Lophotrochozoan phylogeny assessed with LSU and SSU data: Evidence of lophophorate polyphyly

A new eyeless species of Nereis (Annelida, Nereididae) from deep-sea sediments of the northern South China Sea

A variety of nereidid species have been reported from the South China Sea, although little is known about the deep-sea species in this area. Recently, two specimens belonging to a novel nereidid polychaete were collected from a sedimentary habitat during an environmental survey to a deep-sea basin where cold seeps occur. This new species, Nereistricirrata sp. nov., is described herein, based on morphological and molecular analyses. The most noteworthy feature is the absence of eyes on the prostomium; it can be distinguished from other eyeless Nereis species by the arrangement of conical paragnaths on the pharynx, the nature of homogomph falcigers and the shape of notopodial lobes in posterior chaetigers. The reconstructed phylogenetic tree, using concatenated sequences of mtCOI, 16S, and 18S rRNA, showed that all Nereis species included in this study form a monophyletic clade with full support. The mtCOI-based interspecific comparisons revealed a high genetic divergence (23.1%-37.3% K2P) from four-eyed Nereis species with the available sequences. This is the first record of an eyeless Nereis species in the South China Sea.

Polyzoa is back: The effect of complete gene sets on the placement of Ectoprocta and Entoprocta

The phylogenomic approach has largely resolved metazoan phylogeny and improved our knowledge of animal evolution based on morphology, paleontology, and embryology. Nevertheless, the placement of two major lophotrochozoan phyla, Entoprocta (Kamptozoa) and Ectoprocta (Bryozoa), remains highly controversial: Originally considered as a single group named Polyzoa (Bryozoa), they were separated on the basis of morphology. So far, each new study of lophotrochozoan evolution has still consistently proposed different phylogenetic positions for these groups. Here, we reinvestigated the placement of Entoprocta and Ectoprocta using highly complete datasets with rigorous contamination removal. Our results from maximum likelihood, Bayesian, and coalescent analyses strongly support the topology in which Entoprocta and Bryozoa form a distinct clade, placed as a sister group to all other lophotrochozoan clades: Annelida, Mollusca, Brachiopoda, Phoronida, and Nemertea. Our study favors the evolutionary scenario where Entoprocta, Cycliophora, and Bryozoa constitute one of the earliest branches among Lophotrochozoa and thus supports the Polyzoa hypothesis.

The Molecular Profile of Rhadinorhynchus dorsoventrospinosus Amin, Heckmann, and Ha 2011 (Acanthocephala: Rhadinorhynchidae) from Vietnam

Of the 46 known species of Rhadinorhynchus Lühe, 1911, only 6 species, including Rhadinorhynchus dorsoventrospinosus Amin, Heckmann, and Ha, 2011, have dorsal and ventral, as well as lateral, trunk spines in the posterior field of trunk spines. The other 5 species are Rhadinorhynchus erumei Gupta and Fatima, 1981, Rhadinorhynchus adenati (Golvan and Houin, 1964) Golvan, 1969, Rhadinorhynchus lintoni Cable and Linderoth, 1963, Rhadinorhynchus pacificus Amin, Rubtsova, and Ha, 2019, and Rhadinorhynchus multispinosus Amin, Rubtsova, and Ha, 2019. These 5 species are distinguished from R. dorsoventrospinosus by differences in proboscis hook armature, trunk spine organization, and egg size. The distinction of R. dorsoventrospinosus is further demonstrated by its molecular description. We amplified the 18S and ITS1+5.8S+ITS2 rDNA region and cytochrome c oxidase subunit 1 (COI) gene for this study. Unfortunately, no ITS1+5.8S+ITS2 gene sequences are available for comparison with other species of the genus Rhadinorhynchus. Therefore, phylogenetic trees generated from sequences of the 18S nuclear region and COI gene were analyzed for the phylogenetic position of isolates of R. dorsoventrospinosus. Rhadinorhynchus dorsoventrospinosus has been validated as a species based on comparisons of morphological (original description) and molecular features (this paper). The additional genetic data will be useful as more species are described and as more genetic material becomes available to improve taxon sampling in the genetic analysis.

Evaluation of the taxonomic position of the genus Carinina (Nemertea:Palaeonemertea), with descriptions of two new species

The genus Carinina Hubrecht, 1885 has long been considered the most ‘archaic’ nemertean taxon because its members are distinguished by the basiepidermal position of the brain and lateral nerve cords, characters thought to be plesiomorphic for the phylum. Here we describe two new species, Carinina yushini sp. nov. from the Sea of Japan (Russia) and C. chocolata sp. nov. from the north-east Pacific (Oregon, USA), distinguished by brown body colour. A phylogenetic analysis based on partial sequences of five nuclear and mitochondrial gene regions, 18S rRNA, 28S rRNA, histone H3, 16S rRNA and COI, confirms the monophyly of Carinina (Family Carininidae), and points to a close relationship to Carinoma (Family Carinomidae). The two groups together form a sister clade to the rest of the palaeonemerteans (Family Tubulanidae + Family Cephalotrichidae s.l.). Carinina plecta most likely belongs to the Tubulanidae. A morphological synapomorphy of the clade Carininidae + Carinomidae is a larva with a single midventral eye (in contrast to eyeless larvae of the Tubulanidae and two-eyed larvae of the Cephalotrichidae). Our phylogenetic analysis suggests that the basiepidermal position of the central nervous system is an autapomorphy of Carininidae (and, independently, C. plecta), rather than a plesiomorphy of the phylum Nemertea or the class Palaeonemertea, emphasising that the genus Carinina is no more archaic than any other palaeonemertean genus.

Pattern of sucker development in cuttlefishes

Background

Morphological novelties have been acquired through evolutionary processes and related to the adaptation of new life-history strategies with new functions of the bodyparts. Cephalopod molluscs such as octopuses, squids and cuttlefishes possess unique morphological characteristics. Among those novel morphologies, in particular, suckers arranged along the oral side of each arm possess multiple functions, such as capturing prey and locomotion, so that the sucker morphology is diversified among species, depending on their ecological niche. However, the detailed developmental process of sucker formation has remained unclear, although it is known that new suckers are formed or added during both embryonic and postembryonic development. In the present study, therefore, focusing on two cuttlefish species, Sepia esculenta and S. lycidas, in which the sucker morphology is relatively simple, morphological and histological observations were carried out during embryonic and postembryonic development to elucidate the developmental process of sucker formation and to compare them among other cephalopod species.

Results

The observations in both species clearly showed that the newly formed suckers were added on the oral side of the most distal tip of each arm during embryonic and postembryonic development. On the oral side of the arm tip, the epithelial tissue became swollen to form a ridge along the proximal-distal axis (sucker field ridge). Next to the sucker field ridge, there were small dome-shaped bulges that are presumed to be the sucker buds. Toward the proximal direction, the buds became functional suckers, in which the inner tissues differentiated to form the complex sucker structures. During postembryonic development, on both sides of the sucker field ridge, epithelial tissues extended to form a sheath, covering the ridge for protection of undifferentiated suckers.

Conclusions

The developmental process of sucker formation, in which sucker buds are generated from a ridge structure (sucker field ridge) on the oral side at the distal-most arm tip, was shared in both cuttlefish species, although some minor heterochronic shifts of the developmental events were detected between the two species.

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Morphological and genetic description of Moniliformis necromysi sp. n. (Archiacanthocephala) from the wild rodent Necromys lasiurus (Cricetidae: Sigmondontinae) in Brazil

A new species of Moniliformis Travassos, 1915 (Acanthocephala: Moniliformidae) is described from the hairy-tailed bolo mouse, Necromys lasiurus Lund, 1840 (Cricetidae: Sigmondontinae), captured in the Brazilian Cerrado, in Uberlândia, state of Minas Gerais, Brazil. The specimens were studied by light and scanning electron microscopy. Molecular phylogenies were inferred from partial nuclear large subunit ribosomal RNA gene sequences and partial mitochondrial cytochrome c oxidase subunit I gene. The new species is distinguished from other moniliformid species by the number of rows and number of hooks per row, size of the proboscis, size of the eggs, host species and geographical distribution. Molecular phylogenies and genetic distances analyses demonstrated that Moniliformis necromysi sp. n. forms a well-supported monophyletic group with sequences of other species of Moniliformis and is distinguished from them, which agrees with the morphological characteristics, allocating the new species to this genus and to the family Moniliformidae Van Cleave, 1924. This is the first moniliformid acanthocephalan described from a wild rodent in Brazil.

Are hyoliths Palaeozoic lophophorates?

The phylogenetic position of hyoliths has long been unsettled, with recent discoveries of a tentaculate feeding apparatus (‘lophophore’) and fleshy apical extensions from the shell (‘pedicle’) suggesting a lophophorate affinity. Here, we describe the first soft parts associated with the feeding apparatus of an orthothecid hyolith, Triplicatella opimus from the Chengjiang biota of South China. The tuft-like arrangement of the tentacles of T. opimus differs from that of hyolithids, suggesting they collected food directly from the substrate. A reassessment of the feeding organ in hyolithids indicates that it does not represent a lophophore and our analysis of the apical structures associated with some orthothecids show that these represent crushed portions of the shell and are not comparable to the brachiopod pedicle. The new information suggests that hyoliths are more likely to be basal members of the lophotrochozoans rather than lophophorates closely linked with the Phylum Brachiopoda.

Phylogeny of Echiura updated, with a revised taxonomy to reflect their placement in Annelida as sister group to Capitellidae

Echiura (commonly called spoon worms) are derived annelids that have an unsegmented sausage-shaped body with a highly extensible anterior end (i.e. a proboscis). Echiura currently contains two superfamilies: Echiurioidea (with Echiuridae, Urechidae and Thalassematidae) and Bonellioidea (with Bonelliidae, and Ikedidae). Ikedidae contains only Ikeda, which is distinctive in having a huge trunk, a highly elongate proboscis with stripes or dots, and numerous gonoducts. A recent molecular phylogeny of Echiura recovered Ikedidae as the sister group to Bonelliidae. However, due to relatively low support values for the monophyly of Bonelliidae, this relationship remains problematic. In this study, we reinvestigated the relationship of Bonelliidae and Ikedidae using an expanded dataset with more taxa and genes. In contrast to the previous results, our analyses strongly support that Ikeda is nested within Bonelliidae due to the placement of Maxmuelleria. On the basis of this result, we synonymise Ikedidae with Bonelliidae and transfer Ikeda to the latter, the diagnosis of which is amended. In addition, we synonymise Urechidae with its sister group Echiuridae because they share the synapomorphy of having anal chaetae rings. Furthermore, considering that recent phylogenetic studies have consistently recovered Echiura as the sister group to Capitelliidae within Annelida, we drop the rank of the echiuran clade to family-level and propose a revised classification: Thalassematidae with two subfamilies, Thalassematinae (with two tribes Echiurini and Thalassematini) and Bonelliinae. In addition, we identified a sample collected from the deep sea (~1820 m) of Monterey Bay, California, based on its molecular data. This terminal unexpectedly formed the sister group to the eight genera of Thalassematini, most members of which are inhabitants of littoral zones.

New morphological and genetic data of Gigantorhynchus echinodiscus (Diesing, 1851) (Acanthocephala: Archiacanthocephala) in the giant anteater Myrmecophaga tridactyla Linnaeus, 1758 (Pilosa: Myrmecophagidae)

Gigantorhynchus echinodiscus (Diesing, 1851) is a parasite of anteaters in South America. Although described by Diesing in 1851, there is still a lack of taxonomic and phylogenetic information regarding this species. In the present study, we redescribe G. echinodiscus collected from a giant anteater, Myrmecophaga tridactyla Linnaeus, 1758, from the Brazilian Cerrado (Savannah) in the State of São Paulo by light and scanning electron microscopy. In addition, phylogenies were inferred from partial DNA gene sequence of the nuclear large subunit ribosomal RNA gene (28S rRNA). We provide for the first time details of the proboscis with a crown having 18 large hooks and numerous small hooks, a lateral papilla at the base of the proboscis, a ringed pseudo-segmented body, large testes, cemented glands in pairs, and a non-segmented region in the posterior end of the body, which contributed to the diagnosis of the species. Molecular phylogenetic analyses recovered G. echinodiscus forming a well-supported monophyletic group with Mediorhynchus sp., which was congruent with morphological studies that allocate both genera within the family Gigantorhynchidae. In conclusion, the present work adds new morphological and molecular information, emphasizing the importance of adopting integrative taxonomic approaches in studies of Acanthocephala.

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Redescription of Gigantorhynchus echinodischus from Brazilian giant anteater.

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First molecular data of the genus Gigantorhynchus with 28S rRNA partial gene.

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Phylogenetic relationships of Gigantorhynchidae are assessed.

Redescription of Acanthogyrus (Acanthosentis) maroccanus (Dollfus, 1951) (Acanthocephala: Quadrigyridae), a parasite of the Algerian barb Luciobarbus callensis (Valenciennes) (Cyprinidae) in Algeria, and first molecular data

Acanthogyrus (Acanthosentis) maroccanus (Dollfus, 1951), an insufficiently described quadrigyrid acanthocephalan of cyprinid fishes from Northwest Africa, is redescribed based on recently collected specimens from the Algerian barb Luciobarbus callensis (Valenciennes) in Algeria. Newly observed morphological features for A. (A.) maroccanus include the arrangement of proboscis hooks (not in regular circles), the male reproductive structures extending into the copulatory bursa and the presence of a para-receptacle structure and vaginal sleeve. The mechanism of copulation of this acanthocephalan is described based on several copulating pairs. The phylogenetic position of A. (A.) maroccanus within Eoacanthocephala was assessed based on partial 28S rDNA sequences. Maximum likelihood and Bayesian inference analyses placed A. (A.) maroccanus in a clade with Palliolisentis (Demidueterospinus) ophiocephalus (Thapar, 1931), both species included in the Quadrigyridae, the only family within the Gyracanthocephala.

The neuroanatomy of Barentsia discreta (Entoprocta, Coloniales) reveals significant differences between bryozoan and entoproct nervous systems

BACKGROUND

Entoprocta affinities within Lophotrochozoa remain unclear. In different studies, entoprocts are considered to be related to different groups, including Cycliophora, Bryozoa, Annelida, and Mollusca. The use of modern methods to study the neuroanatomy of Entoprocta should provide new information that may be useful for phylogenetic analysis.

RESULTS

The anatomy of the nervous system in the colonial Barentsia discreta was studied using immunocytochemistry and transmission electron microscopy. The ganglion gives rise to several main nerves: paired lateral, aboral, and arcuate nerves, and three pairs of tentacular cords that branch out into tentacular nerves. The serotonergic nervous system includes paired esophageal perikarya and two large peripheral perikarya, each with a complex net of neurites. Each tentacle is innervated by one abfrontal and two laterofrontal neurite bundles. Sensory cells occur regularly along the abfrontal side of each tentacle. Star-like nerve cells are scattered in the epidermis of the calyx. The stalk is innervated by paired stalk nerves.

CONCLUSIONS

The neuroanatomy of the colonial Barentsia discreta is generally similar to that of solitary entoprocts but differs in the anatomy and ultrastructure of the ganglion, the number of neurite bundles in the calyx, and the distribution of serotonin in the nerve elements. A comparison of the organization of the nervous system in the Entoprocta and Bryozoa reveals many differences in tentacle innervations, which may indicate that these groups may not be closely related. Our results can not support with any certainty the homology of nervous system elements in adult entoprocts and adult "basal mollusks".

Phylogenomics of Lophotrochozoa with Consideration of Systematic Error

Phylogenomic studies have improved understanding of deep metazoan phylogeny and show promise for resolving incongruences among analyses based on limited numbers of loci. One region of the animal tree that has been especially difficult to resolve, even with phylogenomic approaches, is relationships within Lophotrochozoa (the animal clade that includes molluscs, annelids, and flatworms among others). Lack of resolution in phylogenomic analyses could be due to insufficient phylogenetic signal, limitations in taxon and/or gene sampling, or systematic error. Here, we investigated why lophotrochozoan phylogeny has been such a difficult question to answer by identifying and reducing sources of systematic error. We supplemented existing data with 32 new transcriptomes spanning the diversity of Lophotrochozoa and constructed a new set of Lophotrochozoa-specific core orthologs. Of these, 638 orthologous groups (OGs) passed strict screening for paralogy using a tree-based approach. In order to reduce possible sources of systematic error, we calculated branch-length heterogeneity, evolutionary rate, percent missing data, compositional bias, and saturation for each OG and analyzed increasingly stricter subsets of only the most stringent (best) OGs for these five variables. Principal component analysis of the values for each factor examined for each OG revealed that compositional heterogeneity and average patristic distance contributed most to the variance observed along the first principal component while branch-length heterogeneity and, to a lesser extent, saturation contributed most to the variance observed along the second. Missing data did not strongly contribute to either. Additional sensitivity analyses examined effects of removing taxa with heterogeneous branch lengths, large amounts of missing data, and compositional heterogeneity. Although our analyses do not unambiguously resolve lophotrochozoan phylogeny, we advance the field by reducing the list of viable hypotheses. Moreover, our systematic approach for dissection of phylogenomic data can be applied to explore sources of incongruence and poor support in any phylogenomic data set. [Annelida; Brachiopoda; Bryozoa; Entoprocta; Mollusca; Nemertea; Phoronida; Platyzoa; Polyzoa; Spiralia; Trochozoa.].

Neuroanatomy of Hyalinella punctata: Common patterns and new characters in phylactolaemate bryozoans

Studies on the bryozoan adult nervous system employing immunocytochemical techniques and confocal laser scanning microscopy are scarce. To gain a better view into the structure and evolution of the nervous system of the Phylactolaemata, the earliest extant branch and sister taxon to the remaining Bryozoa, this work aims to characterize the nervous system of Hyalinella punctata with immunocytochemical techniques and confocal laser scanning microscopy. The cerebral ganglion is located between the anus and the pharynx and contains a lumen. Two ganglionic horns and a circum-oral nerve ring emanate from the cerebral ganglion. The pharynx is innervated by a diffuse neural plexus with two prominent neurite bundles. The caecum is innervated by longitudinal neurite bundles and a peripheral plexus. The intestine is characterized by longitudinal and circular neurite bundles, mostly near the anus. Novel putative sensory cells were found in the foregut and intestine. The tentacle sheath is innervated by a diffuse neural plexus, which emanates from several neurite bundles from the cerebral ganglion, but also parts of the pharyngeal plexus. There are six tentacle neurite bundles of intertentacular origin. The retractor muscles are innervated by two thin neurite bundles. Several characters are described herein for the first time in Phylactolaemata: Longitudinal neurite bundles and a peripheral plexus of the caecum, putative sensory structures of the gut, retractor muscle innervation, specific duplicature band neurite bundles. The tentacle innervation differs from previous descriptions of phylactolaemates regarding the origin of the three abfrontal neurite bundles. In general, most organ systems are innervated by a diffuse plexus in phylactolaemates as opposed to gymnolaemates. In contrast to the Gymnolaemata, representatives of Phylactolaemata show a higher number of tentacle nerves. Although the plesiomorphic condition for zooidal features among bryozoans remains unclear, having a diffuse nerve plexus may represent an ancestral feature for freshwater bryozoans.

Genetic population structure of polychaeta Neanthes glandicincta (Nereididae) of the Mai Po Inner Deep Bay Ramsar Site, Hong Kong

Neanthes glandicincta (Nereididae, Polychaeta) is the first numerically dominant benthic infauna in the Mai Po international Ramsar site, Hong Kong and also an economically important species for food source of birds and fishes. In present study, highly conserved nuclear ribosomal DNA (SSU and LSU rDNA) and mitochondrial COI gene were employed to study the population structure of N. glandicincta in the subtropical mudflat. The specimens were collected from five localities in February 2006, February-August 2007 and preserved at -80 °C, methanol or formalin, respectively. DNA extraction efficiency was the highest in fresh materials and lowest in formalin-fixed samples. The 18S (1774 bp), 28S D1 (383 bp) and COI genes were sequenced and analyzed. Both 18S and 28S D1 rDNA were highly conserved and showed no difference among the populations, whereas COI gene exhibited relatively high-level intraspecific polymorphism (2.2 %). The population from onshore and near mangrove station was phylogenetic different from other sites, indicating restricted gene exchange between the region of river mouth and mangrove forest. The mangrove may form a barrier for the dispersal of pelagic/benthic larvae of the population, which indicates that the population genetic difference is related to different habitats.

Unraveling a 70-year-old taxonomic puzzle: redefining the genus ikedosoma (annelida: echiura) on the basis of morphological and molecular analyses

After a long-standing taxonomic confusion, the echiurid genus Ikedosoma Bock, 1942 , endemic to Japan and surroundings, is redefined on the basis of morphological and molecular analyses of many new Japanese materials and some museum specimens. The re-examination of a syntype of I. elegans ( Ikeda, 1904 ), the type species of the genus, first revealed that its oblique muscle layer is continuous throughout and never fasciculate between longitudinal muscle bands, unlike those described in the definitions that have prevailed for ca. 70 years, making this genus indistinguishable from Listriolobus Spengel, 1912 . Two Japanese species of Ikedosoma, I. elegans and I. gogoshimense (Ikeda, 1904), which were thus redefined, had also been poorly defined in the past to the point of being nearly indistinguishable from each other, largely due to incomplete descriptions and poor collections. Molecular phylogenetic analyses using 18S and 28S ribosomal RNA, histone H3, and cytochrome c oxidase subunit I (COI) genes clearly confirmed the distinction between these two species, their monophyletic origin, and their distinction from L. sorbillans (Lampert, 1883). The genus Ikedosoma thus validated is morphologically distinguishable from Listriolobus by the absence of a rectal caecum. Ikedosoma elegans and I. gogoshimense also differ in the disposition of gonoduct pairs. The third known species, I. qingdaoense Li, Wang and Zhou, 1994 , from Qingdao, North China, lacks information on oblique muscle layers, which makes even its generic affiliation uncertain.

The molecular symplesiomorphies shared by the stem groups of metazoan evolution: can sites as few as 1% have a significant impact on recognizing the phylogenetic position of myzostomida?

Although it is clear that taxon sampling, alignments, gene sampling, tree reconstruction methods and the total length of the sequences used are critical to the reconstruction of evolutionary history, weakly supported or misleading nodes exist in phylogenetic studies with no obvious flaw in those aspects. The phylogenetic studies focusing on the basal part of bilaterian evolution are such a case. During the past decade, Myzostomida has appeared in the basal part of Bilateria in several phylogenetic studies of Metazoa. However, most researchers have entertained only two competing hypotheses about the position of Myzostomida-an affinity with Annelida and an affinity with Platyhelminthes. In this study, dozens of symplesiomorphies were discovered by means of ancestral state reconstruction in the complete 18S and 28S rDNAs shared by the stem groups of Metazoa. By contrastive analysis on the datasets with or without such symplesiomorphic sites, we discovered that Myzostomida and other basal groups are basal lineages of Bilateria due to the corresponding symplesiomorphies shared with earlier lineages. As such, symplesiomorphies account for approximately 1-2% of the whole dataset have an essential impact on phylogenetic inference, and this study reminds molecular systematists of the importance of carrying out ancestral state reconstruction at each site in sequence-based phylogenetic studies. In addition, reasons should be explored for the low support of the hypothesis that Myzostomida belongs to Annelida in the results of phylogenomic studies. Future phylogenetic studies concerning Myzostomida should include all of the basal lineages of Bilateria to avoid directly neglecting the stand-alone basal position of Myzostomida as a potential hypothesis.

Complete mitochondrial genome sequences of two parasitic/commensal nemerteans, Gononemertes parasita and Nemertopsis tetraclitophila (Nemertea: Hoplonemertea)

BACKGROUND

Most nemerteans (phylum Nemertea) are free-living, but about 50 species are known to be firmly associated with other marine invertebrates. For example, Gononemertes parasita is associated with ascidians, and Nemertopsis tetraclitophila with barnacles. There are 12 complete or near-complete mitochondrial genome (mitogenome) sequences of nemerteans available in GenBank, but no mitogenomes of none free-living nemerteans have been determined so far. In the present paper complete mitogenomes of the above two parasitic/commensal nemerteans are reported.

METHODS

The complete mitochondrial genomes (mitogenome) of G. parasita and N. tetraclitophila were amplified by conventional and long PCR. Phylogenetic analyses of maximum likelihood (ML) and Bayesian inference (BI) were performed with both concatenated nucleotide and amino acid sequences.

RESULTS

Complete mitogenomes of G. parasita and N. tetraclitophila are 14742 bp and 14597 bp in size, respectively, which are within the range of published Hoplonemertea mitogenomes. Their gene orders are identical to that of published Hoplonemertea mitogenomes, but different from those of Palaeo- and Heteronemertea species. All the coding genes, as well as major non-coding regions (mNCRs), are AT rich, which is especially pronounced at the third codon position. The AT/GC skew pattern of the coding strand is the same among nemertean mitogenomes, but is variable in the mNCRs. Some slight differences are found between mitogenomes of the present species and other hoplonemerteans: in G. parasita the mNCR is biased toward T and C (contrary to other hoplonemerteans) and the rrnS gene has a unique 58-bp insertion at the 5' end; in N. tetraclitophila the nad3 gene starts with the ATT codon (ATG in other hoplonemerteans). Phylogenetic analyses of the nucleotide and amino acid datasets show early divergent positions of G. parasita and N. tetraclitophila within the analyzed Distromatonemertea species, and provide strong support for the close relationship between Hoplonemertea and Heteronemertea.

CONCLUSION

Gene order is highly conserved within the order Monostilifera, particularly within the Distromatonemertea, and the special lifestyle of G. parasita and N. tetraclitophila does not bring significant variations to the overall structures of their mitogenomes in comparison with free-living hoplonemerteans.

Description and molecular phylogeny of a new species of Phoronis (Phoronida) from Japan, with a redescription of topotypes of P. ijimai Oka, 1897

We describe Phoronis emigisp. n. as the eighth member of the genus based on specimens collected from a sandy bottom at 33.2 m depth in Tomioka Bay, Amakusa, Japan. The new species is morphologically similar to P. psammophila Cori, 1889, but can be distinguished from the latter by the number of longitudinal muscle bundles in the body wall (56–72 vs. 25–50 in P. psammophila) and the position of the nephridiopores (situated level with the anus vs. lower than the anus in P. psammophila). Using sequences of the nuclear 18S and 28S rRNA genes and the mitochondrial cytochrome c oxidase subunit I (COI) gene, we inferred the relationship of P. emigi to other phoronids by the maximum likelihood method and Bayesian analysis. The analyses showed that P. emigi is closely related to P. hippocrepia Wright, 1856 and P. psammophila Cori, 1889. We describe the morphology of the topotypes and additional material for P. ijimai Oka, 1897. Neither our morphological observations of P. ijimai, nor the phylogenetic analyses based on 18S and COI sequences, contradicts that P. vancouverensis Pixell, 1912 is conspecific with P. ijimai, a synonymy that has long been disputed.

Transcriptome data reveal Syndermatan relationships and suggest the evolution of endoparasitism in Acanthocephala via an epizoic stage

The taxon Syndermata comprises the biologically interesting wheel animals ("Rotifera": Bdelloidea + Monogononta + Seisonidea) and thorny-headed worms (Acanthocephala), and is central for testing superordinate phylogenetic hypotheses (Platyzoa, Gnathifera) in the metazoan tree of life. Recent analyses of syndermatan phylogeny suggested paraphyly of Eurotatoria (free-living bdelloids and monogononts) with respect to endoparasitic acanthocephalans. Data of epizoic seisonids, however, were absent, which may have affected the branching order within the syndermatan clade. Moreover, the position of Seisonidea within Syndermata should help in understanding the evolution of acanthocephalan endoparasitism. Here, we report the first phylogenomic analysis that includes all four higher-ranked groups of Syndermata. The analyzed data sets comprise new transcriptome data for Seison spec. (Seisonidea), Brachionus manjavacas (Monogononta), Adineta vaga (Bdelloidea), and Paratenuisentis ambiguus (Acanthocephala). Maximum likelihood and Bayesian trees for a total of 19 metazoan species were reconstructed from up to 410 functionally diverse proteins. The results unanimously place Monogononta basally within Syndermata, and Bdelloidea appear as the sister group to a clade comprising epizoic Seisonidea and endoparasitic Acanthocephala. Our results support monophyly of Syndermata, Hemirotifera (Bdelloidea + Seisonidea + Acanthocephala), and Pararotatoria (Seisonidea + Acanthocephala), rejecting monophyly of traditional Rotifera and Eurotatoria. This serves as an indication that early acanthocephalans lived epizoically or as ectoparasites on arthropods, before their complex lifecycle with arthropod intermediate and vertebrate definite hosts evolved.

New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias

BACKGROUND

Within the complex metazoan phylogeny, the relationships of the three lophophorate lineages, ectoprocts, brachiopods and phoronids, are particularly elusive. To shed further light on this issue, we present phylogenomic analyses of 196 genes from 58 bilaterian taxa, paying particular attention to the influence of compositional heterogeneity.

RESULTS

The phylogenetic analyses strongly support the monophyly of Lophophorata and a sister-group relationship between Ectoprocta and Phoronida. Our results contrast previous findings based on rDNA sequences and phylogenomic datasets which supported monophyletic Polyzoa (= Bryozoa sensu lato) including Ectoprocta, Entoprocta and Cycliophora, Brachiozoa including Brachiopoda and Phoronida as well as Kryptrochozoa including Brachiopoda, Phoronida and Nemertea, thus rendering Lophophorata polyphyletic. Our attempts to identify the causes for the conflicting results revealed that Polyzoa, Brachiozoa and Kryptrochozoa are supported by character subsets with deviating amino acid compositions, whereas there is no indication for compositional heterogeneity in the character subsets supporting the monophyly of Lophophorata.

CONCLUSION

Our results indicate that the support for Polyzoa, Brachiozoa and Kryptrochozoa gathered so far is likely an artifact caused by compositional bias. The monophyly of Lophophorata implies that the horseshoe-shaped mesosomal lophophore, the tentacular feeding apparatus of ectoprocts, phoronids and brachiopods is, indeed, a synapomorphy of the lophophorate lineages. The same may apply to radial cleavage. However, among phoronids also spiral cleavage is known. This suggests that the cleavage pattern is highly plastic and has changed several times within lophophorates. The sister group relationship of ectoprocts and phoronids is in accordance with the interpretation of the eversion of a ventral invagination at the beginning of metamorphosis as a common derived feature of these taxa.

The impact of paralogy on phylogenomic studies - a case study on annelid relationships

Phylogenomic studies based on hundreds of genes derived from expressed sequence tags libraries are increasingly used to reveal the phylogeny of taxa. A prerequisite for these studies is the assignment of genes into clusters of orthologous sequences. Sophisticated methods of orthology prediction are used in such analyses, but it is rarely assessed whether paralogous sequences have been erroneously grouped together as orthologous sequences after the prediction, and whether this had an impact on the phylogenetic reconstruction using a super-matrix approach. Herein, I tested the impact of paralogous sequences on the reconstruction of annelid relationships based on phylogenomic datasets. Using single-partition analyses, screening for bootstrap support, blast searches and pruning of sequences in the supermatrix, wrongly assigned paralogous sequences were found in eight partitions and the placement of five taxa (the annelids Owenia, Scoloplos, Sthenelais and Eurythoe and the nemertean Cerebratulus) including the robust bootstrap support could be attributed to the presence of paralogous sequences in two partitions. Excluding these sequences resulted in a different, weaker supported placement for these taxa. Moreover, the analyses revealed that paralogous sequences impacted the reconstruction when only a single taxon represented a previously supported higher taxon such as a polychaete family. One possibility of a priori detection of wrongly assigned paralogous sequences could combine 1) a screening of single-partition analyses based on criteria such as nodal support or internal branch length with 2) blast searches of suspicious cases as presented herein. Also possible are a posteriori approaches in which support for specific clades is investigated by comparing alternative hypotheses based on differences in per-site likelihoods. Increasing the sizes of EST libraries will also decrease the likelihood of wrongly assigned paralogous sequences, and in the case of orthology prediction methods like HaMStR it is likewise decreased by using more than one reference taxon.

Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida

Myzostomida comprise a group of marine worms associated mainly with echinoderms since the Carboniferous. Due to their unusual morphology the phylogenetic position in relation to other Lophotrochozoa is discussed since their description. According to different morphological and molecular markers the Myzostomida are either close to Platyzoa or Annelida. Here we investigated small non-coding RNAs of Myzostoma cirriferum to infer the phylogenetic position of myzostomids. Based on transcriptomic data collected by Illumina Deep Sequencing we analyzed the microRNA (miRNA) families occurring in M. cirriferum. Phylogenetic analysis revealed the presence of 13 miRNA-families exclusively shared by Annelida (including Sipuncula) and Myzostomida, as such highly significantly supporting an annelid origin of myzostomids. Furthermore, using a mapping-approach and secondary structure models we predicted several miRNA-candidates unique for myzostomids.

Ultrastructure and morphology of the cycliophoran female

Knowledge on the morphology of the cycliophoran female has mostly been based on observations of immature females in brood chambers of feeding stages. With the use of light- and transmission electron microscopy, the morphology and ultrastructure of the free and fully mature female of Cycliophora is described now for the first time. The external morphology is characterized by a ciliation consisting of an anteroventral ciliated field, a posterior ciliated tuft, and four sensory structures extending anteriorly from the anteroventral ciliated field. In addition, a small ciliated structure in the midventral region is interpreted as a round-shaped gonopore. Internally, a bilateral cerebral ganglion is situated in the anterior region and a large oocyte is located medially in the body. Several glands are present anteriorly, while posteriorly a pair of glands is associated with the ciliated tuft. Dorsal and ventral longitudinal muscles, as well as, dorsoventral muscles are identified by electron microscopy. Muscle fibers attach to the endocuticle via the epidermis, by means of attachment fibers. An unknown endosymbiont is present throughout the body of the female. We discuss the functional implications of the morphological and ultrastructural aspects of the cycliophoran female. Finally, we compare this life cycle stage with that fromother phyla, suggested as phylogenetically close.

Spiral cleavage and early embryology of a loxosomatid entoproct and the usefulness of spiralian apical cross patterns for phylogenetic inferences

Background

Among the four major bilaterian clades, Deuterostomia, Acoelomorpha, Ecdysozoa, and Lophotrochozoa, the latter shows an astonishing diversity of bodyplans. While the largest lophotrochozoan assemblage, the Spiralia, which at least comprises Annelida, Mollusca, Entoprocta, Platyhelminthes, and Nemertea, show a spiral cleavage pattern, Ectoprocta, Brachiopoda and Phoronida (the Lophophorata) cleave radially. Despite a vast amount of recent molecular phylogenetic analyses, the interrelationships of lophotrochozoan phyla remain largely unresolved. Thereby, Entoprocta play a key role, because they have frequently been assigned to the Ectoprocta, despite their differently cleaving embryos. However, developmental data on entoprocts employing modern methods are virtually non-existent and the data available rely exclusively on sketch drawings, thus calling for thorough re-investigation.

Results

By applying fluorescence staining in combination with confocal microscopy and 3D-imaging techniques, we analyzed early embryonic development of a basal loxosomatid entoproct. We found that cleavage is asynchronous, equal, and spiral. An apical rosette, typical for most spiralian embryos, is formed. We also identified two cross-like cellular arrangements that bear similarities to both, a "molluscan-like" as well as an "annelid-like" cross, respectively.

Conclusions

A broad comparison of cleavage types and apical cross patterns across Lophotrochozoa shows high plasticity of these character sets and we therefore argue that these developmental traits should be treated and interpreted carefully when used for phylogenetic inferences.

A molecular phylogeny of bryozoans

We present the most comprehensive molecular phylogeny of bryozoans to date. Our concatenated alignment of two nuclear ribosomal and five mitochondrial genes includes 95 taxa and 13,292 nucleotide sites, of which 8297 were included. The number of new sequences generated during this project are for each gene:ssrDNA (32), lsrDNA (22), rrnL (38), rrnS (35), cox1 (37), cox3 (34), and cytb (44). Our multi-gene analysis provides a largely stable topology across the phylum. The major groups were unambiguously resolved as (Phylactolaemata (Cyclostomata (Ctenostomata, Cheilostomata))), with Ctenostomata paraphyletic. Within Phylactolaemata, (Stephanellidae, Lophopodidae) form the earliest divergent clade. Fredericellidae is not resolved as a monophyletic family and forms a clade together with Plumatellidae, Cristatellidae and Pectinatellidae, with the latter two as sister taxa. Hyalinella and Gelatinella nest within the genus Plumatella. Cyclostome taxa fall into three major clades: i. (Favosipora (Plagioecia, Rectangulata)); ii. (Entalophoroecia ((Diplosolen, Cardioecia) (Frondipora, Cancellata))); and iii. (Articulata ((Annectocyma, Heteroporidae) (Tubulipora (Tennysonia, Idmidronea)))), with suborders Tubuliporina and Cerioporina, and family Plagioeciidae each being polyphyletic. Ctenostomata is composed of three paraphyletic clades to the inclusion of Cheilostomata: ((Alcyonidium, Flustrellidra) (Paludicella (Anguinella, Triticella)) (Hislopia (Bowerbankia, Amathia)) Cheilostomata); Flustrellidra nests within the genus Alcyonidium, and Amathia nests within the genus Bowerbankia. Suborders Carnosa and Stolonifera are not monophyletic. Within the cheilostomes, Malacostega is paraphyletic to the inclusion of all other cheilostomes. Conopeum is the most early divergent cheilostome, forming the sister group to ((Malacostega, Scrupariina, Inovicellina) ((Hippothoomorpha, Flustrina) (Lepraliomorpha, Umbonulomorpha))); Flustrina is paraphyletic to the inclusion of the hippothoomorphs; neither Lepraliomorpha nor Umbonulomorpha is monophyletic. Ascophorans are polyphyletic, with hippothoomorphs grouping separately from lepraliomorphs and umbonulomorphs; no cribrimorphs were included in the analysis. Results are discussed in the light of molecular and morphological evidence. Ancestral state reconstruction of larval strategy in Gymnolaemata revealed planktotrophy and lecithotrophy as equally parsimonious solutions for the ancestral condition. More comprehensive taxon sampling is expected to clarify this result. We discuss the extent of non-bryozoan contaminant sequences deposited in GenBank and their impact on the reconstruction of metazoan phylogenies and those of bryozoan interrelationships.

The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships

Background

The phylogenetic relationships of the lophophorate lineages, ectoprocts, brachiopods and phoronids, within Lophotrochozoa are still controversial. We sequenced an additional mitochondrial genome of the most species-rich lophophorate lineage, the ectoprocts. Although it is known that there are large differences in the nucleotide composition of mitochondrial sequences of different lineages as well as in the amino acid composition of the encoded proteins, this bias is often not considered in phylogenetic analyses. We applied several approaches for reducing compositional bias and saturation in the phylogenetic analyses of the mitochondrial sequences.

Results

The complete mitochondrial genome (16,089 bp) of Flustra foliacea (Ectoprocta, Gymnolaemata, Cheilostomata) was sequenced. All protein-encoding, rRNA and tRNA genes are transcribed from the same strand. Flustra shares long intergenic sequences with the cheilostomate ectoproct Bugula, which might be a synapomorphy of these taxa. Further synapomorphies might be the loss of the DHU arm of the tRNA L(UUR), the loss of the DHU arm of the tRNA S(UCN) and the unique anticodon sequence GAG of the tRNA L(CUN). The gene order of the mitochondrial genome of Flustra differs strongly from that of the other known ectoprocts. Phylogenetic analyses of mitochondrial nucleotide and amino acid data sets show that the lophophorate lineages are more closely related to trochozoan phyla than to deuterostomes or ecdysozoans confirming the Lophotrochozoa hypothesis. Furthermore, they support the monophyly of Cheilostomata and Ectoprocta. However, the relationships of the lophophorate lineages within Lophotrochozoa differ strongly depending on the data set and the used method. Different approaches for reducing heterogeneity in nucleotide and amino acid data sets and saturation did not result in a more robust resolution of lophotrochozoan relationships.

Conclusion

The contradictory and usually weakly supported phylogenetic reconstructions of the relationships among lophotrochozoan phyla based on mitochondrial sequences indicate that these alone do not contain enough information for a robust resolution of the relations of the lophotrochozoan phyla. The mitochondrial gene order is also not useful for inferring their phylogenetic relationships, because it is highly variable in ectoprocts, brachiopods and some other lophotrochozoan phyla. However, our study revealed several rare genomic changes like the evolution of long intergenic sequences and changes in the structure of tRNAs, which may be helpful for reconstructing ectoproct phylogeny.

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.

A twist in time--the evolution of spiral cleavage in the light of animal phylogeny

Recent progress in reconstructing animal relationships enables us to draw a better picture of the evolution of important characters such as organ systems and developmental processes. By mapping these characters onto the phylogenetic framework, we can detect changes that have occurred in them during evolution. The spiral mode of development is a complex of characters that is present in many lineages, such as nemerteans, annelids, mollusks, and polyclad platyhelminthes. However, some of these lineages show variations of this general program in which sub-characters are modified without changing the overlying pattern. Recent molecular phylogenies suggest that spiral cleavage was lost, or at least has deviated from its original pattern, in more lineages than was previously thought (e.g., in rotifers, gastrotrichs, bryozoans, brachiopods, and phoronids). Here, I summarize recent progress in reconstructing the spiralian tree of life and discuss its significance for our understanding of the spiral-cleavage character complex. I conclude that more detailed knowledge of the development of spiralian taxa is necessary to understand the mechanisms behind these changes, and to understand the evolutionary changes and adaptations of spiralian embryos.

Comparative myoanatomy of cycliophoran life cycle stages

The metazoan phylum Cycliophora includes small cryptic epibionts that live attached to the mouthparts of clawed lobsters. The life cycle is complex, with alternating sexual and asexual generations, and involves several sessile and free-living stages. So far, the morphological and genetic characterization of cycliophorans has been unable to clarify the phylogenetic position of the phylum. In this study, we add new details on the muscular anatomy of the feeding stage, the attached Prometheus larva, the dwarf male, and the female of one of the two hitherto described species, Symbion pandora. The musculature of the feeding stage is composed of myofibers that run longitudinally in the buccal funnel (two fibers) and in the trunk (variable number of fibers). The mouth opening is lined by a myoepithelial ring musculature. A complex myoepithelial sphincter is situated proximal to the anus. In the attached Prometheus larva, three longitudinal sets of myofilaments run dorsally, laterally, and ventrally along the entire anterior-posterior body axis. The muscular architecture of the dwarf male is complex, especially close to the penis, in the posterior part of the body. An X-shaped muscle structure is found on the dorsal side, whereas on the ventral side, longitudinal muscles and a V-shaped muscle structure are present. These muscles are complemented by additional dorsoventral muscles. The mesodermal muscle fibers attach to the cuticle via the epidermis in all life cycle stages studied herein. The musculature of the female is similar to that of the Pandora larva of Symbion americanus and includes dorsoventral muscles and longitudinal muscles that run in the dorsal and ventral body region. Overall, our results reveal striking similarities in the muscular arrangement of the life cycle stages of both Symbion species.

The slipper snail, Crepidula: an emerging lophotrochozoan model system

Recent developmental and genomic research focused on "slipper snails" in the genus Crepidula has positioned Crepidula fornicata as a de facto model system for lophotrochozoan development. Here we review recent developments, as well as earlier reports demonstrating the widespread use of this system in studies of development and life history. Recent studies have resulted in a well-resolved fate map of embryonic cell lineage, documented mechanisms for axis determination and D quadrant specification, preliminary gene expression patterns, and the successful application of loss- and gain-of-function assays. The recent development of expressed sequence tags and preliminary genomics work will promote the use of this system, particularly in the area of developmental biology. A wealth of comparative information on phylogenetic relationships, variation in mode of development within the family, and numerous studies on larval biology and metamorphosis, primarily in Crepidula fornicata, make these snails a powerful tool for studies of the evolution of the mechanisms of development in the Mollusca and Lophotrochozoa. By bringing a review of the current state of knowledge of Crepidula life histories and development together with some detailed experimental methods, we hope to encourage further use of this system in various fields of investigation.