Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept

Based on embryological and morphological evidence, Lophophorata was long considered to be the sister or paraphyletic stem group of Deuterostomia. By contrast, molecular data have consistently indicated that the three lophophorate lineages, Ectoprocta, Brachiopoda and Phoronida, are more closely related to trochozoans (annelids, molluscs and related groups) than to deuterostomes. For this reason, the lophophorate groups and Trochozoa were united to Lophotrochozoa. However, the relationships of the lophophorate lineages within Lophotrochozoa are still largely unresolved. Maximum-likelihood and Bayesian analyses were performed based on a dataset comprising 11,445 amino acid positions derived from 79 ribosomal proteins of 39 metazoan taxa including new sequences obtained from a brachiopod and a phoronid. These analyses show that the three lophophorate lineages are affiliated with trochozoan rather than deuterostome phyla. All hypotheses claiming that they are more closely related to Deuterostomia than to Protostomia can be rejected by topology testing. Monophyly of lophophorates was not recovered but that of Bryozoa including Ectoprocta and Entoprocta and monophyly of Brachiozoa including Brachiopoda and Phoronida were strongly supported. Alternative hypotheses that are refuted include (i) Brachiozoa as the sister group of Mollusca, (ii) ectoprocts as sister to all other Lophotrochozoa including Platyzoa, and (iii) ectoprocts as sister or to all other protostomes except chaetognaths.     

Phylogenetic analysis of higher taxa of Brachiopoda

Inferred phylogenetic relationships within the Brachiopoda have long been accepted as demonstrating repeated transitions from a phosphatic shell chemistry to a calcareous composition. This interpretation is reflected in the major subdivision of the phylum into the classes Inarticulata and Articulata. Cladistic analysis suggests, however, that the phosphatic-shelled and the calcareous-shelled Brachiopoda are sister groups that have had consistently separated shell chemistries from early in phylogenetic history. This separation is recognized in the class-rank divisions Lingulata and Calciata, the former of which includes the new Subclass Lingulatea, whilst the latter includes the new Subclass Craniformea together with the 'articulates' of previous classifications. □Brachiopoda, cladistic analysis, Lingulata, Lingulatea, Calciata, Craniformea.     

A soft-bodied lophophorate from the Silurian of England

Soft-bodied taxa comprise an important component of the extant lophophorate fauna, but convincing fossils of soft-bodied lophophorates are extremely rare. A small fossil lophophorate, attached to a brachiopod dorsal valve, is described from the Silurian (Wenlock Series) Herefordshire Lagerstätte of England. This unmineralized organism was bilaterally symmetrical and comprised a subconical body attached basally to the host and partially enclosed by a broad ‘hood’; the body bore a small, coiled lophophore. Where the hood attached laterally, there is a series of transverse ridges and furrows. The affinities of this organism probably lie with Brachiopoda; the hood is interpreted as the homologue of a dorsal valve/mantle lobe, and the attachment as the homologue of the ventral valve and/or pedicle. The ridges are arranged in a manner that suggests constructional serial repetition, indicating that they are unlikely to represent mantle canals. Extant brachiopods are not serially structured, but morphological and molecular evidence suggests that their ancestors were. The new organism may belong to the brachiopod stem group, and might also represent a significant element of the Palaeozoic lophophorate fauna.     

Multigene analysis of lophophorate and chaetognath phylogenetic relationships

Maximum likelihood and Bayesian inference analyses of seven concatenated fragments of nuclear-encoded housekeeping genes indicate that Lophotrochozoa is monophyletic, i.e., the lophophorate groups Bryozoa, Brachiopoda and Phoronida are more closely related to molluscs and annelids than to Deuterostomia or Ecdysozoa. Lophophorates themselves, however, form a polyphyletic assemblage. The hypotheses that they are monophyletic and more closely allied to Deuterostomia than to Protostomia can be ruled out with both the approximately unbiased test and the expected likelihood weights test. The existence of Phoronozoa, a putative clade including Brachiopoda and Phoronida, has also been rejected. According to our analyses, phoronids instead share a more recent common ancestor with bryozoans than with brachiopods. Platyhelminthes is the sister group of Lophotrochozoa. Together these two constitute Spiralia. Although Chaetognatha appears as the sister group of Priapulida within Ecdysozoa in our analyses, alternative hypothesis concerning chaetognath relationships could not be rejected.     

Set-aside cells in maximal indirect development: Evolutionary and developmental significance

In the maximal form of indirect development found in many taxa of marine invertebrates, embryonic cell lineages of fixed fate and limited division capacity give rise to the larval structures. The adult arises from set-aside cells in the larva that are held out from the early embryonic specification processes, and that retain extensive proliferative capacity. We review the locations and fates of set-aside cells in two protostomes, a lophophorate and a deuterostome. The distinct adult body plans of many phyla develop from homologous set-aside cells within homologous larvae. We argue that the stocks from which these phyla arose utilized these respective larvae, and the diversity of their adult body plans reflects diverse pattern formation processes executed in their set-aside cell populations. Chordates and arthropods develop directly, but share adult characters with indirectly developing phyla. Thus the deuterostome and protostome stocks that were ancestral to chordates and arthropods, respectively, also utilized maximal indirect development.     

Insights into the Evolution of Nuclear Dualism in the Ciliates Revealed by Phylogenetic Analysis of rRNA Sequences

The small subunit rRNA gene sequences of the karyorelictean ciliates, Loxodes striatus and Protocruzia sp., and the heterotrichian ciliates, Climacostomum virens and Eufolliculina uhligi , were used to test the evolution of nuclear dualism in the Phylum Ciliophora. Phylogenies derived using a least squares distance method, neighbour joining, and maximum parsimony demonstrate that the karyorelictean ciliates sensu Small and Lynn, 1985 do not form a monophyletic group. However, Loxodes and the heterotrich ciliates form the first branch in the ciliate lineage, and Protocruzia branches, in distance methods, basal to the spirotrich lineage. It is proposed that Protocruzia be removed from the Class Karyorelictea, and placed in closer taxonomic association with the spirotrich lineage. The distribution of nuclear division types along the phylogenetic tree is consistent with the notion that macronuclei incapable of division represent a derived rather than a primitive or "karyorelictid" character trait.     

Fine structure of the epistome in Phoronis ovalis: significance for the coelomic organization in Phoronida

Abstract. The hypothesis of a common ancestry of the lophophorate taxa Brachiopoda, Bryozoa, Phoronida, and the Deuterostomia can be traced back to the late 19th century when Masterman recognized a tripartite organization of the body consisting of pro-, meso-, and metasome, along with coelomic body cavities in each compartment, as characteristic for Echinodermata, Pterobranchia, Phoronida, and Brachiopoda. This idea became quite popular under the name "archicoelomate" concept. The organization of the phoronids, and especially of their transparent actinotroch larva, has for a long time been used as a touchstone for the validity of this concept. As a coelomic lining can reliably be recognized only on the ultrastructural level, this technique has been applied for adults of Phoronis ovalis , which is assumed to be a sister species to all other phoronids. Phoronis ovalis contains only two coelomic compartments, a posterior coelom inside the trunk (metasoma), occupying the space between the trunk epidermis and the digestive epithelium, and an anterior lophophoral coelom inside and basal to the tentacular crown (mesosoma). There is no coelomic cavity inside the epistome (prosoma). This part of the body is filled with myoepithelial cells, which are continuous with the epithelial lining of the lophophore cavity. These cells form a lumenless bilayer and possess long, tiny myofilamentous processes, which are completely embedded in an extracellular matrix. A comparison with data on P. muelleri shows that there is no need to assume three different coelomic cavities in Phoronida, in contrast to the predictions of the archicoelomate concept. At least for this taxon, a correspondence to the situation in deuterostomes can hardly be found.     

Phylogenetic analyses of the polycystine Radiolaria based on the 18s rDNA sequences of the Spumellarida and the Nassellarida

Acantharea, Polycystinea, and Phaeodarea have members that are widely distributed in the marine plankton. Many biologists use the conventional term “Radiolaria” to include these three classes. However, on the basis of an 18S rDNA study, Polet et al. (2004, Protist 155, 53–63) recently suggested that the Phaeodarea should be moved into the Phylum Cercozoa. In the present paper, the phylogenetic relationships of the Acantharea and the Polycystinea, especially the phylogenetic positions of Nassellarida and Spumellarida, were inferred from 18S rDNA sequences including those we have determined from the Family Spongodiscidae (Class Polycystinea, Order Spumellarida) and the Family Pterocorythidae (Class Polycystinea, Order Nassellarida). Among major eukaryotic lineages, the Polycystinea were shown to constitute a paraphyletic group: in the phylogenetic trees for the relationships among polycystines, the collosphaerid, sphaerozoid, and thalassicollid spumellarians and the pterocorycid nassellarians constantly formed a monophyletic group, from which the spongodiscid spumellarians were excluded. This conclusion is not consistent with the current taxonomy of the “Radiolaria,” and leads us to consider that the collosphaerid, sphaerozoid, and thalassicollid spumellarians and the pterocorycid nassellarians may have evolved from an ancestor with triradiate branched spicules.     

A new family of inarticulate brachiopods from the Lower Cambrian of northwestern Mongolia

A new genus of calcareous-shelled brachiopods, Egyngolella, with E. lenae sp. nov. selected as the type species, is described from the upper part of the Egiin Gol Formation, Atdabanian Stage, Lower Cambrian of northwestern Mongolia and is assigned to a new family that is tentatively placed in the order Obolellida. E. lenae sp. nov. is characterized by an unusual combination of features typical for different, sometimes widely divergent brachiopod lineages.     

A preliminary overview of the Diaporthales based on large subunit nuclear ribosomal DNA sequences

The ascomycete order Diaporthales includes a number of plant pathogenic fungi such as Cryphonectria parasitica, the chestnut blight fungus, as well as many asexually reproducing fungi without known sexual states. Relationships among genera in the Diaporthales were evaluated as a basis for the recognition of families and to provide a taxonomic framework for the asexually reproducing diaporthalean fungi. Phylogenetic relationships were determined based on analyses of large subunit (LSU) nuclear ribosomal DNA (nrDNA) sequences. Within the Diaporthales 82 sequences representing 69 taxa were analyzed. Results suggest the presence of at least six major lineages within the Diaporthales recognized as the Gnomoniaceae sensu stricto, Melanconidaceae sensu stricto, Schizoparme complex including the anamorph genera Coniella and Pilidiella, Cryphonectria-Endothia complex, Valsaceae sensu stricto, and Diaporthaceae sensu stricto. In addition, six teleomorphic and anamorphic taxa fell within the Diaporthales but were not allied with any of the six lineages.     

Immunological responses from brachiopod skeletal macromolecules; a new technique for assessing taxonomic relationships using shells

The phylogenetic relationships of living, calcareous-shelled brachiopods have been assessed on the basis of immunological responses from intracrystalline macromolecules. Calculations of immunological distances between representatives of the order Terebratulida have revealed a primary threefold division which correlates precisely with a proposed subdivision of the order into three superfamilies but refutes attempts to establish a fourth superfamily. This conclusion was confirmed by carrying out immunological investigations of small shell fragments from other brachiopod genera which were so rare that no antisera could be prepared. The immunological results also indicate a fundamental subdivision of the long-looped brachiopods, with one group perhaps being derived from short-looped terebratuloids rather than long-looped terebratelloids. Sero-taxonomy of skeletal macromolecules provides an ideal method of acquiring molecular phylogenetic data in many groups because a large number of taxa can be surveyed in a short period of time, and microscopic pieces of shell contain sufficient antigenic determinants for many reactions. The technique can also be applied to specimens which have been stored without special treatment in museum collections, making the technique particularly applicable to rare taxa for which no other form of molecular data is available. □ Immunology, Brachiopoda, taxonomy, intracrystalline molecules.     

Fission in sea anemones: integrative studies of life cycle evolution

Sea anemones (Phylum Cnidaria; Class Anthozoa, Order Actiniaria)exhibit a diversity of developmental patterns that include cloningby fission. Because natural histories of clonal and aclonalsea anemones are quite different, the gain and loss of fissionis an important feature of actiniarian lineages. We have usedmitochondrial DNA and nuclear intron DNA phylogenies to investigatethe evolution of longitudinal fission in sixteen species inthe genus Anthopleura, and reconstructed an aclonal ancestorthat has given rise at least four times to clonal descendents.For A. elegantissima from the northeastern Pacific Ocean, atransition to clonality by fission was associated with an up-shorehabitat shift, supporting prior hypotheses that clonal growthis an adaptation to the upper shore. Fission in Actiniaria likelyprecedes its advent in Anthopleura, and its repeated loss andgain is perplexing. Field studies of the acontiate sea anemoneAiptasia californica provided insight to the mechanisms thatregulate fission: subtidal Aiptasia responded to experimentallydestabilized substrata by increasing rates of pedal laceration.We put forth a general hypothesis for actiniarian fission inwhich sustained tissue stretch (a consequence of substratuminstability or intrinsic behavior) induces tissue degradation,which in turn induces regeneration. The gain and loss of fissionin Anthopleura lineages may only require the gain and loss ofsome form of stretching behavior. In this view, tissue stretchinitiates a cascade of developmental events without requiringcomplex gene regulatory linkages.     

Variable pedicle morphology in a population of the Recent brachiopod Terebratulina septentrionalis

Extremely variable pedicle morphology is described in a large sample of the Recent articulate brachiopod Terebratulina septentrionalis (Couthouy) from off the coast of Nova Scotia. The majority of these specimens were attached to the shells of living or dead scaphopods by a dense network of pedicle rootlets. Other brachiopods had been lying on the sea-floor anchored solely by the weight of sediment enmeshed within the bush-like network of pedicle rootlets. Some brachiopod larvae had settled on the exposed pedicle rootlets of adults, presumably because of the scarcity of other suitable substrate. Such a mode of life is thought 'to indicate that these brachiopods could survive a further reduction in the available substrate and it is suggested that, should such conditions persist, changes in hard-part morphology would enable descendants of the species to adopt a predominantly free-lying mode of life. Likely morphological adaptions are suggested, based on examples from the fossil record. This evolutionary trend, from attached to free-lying and perhaps vice versa, has occurred many times in the history of the Phylum Brachiopoda, and it is suggested that the mode of life of this T. septentrionalis population provides an important insight into at least one of the possible evolutionary pathways which bring about such transformations.     

RHYNCHONELLIFORMEAN BRACHIOPODS WITH SOFT-TISSUE PRESERVATION FROM THE EARLY CAMBRIAN CHENGJIANG LAGERSTÄTTE OF SOUTH CHINA

Abstract:  Cosmopolitan kutorginates, the most abundant Early Cambrian rhynchonelliformean brachiopods, became extinct at the end of the Middle Cambrian. Consequently, any information concerning the anatomy of this peculiar lineage of brachiopods has great phylogenetic significance with regard to their extant relatives for analogies with the stem-group clade. Such data have been supplied from fossils of which the soft parts have been preserved in exceptional detail. A new brachiopod, Kutorgina chengjiangensis sp. nov., from the Early Cambrian Chengjiang Lagerstätte of southern China, is described here. It is the first articulated brachiopod species collected from this deposit. The specimens preserve a set of soft-body parts, i.e. lophophore, digestive tract and pedicle, all previously poorly known in almost all Palaeozoic calcareous brachiopod taxa. The lophophore attains an early spirolophe stage, clearly homologous to that in the coeval lingulids. The digestive tract consists of a mouth, oesophagus, swollen stomach, intestine and a terminal anus. The pedicle protruding between the valves is stout and elongate, with annulated lamellae on the surface, and contains a putative cœlomic cavity. K. chengjiangensis displays the characteristics of the stem group of calcareous brachiopods, and illustrates anatomical similarities between Cambrian phosphatic- and calcareous-shelled brachiopods, thus corroborating that the Brachiopoda are a monophyletic group.     

A barcode of life database for the Cephalopoda? Considerations and concerns

The concept of a Barcode of Life Database (BoLD) for the Class Cephalopoda (Phylum Mollusca) was introduced at the Cephalopod International Advisory Council (CIAC) symposium in Hobart, Australia, February 2006. This suggestion was met with significant interest, concern and debate. This review attempts to describe the concept of the BoLD initiative and to outline considerations and concerns specific to a cephalopod BoLD. Jan M. Strugnell and Annie R. Lindgren contributed equally to this work.     

PHYLOGENETIC RELATIONSHIPS AMONG EXTANT BRACHIOPODS

Abstract— The monophyletic status of the Brachiopoda and phylogenetic relationships within the phylum have long been contentious issues for brachiopod systematists. The relationship of brachiopods to other lophophore-bearing taxa is also uncertain; results from recent morphological and molecular studies are in conflict. To test current hypotheses of relationship, a phylogenetic analysis was completed (using PAUP 3.1.1) with 112 morphological and embryological characters that vary among extant representatives of seven brachiopod superfamilies, using bryozoans, phoronids, pterobranchs and sipunculids as outgroups. In the range of analyses performed, brachiopod monophyly is well supported, particularly by characters of soft anatomy. Arguments concerning single or multiple origins of a bivalved shell are not relevant to recognizing brachiopods as a clade. Articulate monophyly is very strongly supported, but inarticulate monophyly receives relatively weak support. Unlike previous studies, the nature of uncertainties about the clade status of Inarticulata are detailed explicitly here, making them easier to test in the future. Calcareous inarticulates appear to share derived characters with the other inarticulates, while sharing many primitive characters with other calcareous brachiopods (the articulates). Experimental manipulation of the data matrix reveals potential sources of bias in previous hypotheses of brachiopod phylogeny. Although not tested explicitly, lophophorate monophyly is very tentatively supported. Molecular systematic studies of a diverse group of brachiopods and other lophophorates will be particularly welcome in providing a test of the conclusions presented here.     

Phylogenetic relationships within the class Anthozoa (phylum Cnidaria) based on nuclear 18S rDNA sequences

Taxonomic relationships within the corals and anemones (Phylum Cnidaria: Class Anthozoa) are based upon few morphological characters. The significance of any given character is debatable, and there is little fossil record available for deriving evolutionary relationships. We analyzed complete 18S ribosomal sequences to examine subclass-level and ordinal-level organization within the Anthozoa. We suggest that the Subclass Ceriantipatharia is not an evolutionarily relevant grouping. The Order Corallimorpharia appears paraphyletic and closely related to the Order Scleractinia. The 18S rRNA gene may be insufficient for establishing robust phylogenetic hypotheses concerning the specific relationships of the Corallimorpharia and the Ceriantharia and the branching sequence for the orders within the Hexacorallia. The 18S rRNA gene has sufficient phylogenetic signal, however, to distinguish among the major groupings within the Class Anthozoa, and we use this information to suggest relationships for the enigmatic taxa Dactylanthus and Dendrobrachia.     

Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades

Background  

The subclass Enoplia (Phylum Nematoda) is purported to be the earliest branching clade amongst all nematode taxa, yet the deep phylogeny of this important lineage remains elusive. Free-living marine species within the order Enoplida play prominent roles in marine ecosystems, but previous molecular phylogenies have provided only the briefest evolutionary insights; this study aimed to firmly resolve internal relationships within the hyper-diverse but poorly understood Enoplida. In addition, we revisited the molecular framework of the Nematoda using a rigorous phylogenetic approach in order to investigate patterns of early splits amongst the oldest lineages (Dorylaimia and Enoplia).     

Palaeontological and Molecular Evidence Linking Arthropods, Onychophorans, and other Ecdysozoa

Membership of Arthropoda in a clade of molting animals, the Ecdysozoa, has received a growing body of support over the past 10 years from analyses of DNA sequences from many genes together with morphological characters involving the cuticle and its molting. Recent analyses based on broad phylogenomic sampling strengthen the grouping of cycloneuralian worms and arthropods as Ecdysozoa, identify the velvet worms (Phylum Onychophora) as the closest living relatives of arthropods, and interpret segmentation as having separate evolutionary origins in arthropods and annelid worms. Determining whether the water bears (Phylum Tardigrada) are more closely related to onychophorans and arthropods or to unsegmented cycloneuralians such as roundworms (Nematoda) is an open question. Fossil taxa such as the Cambrian anomalocaridids provide a combination of arthropod and cycloneuralian characters that is not observed in any living ecdysozoan. Fossils break up long branches and help to resolve the sequence of character acquisition at several critical nodes in the arthropod tree, notably in a suite of Cambrian lobopodians that may include the stem groups of each of the major panarthropod lineages.     

Dismissal of Acoelomorpha: Acoela and Nemertodermatida are separate early bilaterian clades

We used new 18S and 28S rRNA sequences analysed with parsimony, maximum likelihood and Bayesian methods of phylogenetic reconstruction to show that Nemertodermatida, generally classified as the sister group of Acoela within the recently proposed Phylum Acoelomorpha, are a separate basal bilaterian lineage. We used several analytical approaches to control for possible long branch attraction (LBA) artefacts in our results. Parsimony and the model based phylogenetic reconstruction methods that incorporate 'corrections' for substitution rate heterogenities yielded concordant results. When putative long branch taxa were experimentally removed the resulting topologies were consistent with our total evidence analysis. Deletion of fast-evolving nucleotide sites decreased resolution and clade support, but did not support a topology conflicting with the total evidence analysis. Establishment of Acoela and Nemertodermatida as two early lineages facilitates reconstruction of ancestral bilaterian features. The ancestor of extant Bilateria was a small, benthic direct developer without coelom or a planktonic larval stage. The previously proposed Phylum Acoelomorpha is dismissed as paraphyletic.