it has been possible to propose a plausible scenario for the sequence of evolutionary steps that led to the emergence of vertebrate photoreceptors and retina.     

Evolutionary origins of germline segregation in Metazoa: evidence for a germ stem cell lineage in the coral Orbicella faveolata (Cnidaria,Anthozoa)

The ability to segregate a committed germ stem cell (GSC) lineage distinct from somatic cell lineages is a characteristic of bilaterian Metazoans. However, the occurrence of GSC lineage specification in basally branching Metazoan phyla, such as Cnidaria, is uncertain. Without an independently segregated GSC lineage, germ cells and their precursors must be specified throughout adulthood from continuously dividing somatic stem cells, generating the risk of propagating somatic mutations within the individual and its gametes. To address the potential for existence of a GSC lineage in Anthozoa, the sister-group to all remaining Cnidaria, we identified moderate- to high-frequency somatic mutations and their potential for gametic transfer in the long-lived coral Orbicella faveolata (Anthozoa, Cnidaria) using a 2b-RAD sequencing approach. Our results demonstrate that somatic mutations can drift to high frequencies (up to 50%) and can also generate substantial intracolonial genetic diversity. However, these somatic mutations are not transferable to gametes, signifying the potential for an independently segregated GSC lineage in O. faveolata. In conjunction with previous research on germ cell development in other basally branching Metazoan species, our results suggest that the GSC system may be a Eumetazoan characteristic that evolved in association with the emergence of greater complexity in animal body plan organization and greater specificity of stem cell functions.     

Phylogenetic comparison of the myxosporea based on an actin cDNA isolated from Myxobolus cerebralis

The full-length actin gene from Myxobolus cerebralis (McerAct-1), the first characterized from representatives in the phylum Myxozoa, encodes a 378-amino acid polypeptide with an estimated molecular weight of 41,580-Da. A phylogenetic comparison found M. cerebralis to branch outside the metazoans. This finding contrasts with previous reports that suggest an evolutionary affinity of the Myxozoa with either the Bilateria or Cnidaria.     

Evolution and spectral tuning of visual pigments in birds and mammals

Variation in the types and spectral characteristics of visual pigments is a common mechanism for the adaptation of the vertebrate visual system to prevailing light conditions. The extent of this diversity in mammals and birds is discussed in detail in this review, alongside an in-depth consideration of the molecular changes involved. In mammals, a nocturnal stage in early evolution is thought to underlie the reduction in the number of classes of cone visual pigment genes from four to only two, with the secondary loss of one of these genes in many monochromatic nocturnal and marine species. The trichromacy seen in many primates arises from either a polymorphism or duplication of one of these genes. In contrast, birds have retained the four ancestral cone visual pigment genes, with a generally conserved expression in either single or double cone classes. The loss of sensitivity to ultraviolet (UV) irradiation is a feature of both mammalian and avian visual evolution, with UV sensitivity retained among mammals by only a subset of rodents and marsupials. Where it is found in birds, it is not ancestral but newly acquired.     

Taxonomic classification of the reef coral family Lobophylliidae (Cnidaria: Anthozoa: Scleractinia)

Lobophylliidae is a family‐level clade of corals within the ‘robust’ lineage of Scleractinia. It comprises species traditionally classified as Indo‐Pacific ‘mussids’, ‘faviids’, and ‘pectiniids’. Following detailed revisions of the closely related families Merulinidae, Mussidae, Montastraeidae, and Diploastraeidae, this monograph focuses on the taxonomy of Lobophylliidae. Specifically, we studied 44 of a total of 54 living lobophylliid species from all 11 genera based on an integrative analysis of colony, corallite, and subcorallite morphology with molecular sequence data. By examining coral skeletal features at three distinct levels – macromorphology, micromorphology, and microstructure – we built a morphological matrix comprising 46 characters. Data were analysed via maximum parsimony and transformed onto a robust molecular phylogeny inferred using two nuclear (histone H3 and internal transcribed spacers) and one mitochondrial (cytochrome c oxidase subunit I) DNA loci. The results suggest that micromorphological characters exhibit the lowest level of homoplasy within Lobophylliidae. Molecular and morphological trees show that Symphyllia, Parascolymia, and Australomussa should be considered junior synonyms of Lobophyllia, whereas Lobophyllia pachysepta needs to be transferred to Acanthastrea. Our analyses also lend strong support to recent revisions of Acanthastrea, which has been reorganized into five separate genera (Lobophyllia, Acanthastrea, Homophyllia, Sclerophyllia, and Micromussa), and to the establishment of Australophyllia. Cynarina and the monotypic Moseleya remain unchanged, and there are insufficient data to redefine Oxypora, Echinophyllia, and Echinomorpha. Finally, all lobophylliid genera are diagnosed under the phylogenetic classification system proposed here, which will facilitate the placement of extinct taxa on the scleractinian tree of life.     

Prodigies of propagation: the many modes of clonal replication in boloceroidid sea anemones (Cnidaria,Anthozoa, Actiniaria)

Summary

Diverse modes of clonal propagation were documented in tiny zooxanthellate sea anemones from the tropical Pacific. All were boloceroidids, as indicated by the tentacles' basal sphincter and the animals' swimming behavior. In one species, single tentacles were pinched off at the sphincter, shed into the coelenteron, and brooded there while regenerating into minute new polyps in ~4 days. Within a day of release, the propagules fed on live prey and swam by lashing the tentacles. A similar process occurs in another species studied, Bunodeopsis medusoides. In a third species a previously undescribed mode of replication was seen. These anemones bore a primary cycle of tentacles that engaged actively in feeding and swimming, were not shed, and showed no sign of producing polyps. Alternating with these tentacles were fan-like clusters of shorter tentacles that were relatively inactive in feeding and swimming. Despite the sphincter at the base of each of these clustered tentacles, they were never shed singly; instead, each cluster separated as a unit that then regenerated into a new polyp. Two other replicative modes were observed in similar, minute boloceroidid anemones collected together in the same habitat: longitudinal fission, not previously reported in boloceroidids, and pedal scission. Modes of replication in these actinians are more diverse than once thought, but the selective forces behind this variation are so far unexplored. These prolific anemones may regularly be taking advantage of their combination of swimming and regenerative abilities to achieve dispersal, not only by sexually produced larvae, but also by cloned polyps.     

Evolution and dynamics of branching colonial form in marine modular cnidarians: gorgonian octocorals

Multi-branched arborescent networks are common patterns for many sessile marine modular organisms but no clear understanding of their development is yet available. This paper reviews new findings in the theoretical and comparative biology of branching modular organisms (e.g. Octocorallia Cnidaria) and new hypotheses on the evolution of form are discussed. A particular characteristic of branching Caribbean gorgonian octocorals is a morphologic integration at two levels of colonial organization based on whether the traits are at the module or colony level. This revealed an emergent level of integration and modularity produced by the branching process itself and not entirely by the module replication. In essence, not just a few changes at the module level could generate changes in colony architecture, suggesting uncoupled developmental patterning for the polyp and branch level traits. Therefore, the evolution of colony form in octocorals seems to be related to the changes affecting the process of branching. Branching in these organisms is sub-apical, coming from mother branches, and the highly self-organized form is the product of a dynamic process maintaining a constant ratio between mother and daughter branches. Colony growth preserves shape but is a logistic growth-like event due to branch interference and/or allometry. The qualitative branching patterns in octocorals (e.g. sea feathers, fans, sausages, and candelabra) occurred multiple times when compared with recent molecular phylogenies, suggesting independence of common ancestry to achieve these forms. A number of species with different colony forms, particularly alternate species (e.g. sea candelabrum), shared the same value for an important branching parameter (the ratio of mother to total branches). According to the way gorgonians branch and achieve form, it is hypothesized that the diversity of alternate species sharing the same narrow variance in that critical parameter for growth might be the product of canalization (or a developmental constraint), where uniform change in growth rates and maximum colony size might explain colony differences among species. If the parameter preserving shape in the colonies is fixed but colonies differ in their growth rates and maximum sizes, heterochrony could be responsible for the evolution among some gorgonian corals with alternate branching.