Earliest known ophiuroids from high palaeolatitude, southern Gondwana, recovered from the Pragian to earliest Emsian Baviaanskloof Formation (Table Mountain Group, Cape Supergroup) South Africa

For the first time, ophiuroids have been found in South African strata predating the lowermost Bokkeveld Group. These comprise natural moulds and casts from two localities in the 'upper unit' of the Baviaanskloof Formation (Table Mountain Group). As a Pragian to earliest Emsian age has been inferred for this member, the new taxa comprise the earliest high-palaeolatitude ophiuroid records from southern Gondwana. Morphological analysis of the specimens revealed the presence of two distinct taxa. One is here described as Krommaster spinosus gen. et sp. nov., a new encrinasterid characterised by very large spines on the dorsal side of the disc, the ventral interradial marginal plates and the arm midlines. The second taxon is a poorly preserved specimen of Hexuraster weitzi, a cheiropterasterid previously described from the slightly younger Bokkeveld Group.

Miniaturization during a Silurian environmental crisis generated the modern brittle star body plan

Pivotal anatomical innovations often seem to appear by chance when viewed through the lens of the fossil record. As a consequence, specific driving forces behind the origination of major organismal clades generally remain speculative. Here, we present a rare exception to this axiom by constraining the appearance of a diverse animal group (the living Ophiuroidea) to a single speciation event rather than hypothetical ancestors. Fossils belonging to a new pair of temporally consecutive species of brittle stars (Ophiopetagno paicei gen. et sp. nov. and Muldaster haakei gen. et sp. nov.) from the Silurian (444-419 Mya) of Sweden reveal a process of miniaturization that temporally coincides with a global extinction and environmental perturbation known as the Mulde Event. The reduction in size from O. paicei to M. haakei forced a structural simplification of the ophiuroid skeleton through ontogenetic retention of juvenile traits, thereby generating the modern brittle star bauplan.

Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms

Echinobase (www.echinobase.org) is a third generation web resource supporting genomic research on echinoderms. The new version was built by cloning the mature Xenopus model organism knowledgebase, Xenbase, refactoring data ingestion pipelines and modifying the user interface to adapt to multispecies echinoderm content. This approach leveraged over 15 years of previous database and web application development to generate a new fully featured informatics resource in a single year. In addition to the software stack, Echinobase uses the private cloud and physical hosts that support Xenbase. Echinobase currently supports six echinoderm species, focused on those used for genomics, developmental biology and gene regulatory network analyses. Over 38 000 gene pages, 18 000 publications, new improved genome assemblies, JBrowse genome browser and BLAST + services are available and supported by the development of a new echinoderm anatomical ontology, uniformly applied formal gene nomenclature, and consistent orthology predictions. A novel feature of Echinobase is integrating support for multiple, disparate species. New genomes from the diverse echinoderm phylum will be added and supported as data becomes available. The common code development design of the integrated knowledgebases ensures parallel improvements as each resource evolves. This approach is widely applicable for developing new model organism informatics resources.

Biomineralization by particle attachment in early animals

Crystallization by particle attachment (CPA) of amorphous precursors has been demonstrated in modern biomineralized skeletons across a broad phylogenetic range of animals. Precisely the same precursors, hydrated (ACC-H2O) and anhydrous calcium carbonate (ACC), have been observed spectromicroscopically in echinoderms, mollusks, and cnidarians, phyla drawn from the 3 major clades of eumetazoans. Scanning electron microscopy (SEM) here also shows evidence of CPA in tunicate chordates. This is surprising, as species in these clades have no common ancestor that formed a mineralized skeleton and appear to have evolved carbonate biomineralization independently millions of years after their late Neoproterozoic divergence. Here we correlate the occurrence of CPA from ACC precursor particles with nanoparticulate fabric and then use the latter to investigate the antiquity of the former. SEM images of early biominerals from Ediacaran and Cambrian shelly fossils show that these early calcifiers used attachment of ACC particles to form their biominerals. The convergent evolution of biomineral CPA may have been dictated by the same thermodynamics and kinetics as we observe today.

On the impact of Citizen Science-derived data quality on deep learning based classification in marine images

The evaluation of large amounts of digital image data is of growing importance for biology, including for the exploration and monitoring of marine habitats. However, only a tiny percentage of the image data collected is evaluated by marine biologists who manually interpret and annotate the image contents, which can be slow and laborious. In order to overcome the bottleneck in image annotation, two strategies are increasingly proposed: “citizen science” and “machine learning”. In this study, we investigated how the combination of citizen science, to detect objects, and machine learning, to classify megafauna, could be used to automate annotation of underwater images. For this purpose, multiple large data sets of citizen science annotations with different degrees of common errors and inaccuracies observed in citizen science data were simulated by modifying “gold standard” annotations done by an experienced marine biologist. The parameters of the simulation were determined on the basis of two citizen science experiments. It allowed us to analyze the relationship between the outcome of a citizen science study and the quality of the classifications of a deep learning megafauna classifier. The results show great potential for combining citizen science with machine learning, provided that the participants are informed precisely about the annotation protocol. Inaccuracies in the position of the annotation had the most substantial influence on the classification accuracy, whereas the size of the marking and false positive detections had a smaller influence.

Cell type phylogenetics informs the evolutionary origin of echinoderm larval skeletogenic cell identity

The multiplicity of cell types comprising multicellular organisms begs the question as to how cell type identities evolve over time. Cell type phylogenetics informs this question by comparing gene expression of homologous cell types in distantly related taxa. We employ this approach to inform the identity of larval skeletogenic cells of echinoderms, a clade for which there are phylogenetically diverse datasets of spatial gene expression patterns. We determined ancestral spatial expression patterns of alx1, ets1, tbr, erg, and vegfr, key components of the skeletogenic gene regulatory network driving identity of the larval skeletogenic cell. Here we show ancestral state reconstructions of spatial gene expression of extant eleutherozoan echinoderms support homology and common ancestry of echinoderm larval skeletogenic cells. We propose larval skeletogenic cells arose in the stem lineage of eleutherozoans during a cell type duplication event that heterochronically activated adult skeletogenic cells in a topographically distinct tissue in early development.

Atlantic West Ophiothrix spp. in the scope of integrative taxonomy: Confirming the existence of Ophiothrix trindadensis Tommasi, 1970

We re-describe and confirm the validity of Ophiothrix trindadensis Tommasi, 1970 (Echinodermata: Ophiuroidea). This is a native species from Brazil, however it lacked a type series deposited in scientific collections. The recognition of O. trindadensis was made possible using integrative taxonomy applied to many specimens from the type locality (Trindade Island) as well as from different locations along the Brazilian coast (Araçá Bay and Estuarine Complex of Paranaguá). Initially, 835 specimens were studied and divided into four candidate species (CS) inferred from external morphological characters. Afterwards, the CSs were compared using integrative taxonomy based on external morphology, arm microstructures morphology (arm ossicle), morphometry, and molecular studies (fragments of the mitochondrial genes 16S and COI). Analyses indicated CS1 and CS2 as O. trindadensis, and CS3 as O. angulata, both valid species. CS4 remains O. cf. angulata as more data, including their ecology and physiology, are needed to be definitively clarified. Our integrative investigation using specimens from the type locality overcame the lack of type specimens and increased the reliable identification of O. trindadensis and O. angulata.

Two more Posterior Hox genes and Hox cluster dispersal in echinoderms

BACKGROUND

Hox genes are key elements in patterning animal development. They are renowned for their, often, clustered organisation in the genome, with supposed mechanistic links between the organisation of the genes and their expression. The widespread distribution and comparable functions of Hox genes across the animals has led to them being a major study system for comparing the molecular bases for construction and divergence of animal morphologies. Echinoderms (including sea urchins, sea stars, sea cucumbers, feather stars and brittle stars) possess one of the most unusual body plans in the animal kingdom with pronounced pentameral symmetry in the adults. Consequently, much interest has focused on their development, evolution and the role of the Hox genes in these processes. In this context, the organisation of echinoderm Hox gene clusters is distinctive. Within the classificatory system of Duboule, echinoderms constitute one of the clearest examples of Disorganized (D) clusters (i.e. intact clusters but with a gene order or orientation rearranged relative to the ancestral state).

RESULTS

Here we describe two Hox genes (Hox11/13d and e) that have been overlooked in most previous work and have not been considered in reconstructions of echinoderm Hox complements and cluster organisation. The two genes are related to Posterior Hox genes and are present in all classes of echinoderm. Importantly, they do not reside in the Hox cluster of any species for which genomic linkage data is available.

CONCLUSION

Incorporating the two neglected Posterior Hox genes into assessments of echinoderm Hox gene complements and organisation shows that these animals in fact have Split (S) Hox clusters rather than simply Disorganized (D) clusters within the Duboule classification scheme. This then has implications for how these genes are likely regulated, with them no longer covered by any potential long-range Hox cluster-wide, or multigenic sub-cluster, regulatory mechanisms.

Conservation of mitochondrial genome arrangements in brittle stars (Echinodermata, Ophiuroidea)

Brittle stars are conspicuous members of benthic ecosystems, fill many ecological niches and are the most speciose of all classes of echinoderms. With high levels of biodiversity, elucidating the evolutionary history of this group is important. Understanding of higher-level relationships within Ophiuroidea has been aided by multilocus nuclear data and DNA barcoding. However, the degree of consistency between mitochondrial and nuclear data within ophiuroids remains unclear and deserves further assessment. In this study, 17 mitochondrial genomes spanning the taxonomic breadth of Ophiuroidea were utilized to explore evolutionary relationships through maximum likelihood analyses, Bayesian inference and comparative assessment of gene order. Our phylogenetic analyses, based on both nucleotide and amino acid residues, support recent findings based on multilocus nuclear data and morphology, in that the brittle star clades Ophintegrida and Euryophiurida were recovered as monophyletic with the latter comprising Euyalida, Ophiuridae and Ophiopyrgidae. Only three different arrangements of the 13 protein coding and 2 ribosomal RNA genes were observed. As expected, tRNA genes were more likely to have undergone rearrangement but the order of all 37 genes was found to be conserved in all sampled Euryalida and Ophiuridae. Both Euryalida and the clade comprised of Ophiuridae and Ophiopyrgidae, each had their own conserved rearrangement of protein coding genes and ribosomal genes, after divergence from their last common ancestor. Euryalida has a rearrangement of the two ribosomal RNA genes, rrnS and rrnL, in contrast to Ophiuridae and Ophiopyrgidae, which had an inversion of the genes nad1, nad2, and cob relative to Ophintegrida. Further, our data support the gene order found in all sampled Euryalida as the most likely ancestral order for all Ophiuroidea.

The peristomial plates of ophiuroids (Echinodermata: Ophiuroidea) highlight an incongruence between morphology and proposed phylogenies

The peristomial plates are skeletal components of the interbrachial frame (or mouth frame), which is located below the true mouth of ophiuroids. Whilst the peristomial plates were extensively described and used as diagnostic characters by some early workers, for the past 100 years they have been largely neglected as a taxonomic resource. In this investigation the peristomial plates of 48 species representing 21 families were examined directly, and information on a further 61 species, including representatives of another eight families, was obtained from the published literature. Observations were made with regard to fragmentation state, relative size and orientation of the peristomial plates. Although fragmentation state showed little consistency at any taxonomic level, relative size and orientation segregated a group of families comprising species with relatively small, inclined peristomial plates, viz. Ophiotrichidae, Ophiopholidae, Ophiactidae, Amphiuridae and Ophiocomidae, together with a single hemieuryalid species-Ophioplocus januarii. The distribution of peristomial plate traits was strongly correlated with that of several other character states pertaining to the interbrachial frame. This supported the proposition that two major types of interbrachial frame are present in ophiuroids (designated 'A' and 'B'). Current phylogenies inferred from both morphological and molecular data imply that type B is derived and has evolved independently at least twice in the orders Amphilepidida and Ophiacanthida. This represents a remarkable example of evolutionary convergence. An analysis of the distribution of all interbrachial frame character states suggested that within the Amphilepidida paedomorphosis was probably responsible for the complete reversion of the interbrachial frame to the ancestral type A condition in two families (Ophiothamnidae and Amphilepididae) of suborder Gnathophiurina and possibly responsible for varying degrees of trait reversal in the four families of suborder Ophionereidina. Such paedomorphic events may have been associated with a secondary return to the deep-sea from shallow-sea environments.

Molecular mechanisms of fission in echinoderms: Transcriptome analysis

Echinoderms are capable of asexual reproduction by fission. An individual divides into parts due to changes in the strength of connective tissue of the body wall. The structure of connective tissue and the mechanisms of variations in its strength in echinoderms remain poorly studied. An analysis of transcriptomes of individuals during the process of fission provides a new opportunity to understand the mechanisms of connective tissue mutability. In the holothurian Cladolabes schmeltzii, we have found a rather complex organization of connective tissue. Transcripts of genes encoding a wide range of structural proteins of extracellular matrix, as well as various proteases and their inhibitors, have been discovered. All these molecules may constitute a part of the mechanism of connective tissue mutability. According to our data, the extracellular matrix of echinoderms is substantially distinguished from that of vertebrates by the lack of elastin, fibronectins, and tenascins. In case of fission, a large number of genes of transcription factors and components of different signaling pathways are expressed. Products of these genes are probably involved in regulation of asexual reproduction, connective tissue mutability, and preparation of tissues for subsequent regeneration. It has been shown that holothurian tensilins are a special group of tissue inhibitors of metalloproteinases, which has formed within the class Holothuroidea and is absent from other echinoderms. Our data can serve a basis for the further study of the mechanisms of extracellular matrix mutability, as well as the mechanisms responsible for asexual reproduction in echinoderms.

Regeneration in Stellate Echinoderms: Crinoidea, Asteroidea and Ophiuroidea

Reparative regeneration is defined as the replacement of lost adult body parts and is a phenomenon widespread yet highly variable among animals. This raises the question of which key cellular and molecular mechanisms have to be implemented in order to efficiently and correctly replace entire body parts in any animal. To address this question, different studies using an integrated cellular and functional genomic approach to study regeneration in stellate echinoderms (crinoids, asteroids and ophiuroids) had been carried out over the last few years. The phylum Echinodermata is recognized for the striking regeneration potential shown by the members of its different clades. Indeed, stellate echinoderms are considered among the most useful and tractable experimental models for carrying comprehensive studies focused on ecological, developmental and evolutionary aspects. Moreover, most of them are tractable in the laboratory and, thus, should allow us to understand the underlying mechanisms, cellular and molecular, which are involved. Here, a comprehensive analysis of the cellular/histological components of the regenerative process in crinoids, asteroids and ophiuroids is described and compared. However, though this knowledge provided us with some clear insights into the global distribution of cell types at different times, it did not explain us how the recruited cells are specified (and from which precursors) over time and where are they located in the animal. The precise answer to these queries needs the incorporation of molecular approaches, both descriptive and functional. Yet, the molecular studies in stellate echinoderms are still limited to characterization of some gene families and protein factors involved in arm regeneration but, at present, have not shed light on most of the basic mechanisms. In this context, further studies are needed specifically to understand the role of regulatory factors and their spatio-temporal deployment in the growing arms. A focus on developing functional tools over the next few years should be of fundamental importance.

Evolution of thyroid hormone signaling in animals: Non-genomic and genomic modes of action

Much research has focused on vertebrate thyroid hormone (TH) synthesis and their function in development and metabolism. While important differences in TH synthesis and signaling exist, comparative studies between vertebrates fail to explain the evolutionary origins of this important regulatory axis. For that, one needs to make sense out of the diverse TH effects which have been described in invertebrate phyla but for which a mechanistic understanding is largely missing. Almost every major group of non-vertebrate animals possesses the capability to synthesize and metabolize thyroid hormones and there is evidence for a nuclear thyroid hormone receptor mediated mechanism in the bilateria, especially in molluscs, echinoderms, cephalochordates and ascidians. Still, genomic pathways cannot fully explain many observed effects of thyroid hormones in groups such as cnidarians, molluscs, and echinoderms and it is therefore possible that TH may signal via other mechanisms, such as non-genomic signaling systems via membrane bound or cytoplasmic receptors. Here we provide a brief review of TH actions in selected invertebrate species and discuss the hypothesis that non-genomic TH action may have played a critical role in TH signaling throughout animal evolution.

The importance of offshore origination revealed through ophiuroid phylogenomics

Our knowledge of macro-evolutionary processes in the deep sea is poor, leading to much speculation about whether the deep sea is a source or sink of evolutionary adaptation. Here, we use a phylogenetic approach, on large molecular (688 species, 275 kbp) and distributional datasets (104 513 records) across an entire class of marine invertebrates (Ophiuroidea), to infer rates of bathymetric range shift over time between shallow and deep water biomes. Biome conservation is evident through the phylogeny, with the majority of species in most clades distributed within the same bathome. Despite this, bathymetric shifts have occurred. We inferred from ancestral reconstructions that eurybathic or intermediate distributions across both biomes were a transitional state and direct changes between shallow and deep sea did not occur. The macro-evolutionary pattern of bathome shift appeared to reflect micro-evolutionary processes of bathymetric speciation. Results suggest that most of the oldest clades have a deep-sea origin, but multiple colonization events indicate that the evolution of this group conforms neither to a simple onshore-offshore hypothesis, nor the opposite pattern. Both shallow and deep bathomes have played an important role in generating the current diversity of this major benthic class.

The skeletal proteome of the sea star Patiria miniata and evolution of biomineralization in echinoderms

BACKGROUND

Proteomic studies of skeletal proteins have revealed large, complex mixtures of proteins occluded within the mineral. Many skeletal proteomes contain rapidly evolving proteins with repetitive domains, further complicating our understanding. In echinoderms, proteomic analysis of the skeletal proteomes of mineralized tissues of the sea urchin Strongylocentrotus purpuratus prominently featured spicule matrix proteins with repetitive sequences linked to a C-type lectin domain. A comparative study of the brittle star Ophiocoma wendtii skeletal proteome revealed an order of magnitude fewer proteins containing C-type lectin domains. A number of other proteins conserved in the skeletons of the two groups were identified. Here we report the complete skeletal proteome of the sea star Patiria miniata and compare it to that of the other echinoderm groups.

RESULTS

We have identified eighty-five proteins in the P. miniata skeletal proteome. Forty-two percent of the proteins were determined to be homologous to proteins found in the S. purpuratus skeletal proteomes. An additional 34 % were from similar functional classes as proteins in the urchin proteomes. Thirteen percent of the P. miniata proteins had homologues in the O. wendtii skeletal proteome with an additional 29% showing similarity to brittle star skeletal proteins. The P. miniata skeletal proteome did not contain any proteins with C-lectin domains or with acidic repetitive regions similar to the sea urchin or brittle star spicule matrix proteins. MSP130 proteins were also not found. We did identify a number of proteins homologous between the three groups. Some of the highly conserved proteins found in echinoderm skeletons have also been identified in vertebrate skeletons.

CONCLUSIONS

The presence of proteins conserved in the skeleton in three different echinoderm groups indicates these proteins are important in skeleton formation. That a number of these proteins are involved in skeleton formation in vertebrates suggests a common origin for some of the fundamental processes co-opted for skeleton formation in deuterostomes. The proteins we identify suggest transport of proteins and calcium via endosomes was co-opted to this function in a convergent fashion. Our data also indicate that modifications to the process of skeleton formation can occur through independent co-option of proteins following species divergence as well as through domain shuffling.

Crossing the Divide: Admixture Across the Antarctic Polar Front Revealed by the Brittle Star Astrotoma agassizii

The Antarctic Polar Front (APF) is one of the most well-defined and persistent oceanographic features on the planet and serves as a barrier to dispersal between the Southern Ocean and lower latitudes. High levels of endemism in the Southern Ocean have been attributed to this barrier, whereas the accompanying Antarctic Circumpolar Current (ACC) likely promotes west-to-east dispersal. Previous phylogeographic work on the brittle star Astrotoma agassizii Lyman, 1875 based on mitochondrial genes suggested isolation across the APF, even though populations in both South American waters and the Southern Ocean are morphologically indistinguishable. Here, we revisit this finding using a high-resolution 2b-RAD (restriction-site-associated DNA) single-nucleotide polymorphism (SNP)-based approach, in addition to enlarged mitochondrial DNA data sets (16S rDNA, COI, and COII), for comparison to previous work. In total, 955 biallelic SNP loci confirmed the existence of strongly divergent populations on either side of the Drake Passage. Interestingly, genetic admixture was detected between South America and the Southern Ocean in five individuals on both sides of the APF, revealing evidence of recent or ongoing genetic contact. We also identified two differentiated populations on the Patagonian Shelf with six admixed individuals from these two populations. These findings suggest that the APF is a strong but imperfect barrier. Fluctuations in location and strength of the APF and ACC due to climate shifts may have profound consequences for levels of admixture or endemism in this region of the world.

Exploring Canadian Echinoderm Diversity through DNA Barcodes

DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold) between mean intra- (0.48%) and inter- (12.0%) specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs.

Paedomorphosis as an Evolutionary Driving Force: Insights from Deep-Sea Brittle Stars

Heterochronic development has been proposed to have played an important role in the evolution of echinoderms. In the class Ophiuroidea, paedomorphosis (retention of juvenile characters into adulthood) has been documented in the families Ophiuridae and Ophiolepididae but not been investigated on a broader taxonomic scale. Historical errors, confusing juvenile stages with paedomorphic species, show the difficulties in correctly identifying the effects of heterochrony on development and evolution. This study presents a detailed analysis of 40 species with morphologies showing various degrees of juvenile appearance in late ontogeny. They are compared to a range of early ontogenetic stages from paedomorphic and non-paedomorphic species. Both quantitative and qualitative measurements are taken and analysed. The results suggest that strongly paedomorphic species are usually larger than other species at comparable developmental stage. The findings support recent notions of polyphyletic origin of the families Ophiuridae and Ophiolepididae. The importance of paedomorphosis and its correct recognition for the practice of taxonomy and phylogeny are emphasized.

The diversity of nanos expression in echinoderm embryos supports different mechanisms in germ cell specification

Specification of the germ cell lineage is required for sexual reproduction in all animals. However, the timing and mechanisms of germ cell specification is remarkably diverse in animal development. Echinoderms, such as sea urchins and sea stars, are excellent model systems to study the molecular and cellular mechanisms that contribute to germ cell specification. In several echinoderm embryos tested, the germ cell factor Vasa accumulates broadly during early development and is restricted after gastrulation to cells that contribute to the germ cell lineage. In the sea urchin, however, the germ cell factor Vasa is restricted to a specific lineage by the 32-cell stage. We therefore hypothesized that the germ cell specification program in the sea urchin/Euechinoid lineage has evolved to an earlier developmental time point. To test this hypothesis we determined the expression pattern of a second germ cell factor, Nanos, in four out of five extant echinoderm clades. Here we find that Nanos mRNA does not accumulate until the blastula stage or later during the development of all other echinoderm embryos except those that belong to the Echinoid lineage. Instead, Nanos is expressed in a restricted domain at the 32-128 cell stage in Echinoid embryos. Our results support the model that the germ cell specification program underwent a heterochronic shift in the Echinoid lineage. A comparison of Echinoid and non-Echinoid germ cell specification mechanisms will contribute to our understanding of how these mechanisms have changed during animal evolution.

A New Morphological Phylogeny of the Ophiuroidea (Echinodermata) Accords with Molecular Evidence and Renders Microfossils Accessible for Cladistics

Ophiuroid systematics is currently in a state of upheaval, with recent molecular estimates fundamentally clashing with traditional, morphology-based classifications. Here, we attempt a long overdue recast of a morphological phylogeny estimate of the Ophiuroidea taking into account latest insights on microstructural features of the arm skeleton. Our final estimate is based on a total of 45 ingroup taxa, including 41 recent species covering the full range of extant ophiuroid higher taxon diversity and 4 fossil species known from exceptionally preserved material, and the Lower Carboniferous Aganaster gregarius as the outgroup. A total of 130 characters were scored directly on specimens. The tree resulting from the Bayesian inference analysis of the full data matrix is reasonably well resolved and well supported, and refutes all previous classifications, with most traditional families discredited as poly- or paraphyletic. In contrast, our tree agrees remarkably well with the latest molecular estimate, thus paving the way towards an integrated new classification of the Ophiuroidea. Among the characters which were qualitatively found to accord best with our tree topology, we selected a list of potential synapomorphies for future formal clade definitions. Furthermore, an analysis with 13 of the ingroup taxa reduced to the lateral arm plate characters produced a tree which was essentially similar to the full dataset tree. This suggests that dissociated lateral arm plates can be analysed in combination with fully known taxa and thus effectively unlocks the extensive record of fossil lateral arm plates for phylogenetic estimates. Finally, the age and position within our tree implies that the ophiuroid crown-group had started to diversify by the Early Triassic.

When Ontogeny Matters: A New Japanese Species of Brittle Star Illustrates the Importance of Considering both Adult and Juvenile Characters in Taxonomic Practice

Current taxonomy offers numerous approaches and methods for species delimitation and description. However, most of them are based on the adult characters and rarely suggest a dynamic representation of developmental transformations of taxonomically important features. Here we show how the underestimation of ontogenetic changes may result in long term lack of recognition of a new species of one of the most common ophiacanthid brittle stars (Echinodermata: Ophiuroidea) from the North Pacific. Based on vast material collected predominantly by various Japanese expeditions in the course of more than 50 years, and thorough study of appropriate type material, we revise the complex of three common species of the ophiuroid genus Ophiacantha which have been persistently confused with each other. The present study thus reveals the previously unrecognized new species Ophiacantha kokusai sp.nov. which is commonly distributed off the Pacific coast of Japan. The new species shows developmental differentiation from the closely related species Ophiacantha rhachophora H. L. Clark, 1911 and retains clearly expressed early juvenile features in the adult morphology. Another species, Ophiacantha clypeata Kyte, 1977, which had been separated from O. rhachophora, is in turn shown to be just a juvenile stage of another North Pacific species, Ophiacantha trachybactra H.L. Clark, 1911. For every species, detailed morphological data from both adult and juvenile specimens based on scanning electron microscopy are presented. A special grinding method showing complex internal features has been utilized for the first time. For all three species in this complex, a clear bathymetric differentiation is revealed: O. rhachophora predominantly inhabits shallow waters, 0-250 m, the new species O. kokusai lives deeper, at 250-600 m, and the third species, O. trachybactra, is found at 500-2,000 m. The present case clearly highlights the importance of considering developmental transformations, not only for a limited number of model organisms, but as part of the taxonomic process.

Troglomorphism in the middle Triassic crinoids from Poland

In this paper, we document the Middle Triassic marine fauna recovered from the fissure/cave system of Stare Gliny (southern Poland) developed in the Devonian host dolomite. The fossils are mostly represented by in situ preserved and small-sized holdfasts of crinoids (Crinoidea) that are attached to the cave walls. Other fossils found in the cave infills include articulated brittle stars and brachiopods. Our findings constitute the oldest Mesozoic evidence for troglophile crinoids. We suggest that troglomorphism in these echinoderms was likely related to protection against predation, which underscores the magnitude of anti-predatory adaptations to increased predation pressure that occurred during the Early Mesozoic Marine Revolution.

Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa

Echinoderms (sea urchins, sea stars, brittle stars, sea lilies and sea cucumbers) are a group of diverse organisms, second in number within deuterostome species to only the chordates. Echinoderms serve as excellent model systems for developmental biology due to their diverse developmental mechanisms, tractable laboratory use, and close phylogenetic distance to chordates. In addition, echinoderms are very well represented in the fossil record, including some larval features, making echinoderms a valuable system for studying evolutionary development. The internal relationships of Echinodermata have not been consistently supported across phylogenetic analyses, however, and this has hindered the study of other aspects of their biology. In order to test echinoderm phylogenetic relationships, we sequenced 23 de novo transcriptomes from all five clades of echinoderms. Using multiple phylogenetic methods at a variety of sampling depths we have constructed a well-supported phylogenetic tree of Echinodermata, including support for the sister groups of Asterozoa (sea stars and brittle stars) and Echinozoa (sea urchins and sea cucumbers). These results will help inform developmental and evolutionary studies specifically in echinoderms and deuterostomes in general.

Conservation of sequence and function in fertilization of the cortical granule serine protease in echinoderms

Conservation of the cortical granule serine protease during fertilization in echinoderms was tested both functionally in sea stars, and computationally throughout the echinoderm phylum. We find that the inhibitor of serine protease (soybean trypsin inhibitor) effectively blocks proper transition of the sea star fertilization envelope into a protective sperm repellent, whereas inhibitors of the other main types of proteases had no effect. Scanning the transcriptomes of 15 different echinoderm ovaries revealed sequences of high conservation to the originally identified sea urchin cortical serine protease, CGSP1. These conserved sequences contained the catalytic triad necessary for enzymatic activity, and the tandemly repeated LDLr-like repeats. We conclude that the protease involved in the slow block to polyspermy is an essential and conserved element of fertilization in echinoderms, and may provide an important reagent for identification and testing of the cell surface proteins in eggs necessary for sperm binding.

Oral region homologies in paleozoic crinoids and other plesiomorphic pentaradial echinoderms

The phylogenetic relationships between major groups of plesiomorphic pentaradial echinoderms, the Paleozoic crinoids, blastozoans, and edrioasteroids, are poorly understood because of a lack of widely recognized homologies. Here, we present newly recognized oral region homologies, based on the Universal Elemental Homology model for skeletal plates, in a wide range of fossil taxa. The oral region of echinoderms is mainly composed of the axial, or ambulacral, skeleton, which apparently evolved more slowly than the extraxial skeleton that forms the majority of the body. Recent phylogenetic hypotheses have focused on characters of the extraxial skeleton, which may have evolved too rapidly to preserve obvious homologies across all these groups. The axial skeleton conserved homologous suites of characters shared between various edrioasteroids and specific blastozoans, and between other blastozoans and crinoids. Although individual plates can be inferred as homologous, no directly overlapping suites of characters are shared between edrioasteroids and crinoids. Six different systems of mouth (peristome) plate organization (Peristomial Border Systems) are defined. These include four different systems based on the arrangement of the interradially-positioned oral plates and their peristomial cover plates, where PBS A1 occurs only in plesiomorphic edrioasteroids, PBS A2 occurs in plesiomorphic edrioasteroids and blastozoans, and PBS A3 and PBS A4 occur in blastozoans and crinoids. The other two systems have radially-positioned uniserial oral frame plates in construction of the mouth frame. PBS B1 has both orals and uniserial oral frame plates and occurs in edrioasterid and possibly edrioblastoid edrioasteroids, whereas PBS B2 has exclusively uniserial oral frame plates and is found in isorophid edrioasteroids and imbricate and gogiid blastozoans. These different types of mouth frame construction offer potential synapomorphies to aid in parsimony-based phylogenetics for exploring branching order among stem groups on the echinoderm tree of life.

[Composition and structure of the macrofauna associated with beds of two bivalve species in Cubagua Island, Venezuela]

Bivalve aggregations constitute a microhabitat for a wide variety of organisms in intertidal, subtidal and deep-water marine benthic habitats. Increase in density of bivalve beds could offer more crevices and substratum for the associated fauna, affecting community composition. Beds of the Atlantic Pearl Oyster (Pinctada imbricata) and the Turkey Wing (Arca zebra) of contrasting population densities were evaluated to determine the composition and structure of the associated macrofauna of three taxa (Crustacea Decapoda, Mollusca and Echinodermata). We evaluated plots of three levels of bed density in both species, the associated fauna were identified and counted. Other species were collected by qualitative samples. Univariate and multivariate descriptors were tested comparing the associated fauna between the beds of two species at three levels of density. In these beds a total of 104 species belonging to 58 families were recorded. Mithraculus forceps (Majidae), Crucibulum auricula (Calyptraeidae) and Ophiotrix angulata (Ophiothrichidae) were the most common species found in these assemblages. The medium and high-density bivalve beds exhibited greater species number, abundance, Shannon diversity, evenness, taxonomic diversity, and taxonomic distinctness of associated fauna, than low-density bivalve beds. Moreover, multivariate analysis detected different assemblages of associated fauna between beds with different densities. Additionally, similarities were found in the communities of macrofauna in both beds of P imbricata and Area zebra. Our results suggest that bivalve aggregations at Cubagua Island provide additional habitat for macrofauna living in other shallow habitats such as Thalassia beds, corals and rocky environments. Bed density, associated with topographic complexity, represents an important factor for the composition and complexity of the associated fauna.

Ancient origin of the modern deep-sea fauna

The origin and possible antiquity of the spectacularly diverse modern deep-sea fauna has been debated since the beginning of deep-sea research in the mid-nineteenth century. Recent hypotheses, based on biogeographic patterns and molecular clock estimates, support a latest Mesozoic or early Cenozoic date for the origin of key groups of the present deep-sea fauna (echinoids, octopods). This relatively young age is consistent with hypotheses that argue for extensive extinction during Jurassic and Cretaceous Oceanic Anoxic Events (OAEs) and the mid-Cenozoic cooling of deep-water masses, implying repeated re-colonization by immigration of taxa from shallow-water habitats. Here we report on a well-preserved echinoderm assemblage from deep-sea (1000-1500 m paleodepth) sediments of the NE-Atlantic of Early Cretaceous age (114 Ma). The assemblage is strikingly similar to that of extant bathyal echinoderm communities in composition, including families and genera found exclusively in modern deep-sea habitats. A number of taxa found in the assemblage have no fossil record at shelf depths postdating the assemblage, which precludes the possibility of deep-sea recolonization from shallow habitats following episodic extinction at least for those groups. Our discovery provides the first key fossil evidence that a significant part of the modern deep-sea fauna is considerably older than previously assumed. As a consequence, most major paleoceanographic events had far less impact on the diversity of deep-sea faunas than has been implied. It also suggests that deep-sea biota are more resilient to extinction events than shallow-water forms, and that the unusual deep-sea environment, indeed, provides evolutionary stability which is very rarely punctuated on macroevolutionary time scales.

Plated Cambrian bilaterians reveal the earliest stages of echinoderm evolution

Echinoderms are unique in being pentaradiate, having diverged from the ancestral bilaterian body plan more radically than any other animal phylum. This transformation arises during ontogeny, as echinoderm larvae are initially bilateral, then pass through an asymmetric phase, before giving rise to the pentaradiate adult. Many fossil echinoderms are radial and a few are asymmetric, but until now none have been described that show the original bilaterian stage in echinoderm evolution. Here we report new fossils from the early middle Cambrian of southern Europe that are the first echinoderms with a fully bilaterian body plan as adults. Morphologically they are intermediate between two of the most basal classes, the Ctenocystoidea and Cincta. This provides a root for all echinoderms and confirms that the earliest members were deposit feeders not suspension feeders.

Global diversity and phylogeny of the Asteroidea (Echinodermata)

Members of the Asteroidea (phylum Echinodermata), popularly known as starfish or sea stars, are ecologically important and diverse members of marine ecosystems in all of the world's oceans. We present a comprehensive overview of diversity and phylogeny as they have figured into the evolution of the Asteroidea from Paleozoic to the living fauna. Living post-Paleozoic asteroids, the Neoasteroidea, are morphologically separate from those in the Paleozoic. Early Paleozoic asteroid faunas were diverse and displayed morphology that foreshadowed later living taxa. Preservation presents significant difficulties, but fossil occurrence and current accounts suggests a diverse Paleozoic fauna, which underwent extinction around the Permian-Triassic interval was followed by re-diversification of at least one surviving lineage. Ongoing phylogenetic classification debates include the status of the Paxillosida and the Concentricycloidea. Fossil and molecular evidence has been and continues to be part of the ongoing evolution of asteroid phylogenetic research. The modern lineages of asteroids include the Valvatacea, the Forcipulatacea, the Spinlosida, and the Velatida. We present an overview of diversity in these taxa, as well as brief notes on broader significance, ecology, and functional morphology of each. Although much asteroid taxonomy is stable, many new taxa remain to be discovered with many new species currently awaiting description. The Goniasteridae is currently one of the most diverse families within the Asteroidea. New data from molecular phylogenetics and the advent of global biodiversity databases, such as the World Asteroidea Database (http://www.marinespecies.org/Asteroidea/) present important new springboards for understanding the global biodiversity and evolution of asteroids.

Global diversity of brittle stars (Echinodermata: Ophiuroidea)

This review presents a comprehensive overview of the current status regarding the global diversity of the echinoderm class Ophiuroidea, focussing on taxonomy and distribution patterns, with brief introduction to their anatomy, biology, phylogeny, and palaeontological history. A glossary of terms is provided. Species names and taxonomic decisions have been extracted from the literature and compiled in The World Ophiuroidea Database, part of the World Register of Marine Species (WoRMS). Ophiuroidea, with 2064 known species, are the largest class of Echinodermata. A table presents 16 families with numbers of genera and species. The largest are Amphiuridae (467), Ophiuridae (344 species) and Ophiacanthidae (319 species). A biogeographic analysis for all world oceans and all accepted species was performed, based on published distribution records. Approximately similar numbers of species were recorded from the shelf (n = 1313) and bathyal depth strata (1297). The Indo-Pacific region had the highest species richness overall (825 species) and at all depths. Adjacent regions were also relatively species rich, including the North Pacific (398), South Pacific (355) and Indian (316) due to the presence of many Indo-Pacific species that partially extended into these regions. A secondary region of enhanced species richness was found in the West Atlantic (335). Regions of relatively low species richness include the Arctic (73 species), East Atlantic (118), South America (124) and Antarctic (126).

Pelagic crinoids (Roveacrinida, Crinoidea) discovered in the Neogene of Poland

Until recently, it has been assumed that pelagic crinoids, the roveacrinids (Roveacrinida, Crinoidea), became extinct during the Cretaceous-Paleogene boundary event. Recent finds of well-preserved roveacrinidal remains (brachials and radials) in the Danian (Early Paleogene) of Poland showed that they survived into the earliest Cenozoic. This group was thus characterized as a "dead clade walking". Here, we present fossil evidence that these pelagic crinoids survived in Poland until at least the Middle Miocene (Badenian, ca. 14 Myr ago)-more than 50 Myr after their supposed extinction. These Miocene roveacrinids constitute the first documented evidence of Roveacrinida in strata of Neogene age, thus prolonging the stratigraphic range of pelagic crinoids. This find characterizes the order as a "Lazarus taxon" rather than a "dead clade walking" group.

Influence of Diadema antillarum populations (Echinodermata: Diadematidae) on algal community structure in Jardines de la Reina, Cuba

The 1983-1984 mass mortality of Diadema antillarum produced severe damages on Caribbean reefs contributing to substantial changes in community structure that still persist. Despite the importance of Diadema grazing in structuring coral reefs, available information on current abundances and algal-urchin interactions in Cuba is scarce. We analyzed spatial variations in Diadema abundance and its influence on algal community structure in 22 reef sites in Jardines de la Reina, in June/2004 and April/2005. Urchins were counted in five 30 x 2m transects per site, and algal coverage was estimated in randomly located 0.25m side quadrats (15 per site). Abundances of Diadema were higher at reef crests (0.013-1.553 ind/m2), while reef slope populations showed values up to three orders of magnitude lower and were overgrown by macroalgae (up to 87%, local values). Algal community structure at reef slopes were dominated by macroalgae, especially Dictyota, Lobophora and Halimeda while the most abundant macroalgae at reef crests were Halimeda and Amphiroa. Urchin densities were negatively and positively correlated with mean coverage of macroalgae and crustose coralline algae, respectively, when analyzing data pooled across all sites, but not with data from separate habitats (specially reef crest), suggesting, along with historical fish biomass, that shallow reef community structure is being shaped by the synergistic action of other factors (e.g. fish grazing) rather than the influence of Diadema alone. However, we observed clear signs of Diadema grazing at reef crests and decreased macroalgal cover according to 2001 data, what suggest that grazing intensity at this habitat increased at the same time that Diadema recruitment began to be noticeable. Furthermore, the excessive abundance of macroalgae at reef slopes and the scarcity of crustose coralline algae seems to be due by the almost complete absence of D. antillarum at mid depth reefs, where local densities of this urchin were predominantly low.

Large-scale spatial distribution patterns of echinoderms in nearshore rocky habitats

This study examined echinoderm assemblages from nearshore rocky habitats for large-scale distribution patterns with specific emphasis on identifying latitudinal trends and large regional hotspots. Echinoderms were sampled from 76 globally-distributed sites within 12 ecoregions, following the standardized sampling protocol of the Census of Marine Life NaGISA project (www.nagisa.coml.org). Sample-based species richness was overall low (<1-5 species per site), with a total of 32 asteroid, 18 echinoid, 21 ophiuroid, and 15 holothuroid species. Abundance and species richness in intertidal assemblages sampled with visual methods (organisms >2 cm in 1 m(2) quadrats) was highest in the Caribbean ecoregions and echinoids dominated these assemblages with an average of 5 ind m(-2). In contrast, intertidal echinoderm assemblages collected from clearings of 0.0625 m(2) quadrats had the highest abundance and richness in the Northeast Pacific ecoregions where asteroids and holothurians dominated with an average of 14 ind 0.0625 m(-2). Distinct latitudinal trends existed for abundance and richness in intertidal assemblages with declines from peaks at high northern latitudes. No latitudinal trends were found for subtidal echinoderm assemblages with either sampling technique. Latitudinal gradients appear to be superseded by regional diversity hotspots. In these hotspots echinoderm assemblages may be driven by local and regional processes, such as overall productivity and evolutionary history. We also tested a set of 14 environmental variables (six natural and eight anthropogenic) as potential drivers of echinoderm assemblages by ecoregions. The natural variables of salinity, sea-surface temperature, chlorophyll a, and primary productivity were strongly correlated with echinoderm assemblages; the anthropogenic variables of inorganic pollution and nutrient contamination also contributed to correlations. Our results indicate that nearshore echinoderm assemblages appear to be shaped by a network of environmental and ecological processes, and by the differing responses of various echinoderm taxa, making generalizations about the patterns of nearshore rocky habitat echinoderm assemblages difficult.

Temporal and spatial distribution patterns of echinoderm larvae in La Parguera, Puerto Rico

This study describes temporal and spatial abundance patterns of echinoderm larvae in La Parguera, Puerto Rico. For the temporal study, larvae were sampled by a series of monthly tows taken with a 64 microm mesh net between the new and full moon from April 2005 to July 2006, September 2006 and August 2007. In order to measure spatial variation of echinoderm larval abundances, oblique tows were taken with 64 and 202 microm mesh nets at seven different sites within the shelf, at the shelf-edge, and at a nearby oceanic stations during August 2007. Overall, Echinoidea (sea urchin) exhibited the highest abundance with a total of 11 921 larvae, representing 52.5% of the total collection. Ophiuroidea (brittle star) ranked second in abundance with 45.6% of the total larvae. Holothuroidea (sea cucumber) and Asteroidea larvae (sea star) accounted for less than 2% of the total echinoderm larval collection. Early larval stages (2-8 day old) of Diadema antillarum represented 20% of the total Echinoidea larvae. There was no marked seasonal trend of echinoderm larval abundance; Echinoidea and Ophiuroidea larvae were present in all monthly samples indicating that reproduction occurs year-round. Peak abundances of later-stage Echinoidea larvae were observed during January, July and October and of later-stage Ophiuroidea larvae during June, August and October. The observed peaks of later-stage larval abundances may be indicative of higher recruitment activity during these months. There was a significant difference of echinoderm larval abundance between spatial stations, with higher abundances collected at the shelf-edge. Later-stage (approximately 24 day old) D. antillarum larvae were mostly collected at shelf-edge and oceanic locations. In addition, the 64 microm mesh net was more efficient for collection of echinoderm larvae than the 202 microm mesh net.

Echinoderms: potential model systems for studies on muscle regeneration

Organisms of the phylum Echinodermata show some of the most impressive regenerative feats within the animal kingdom. Following injury or self-induced autotomy, species in this phylum can regenerate most tissues and organs, being the regeneration of the muscular systems one of the best studied. Even though echinoderms are closely related to chordates, they are little known in the biomedical field, and therefore their uses to study pharmacological effects on muscle formation and/or regeneration have been extremely limited. In order to rectify this lack of knowledge, we describe here the echinoderm muscular systems, particularly the somatic and visceral muscle components. In addition, we provide details of the processes that are known to take place during muscle regeneration, namely dedifferentiation, myogenesis and new muscle formation. Finally, we provide the available information on molecular and pharmacological studies that involve echinoderm muscle regeneration. We expect that by making this information accessible, researchers consider the use of echinoderms as model systems for pharmacological studies in muscle development and regeneration.

[The role of heterochrony in the establishment of archetype in higher Echinoderm taxa]

The analysis based on paleontological data shows that the body plans of higher echinoderm taxa were established through the combination of previously developed characters. These combinations appeared due to various heterochronies and resulted in more or less complete filling of the morphological space of logical capabilities. The maximum rank of new taxa decreased with time. New body plans of higher taxa did not replace the old plans but rather overlay them, extending the hierarchy of body plans and the respective hierarchy of taxa. The macroevolution of echinoderms and other metazoans progressed from the formation of an archetype (a general body plan) to individual details, the development of structural plans of lower levels. Heterochrony resulted in mosaic evolution and obscurity of intermediate forms.

Apical organs in echinoderm larvae: insights into larval evolution in the Ambulacraria

The anatomy and cellular organization of serotonergic neurons in the echinoderm apical organ exhibits class-specific features in dipleurula-type (auricularia, bipinnaria) and pluteus-type (ophiopluteus, echinopluteus) larvae. The apical organ forms in association with anterior ciliary structures. Apical organs in dipleurula-type larvae are more similar to each other than to those in either of the pluteus forms. In asteroid bipinnaria and holothuroid auricularia the apical organ spans ciliary band sectors that traverse the anterior-most end of the larvae. The asteroid apical organ also has prominent bilateral ganglia that connect with an apical network of neurites. The simple apical organ of the auricularia is similar to that in the hemichordate tornaria larva. Apical organs in pluteus forms differ markedly. The echinopluteus apical organ is a single structure on the oral hood between the larval arms comprised of two groups of cells joined by a commissure and its cell bodies do not reside in the ciliary band. Ophioplutei have a pair of lateral ganglia associated with the ciliary band of larval arms that may be the ophiuroid apical organ. Comparative anatomy of the serotonergic nervous systems in the dipleurula-type larvae of the Ambulacraria (Echinodermata+Hemichordata) suggests that the apical organ of this deuterostome clade originated as a simple bilaterally symmetric nerve plexus spanning ciliary band sectors at the anterior end of the larva. From this structure, the apical organ has been independently modified in association with the evolution of class-specific larval forms.

[Amphioxus: how to become a vertebrate]

Evo-devo is a young disciplin, which aims to explain the morphological evolution of organisms through developmental mechanisms and genes networks. A major question within this discipline is the origin of vertebrates. It seems now admitted that vertebrates derive from an invertebrate chordate ancestor. Several models among living chordate representatives are used today to answer this question. The small world of evo-evo interested in the emergence of vertebrates is ebullient about the advent of several totally sequenced genomes allowing comparative analyses to become evermore reliable. Furthermore "non classical" models are developed which can be submitted to refined developmental analysis. One of these is amphioxus (genus Branchyostoma), "a peaceful anchory fillet to illuminate chordate evolution" (Garcia-Fernandez, 2006a, b). The features of this model are described in this review.

Ribosomal RNA genes and deuterostome phylogeny revisited: More cyclostomes, elasmobranchs, reptiles, and a brittle star

This is an expanded study of the relationships among the deuterostome animals based on combined, nearly complete 28S and 18S rRNA genes (>3925 nt.). It adds sequences from 20 more taxa to the approximately 45 sequences used in past studies. Seven of the new taxa were sequenced here (brittle star Ophiomyxa, lizard Anolis, turtle Chrysemys, sixgill shark Hexanchus, electric ray Narcine, Southern Hemisphere lamprey Geotria, and Atlantic hagfish Myxine for 28S), and the other 13 were from GenBank and the literature (from a chicken, dog, rat, human, three lungfishes, and several ray-finned fishes, or Actinopterygii). As before, our alignments were based on secondary structure but did not account for base pairing in the stems of rRNA. The new findings, derived from likelihood-based tree-reconstruction methods and by testing hypotheses with parametric bootstrapping, include: (1) brittle star joins with sea star in the echinoderm clade, Asterozoa; (2) with two hagfishes and two lampreys now available, the cyclostome (jawless) fishes remain monophyletic; (3) Hexanchiform sharks are monophyletic, as Hexanchus groups with the frilled shark, Chlamydoselachus; (4) turtle is the sister taxon of all other amniotes; (5) bird is closer to the lizard than to the mammals; (6) the bichir Polypterus is in a monophyletic Actinopterygii; (7) Zebrafish Danio is the sister taxon of the other two teleosts we examined (trout and perch); (8) the South American and African lungfishes group together to the exclusion of the Australian lungfish. Other findings either upheld those of the previous rRNA-based studies (e.g., echinoderms and hemichordates group as Ambulacraria; orbitostylic sharks; batoids are not derived from any living lineage of sharks) or were obvious (monophyly of mammals, gnathostomes, vertebrates, echinoderms, etc.). Despite all these findings, the rRNA data still fail to resolve the relations among the major groups of deuterostomes (tunicates, Ambulacraria, cephalochordates and vertebrates) and of gnathostomes (chondrichthyans, lungfishes, coelacanth, actinopterygians, amphibians, and amniotes), partly because tunicates and lungfishes are rogue taxa that disrupt the tree. Nonetheless, parametric bootstrapping showed our RNA-gene data are only consistent with these dominant hypotheses: (1) deuterostomes consist of Ambulacraria plus Chordata, with Chordata consisting of tunicates and 'vertebrates plus cephalochordates'; and (2) lungfishes are the closest living relatives of tetrapods.

The echinoderm adhesome

Although the development of sea urchin embryos has been studied extensively and clearly involves both cell adhesion and cell migration, rather little is known about the adhesion receptors and extracellular matrix molecules involved. The completion of the genome of Strongylocentrotus purpuratus allows a comprehensive survey of the complement of cell-cell and cell-matrix adhesion molecules in this organism. Furthermore, the phylogenetic position of echinoderms offers the opportunity to compare the complement of adhesion proteins between protostome and deuterostome invertebrates and between invertebrate and vertebrate deuterostomes. Many aspects of development and cell interactions differ among these different taxa and it is likely that analysis of the spectrum of adhesion receptors and extracellular matrix proteins can open up new insights into which molecules have evolved to suit particular developmental processes. In this paper, we report the results of an initial analysis along these lines. The echinoderm adhesome (complement of adhesion-related genes/proteins) is similar overall to that of other invertebrates although there are significant deuterostome-specific innovations and some interesting features previously thought to be chordate or vertebrate specific.

Genetic connectivity in the Florida reef system: comparative phylogeography of commensal invertebrates with contrasting reproductive strategies

Effective spatial management of coral reefs including design of marine protected areas requires an understanding of interpopulation genetic connectivity. We assessed gene flow along 355 km of the Florida reef system and between Florida and Belize in three commensal invertebrates occupying the same host sponge (Callyspongia vaginalis) but displaying contrasting reproductive dispersal strategies: the broadcast-spawning brittle star Ophiothrix lineata and two brooding amphipods Leucothoe kensleyi and Leucothoe ashleyae. Multiple analytical approaches to sequence variation in the mitochondrial COI gene demonstrated a high degree of overall connectivity for all three species along the Florida reef system. Ophiothrix lineata showed significant genetic structuring between Florida and Belize, and a pattern of isolation by distance but no significant genetic structuring along the Florida coastline. Bayesian estimates of migration detected a strong southerly dispersal bias for O. lineata along the Florida reef system, contrary to the general assumption of northerly gene flow in this region based on the direction of the Florida Current. Both amphipods, despite direct development, also showed high gene flow along the Florida reef system. Multiple inferences of long-distance dispersal from a nested clade analysis support the hypothesis that amphipod transport, possibly in detached sponge fragments, could generate the high levels of overall gene flow observed. However, this transport mechanism appears much less effective across deep water as connectivity between Florida and Belize (1072 km) is highly restricted.

The active evolutionary lives of echinoderm larvae

Echinoderms represent a researchable subset of a dynamic larval evolutionary cosmos. Evolution of echinoderm larvae has taken place over widely varying time scales from the origins of larvae of living classes in the early Palaeozoic, approximately 500 million years ago, to recent, rapid and large-scale changes that have occurred within living genera within a span of less than a million years to a few million years. It is these recent evolutionary events that offer a window into processes of larval evolution operating at a micro-evolutionary level of evolution of discrete developmental mechanisms. We review the evolution of the diverse larval forms of living echinoderms to outline the origins of echinoderm larval forms, their diversity among living echinoderms, molecular clocks and rates of larval evolution, and finally current studies on the roles of developmental regulatory mechanisms in the rapid and radical evolutionary changes observed between closely related congeneric species.

Sclerites in Different Tissues of Mediterranean Echinodermata

The presence of sclerites in different mesodermal tissues was studied in thirteen species of Mediterranean echinoderms representing the five living classes. In the species of Asteroidea and Crinoidea examined, sclerites were present only in specific tissues. In the species of Ophiuroidea and, especially, Echinoidea and Holothuroidea examined, sclerites were present in almost every tissue, but with considerable variation among species and tissues. Data on sclerite shape, size, and relative abundance (measured as tissue abundance) are presented. The data support the possible functional role of sclerites as reinforcing structures, as well as their possible use as taxonomic characters. Finally, the need of more studies to elucidate the ontogenetic and phylogenetic implications of sclerites is discussed.

The complete mitochondrial genomes of the sea lily Gymnocrinus richeri and the feather star Phanogenia gracilis: Signature nucleotide bias and unique nad4L gene rearrangement within crinoids

Complete DNA sequences have been determined for the mitochondrial genomes of the crinoids Phanogenia gracilis (15892 bp) and Gymnocrinus richeri (15966 bp). The mitochondrial genetic map of the stalkless feather star P. gracilis is identical to that of the comatulid feather star Florometra serratissima (Scouras, A., Smith, M.J., 2001. Mol. Biol. Evol. 18, 61-73). The mitochondrial gene order of the stalked crinoid G. richeri differs from that of F. serratissima and P. gracilis by the transposition of the nad4L protein gene. The G. richeri nad4L mitochondrial map position is unique among metazoa and is likely a derived feature in this stalked crinoid. Nucleotide compositional analyses of protein genes encoded on the major sense strand confirm earlier conclusions regarding a crinoid-distinctive T over C bias. All three crinoids exhibit high T levels in third codon positions, whereas other echinoderm classes favor A or C in the third codon position. The nucleotide bias is reflected in the relative synonymous codon usage patterns of crinoids versus other echinoderms. We suggest that the nucleotide bias of crinoids, in comparison to other echinoderms, indicates that a physical inversion of the origin of replication has occurred in the crinoid lineage. Evolutionary rate tests support the use of the cytochrome b (cob) gene in molecular phylogenetic analyses of echinoderms. A consensus echinoderm tree was generated based on cytochrome b nucleotide alignments that placed the asteroids as a sister group to a clade containing the ophiuroids and the (echinoids+holothuroids) with the crinoids basal to the rest of the echinoderm classes: [Crinoid,(Asteroid,(Ophiuroid,(Echinoid,Holothuroid)))].

Metaphylogeny of 82 gene families sheds a new light on chordate evolution

Achieving a better comprehension of the evolution of species has always been an important matter for evolutionary biologists. The deuterostome phylogeny has been described for many years, and three phyla are distinguishable: Echinodermata (including sea stars, sea urchins, etc...), Hemichordata (including acorn worms and pterobranchs), and Chordata (including urochordates, cephalochordates and extant vertebrates). Inside the Chordata phylum, the position of vertebrate species is quite unanimously accepted. Nonetheless, the position of urochordates in regard with vertebrates is still the subject of debate, and has even been suggested by some authors to be a separate phylum from cephalochordates and vertebrates. It was also the case for agnathans species -myxines and hagfish- for which phylogenetic evidence was recently given for a controversial monophyly. This raises the following question: which one of the cephalochordata or urochordata is the sister group of vertebrates and what are their relationships? In the present work, we analyzed 82 protein families presenting homologs between urochordata and other deuterostomes and focused on two points: 1) testing accurately the position of urochordata and cephalochordata phyla in regard with vertebrates as well as chordates monophyly, 2) performing an estimation of the rate of gene loss in the Ciona intestinalis genome. We showed that the urochordate phyla is the vertebrate sister group and that gene loss played a major role in structuring the urochordate genome.

Butyltin species in benthic and pelagic organisms of the Saguenay Fjord (Canada) and Imposex occurrence in common whelk (Buccinum undatum)

The distribution and accumulation of butyltins in various tissues of 13 benthic and pelagic species living in the sub-Arctic Saguenay Fjord (Canada) were investigated. Butyltin contamination was ubiquitous in this ecosystem with tributyltin (TBT) biota to sediment accumulation factors (BSAF) ranging between 0.22 and 11, but without any important biomagnification between trophic levels. The large range of butyltin compounds accumulating within different tissues of the species collected from all trophic levels was from 7 to 1238 ng Sn g(-1) d.w. and indicates an exceptional contamination level only found in northern coastal areas exposed to an intensive traffic of commercial ships. Results show that bioaccumulation in organisms depends on three main factors: (1) the actual contamination level in their habitat, (2) their assimilation pathway by water, sediment or diet, and (3) their ability to metabolize TBT and excrete metabolites. By their lack of an efficient TBT degradation system, bivalves are subject to accumulate more butyltins (from 890 to 993 ng Sn g(-1) d.w. for TBT and from n.d to 138 ng Sn g(-1) d.w. for metabolites) whereas most burrow-dwelling organisms are able to degrade TBT and their butyltin levels ranged from 86 to 239 ng Sn g(-1) d.w. for TBT and from 7 to 106 ng Sn g(-1) d.w. for metabolites. Acadian redfish (Sebastes fasciatus) feeding preferentially on shrimps and small crustaceans rich in TBT showed a contamination level about three times higher than eelpout (Licodes vahlii). The latter species living in contact with the sediment and feeding on worms and other burrowing species had a lower proportion of TBT in their tissues. Finally, deleterious effects of butyltins in the Saguenay Fjord were assessed by the significant occurrence of Imposex in common whelk (Bucinum undatum) in two sites from Baie des Ha! Ha!. Results revealed that the effects of Imposex were accentuated close to the source of contamination, at Port-Alfred harbour, since the total of imposexed whelks collected at site A (the mouth of Baie des Ha! Ha!) was 12.5% and reached 52.6% at site B (Port Alfred). Although the incidence or frequency of imposex was low in site A compared to site B, the relative penile length index (RPL) values, a measure of the degree or severity of imposex, was similar at both sites indicating the presence of TBT with higher concentrations in site B.

The phylogenetic status of Paxillosida (Asteroidea) based on complete mitochondrial DNA sequences

One of the most important issues in asteroid phylogeny is the phylogenetic status of Paxillosida. This group lacks an anus and suckers on the tube feet in adults and does not develop the brachiolaria stage in early development. Two controversial hypotheses have been proposed for the phylogenetic status of Paxillosida, i.e., Paxillosida is primitive or rather specialized in asteroids. In this study, we determined the complete mitochondrial DNA nucleotide sequences from two paxillosidans (Astropecten polyacanthus and Luidia quinaria) and one forcipulatidan (Asterias amurensis). The mitochondrial genomes of the three asteroids were identical with respect to gene order and transcription direction, and were identical to the previously reported mitochondrial genomes of Asterina pectinifera (Valvatida) and Pisaster ochraceus (Forcipulatida) in this respect. Therefore, the comparison of genome structures was uninformative for the purposes of asteroid phylogeny. However, molecular phylogenetic analyses based on the amino acid sequences and the nucleotide sequences from the five asteroids supported the monophyly of the clade that included the two paxillosidans and Asterina. This suggests that the paxillosidan characters are secondarily derived ones.

Palaeoanatomy and biological affinities of a Cambrian deuterostome (Stylophora)

Stylophora are a peculiar extinct group of asymmetrical deuterostomes whose biological affinity has been fiercely debated. Disarticulated skeletal elements of a ceratocystid stylophoran recovered from the earliest Middle Cambrian of Morocco are not only the oldest stylophorans in the fossil record, but their exceptional preservation provides crucial data on the microstructure of its skeleton. Stylophoran plates are constructed of a three-dimensional mesh, termed 'stereom', identical to that of living echinoderms in which stereom microstructure provides a reliable guide to the nature of the investing soft tissues. Using modern echinoderm anatomy to interpret stereom microstructure of stylophoran elements, here we show that the large proximal lumen of their appendage was filled with muscle and that ligamentary tissues bound distal elements firmly together. We find no evidence for a mouth in the proximal lumen and no evidence that the covering plates of the appendage were articulated. Thus, although skeletal structure suggests that stylophorans are echinoderms, their appendage was not a feeding arm but a muscular locomotory organ.

[Echinoderms (Echinodermata) from the Gulf of California, Mexico]

A systematic list of the echinoderms of the Gulf of California, based on museum specimens of the Colección Nacional de Equinodermos, Instituto de Ciencias del Mar y Limnologia, Universidad Nacional Autónoma de México and the National Museum of Natural History, Smithsonian Institution, Washington, D.C. is presented. A total of 193 echinoderm species is recorded, distributed in 108 genera, 51 families and 19 orders. 12 new records for the Gulf of California are presented: Asteroidea (four), Ophiuroidea (three) and Holothuroidea (five).