Exceptionally Preserved Setae: A Possible Morphological Synapomorphy of Cambrian Lophotrochozoans

Cambrian Lagerstätten yield exceptionally preserved fossils that have greatly improved our understanding of the origin and evolution of animal groups. Brachiopoda, a phylum of bivalved marine invertebrates nested firmly within the lophotrochozoan protostomes, are widely recovered in such Lagerstätten. The marginal chitinous setae (or chaetae) of brachiopods are the most commonly described soft tissue and have been interpreted as performing a defensive and/or sensory role. Despite their relatively common appearance in Cambrian Lagerstätten, the origin, function, and evolution of setae in the Brachiopoda is poorly known. Here, we document exquisitely preserved setal structures from South China and Laurentia paleocontinents giving new insights into their formation, microstructure and preservation mode. New setae typically make their appearance within the follicle of a neighbouring older seta and then branches off laterally forming its own follicle. Setal microstructure is likely to be composed of many canals, highly comparable to setae of their recent counterparts. Moreover, setae recovered from these palaeo-continents present different preservation: aside from the normal preservation of iron oxides and carbonaceous ingredients, some compositions of calcium are also detected in this originally chitinous organization. Investigating the evolutionary origins of chitinous setae, a specialized type found notably in lophotrochozoans such as brachiopods and annelids, reveals its presence in early Cambrian stem groups. This character likely serves as a morphological synapomorphy in lophotrochozoan evolution. However, the dearth of morpho-ultrastructure and comparative studies in Cambrian fossils presents a challenge in fully understanding this evolutionary development.

Development Features on the Selection of Animal Models for Teratogenic Testing

Today, the use of animal models from different species continues to represent a fundamental step in teratogenic testing, despite the increase in alternative solutions that provide an important screening to the enormous quantity of new substances that aim to enter the market every year. The maintenance of these models is due to the sharing of similar development processes with humans, and in this way they represent an important contribution to the safety in the use of the compounds tested. Furthermore, the application of advances in embryology to teratology, although hampered by the complexity of reproductive processes, continues to prove the importance of sensitivity during embryonic and fetal development to detect potential toxicity, inducing mortality/abortion and malformations.In this chapter, essential periods of development in different models are outlined, highlighting the similarities and differences between species, the advantages and disadvantages of each group, and specific sensitivities for teratogenic testing. Models can be divided into invertebrate species such as earthworms of the species Eisenia fetida/Eisenia andrei, Caenorhabditis elegans, and Drosophila melanogaster, allowing for rapid results and minor ethical concerns. Vertebrate nonmammalian species Xenopus laevis and Danio rerio are important models to assess teratogenic potential later in development with fewer ethical requirements. Finally, the mammalian species Mus musculus, Rattus norvegicus, and Oryctolagus cuniculus, phylogenetically closer to humans, are essential for the assessment of complex specialized processes, occurring later in development.Regulations for the development of toxicology tests require the use of mammalian species. Although ethical concerns and costs limit their use in large-scale screening. On the other hand, invertebrate and vertebrate nonmammalian species are increasing as alternative animal models, as these organisms combine low cost, less ethical requirements, and culture conditions compatible with large-scale screening. Their main advantage is to allow high-throughput screening in a whole-animal context, in contrast to the in vitro techniques, not dependent on the prior identification of a target. Better knowledge of the development pathways of animal models will allow to maximize human translation and reduce the number of animals used, leading to a selection of compounds with an improved safety profile and reduced time to market for new drugs.

Form function of sulcus acusticus of the sagittal otolith in seven Sciaenidae (Acanthuriformes) species using geometric morphometrics (southwestern Atlantic)

The morphology of otoliths determines the function they perform, and it is influenced by genetic and environmental factors. Knowing those relationships is necessary to understand the role of hearing in fish. The objectives of this work were: exploring the shape of the sulcus of the sagittal otolith in seven species of Sciaenidae, in relation to sound production, and analyzing whether the shape and size of the sulcus can be used as a phylogenetic character. For this purpose, geometric morphometry analysis was carried out using landmarks data. It was found that there is an influence of size on the shape of the sulcus, and significant differences were found between the shapes of the sulcus (permutational multivariate analysis of variance). Three general shapes of the sulcus were identified (using principal component analysis, canonical variate analysis, and clustering): (1) in species that produce sounds at dominant frequencies <350 Hz, the deformation of the sulcus showed a tendency towards circularity of the ostium; (2) in those species that produce sounds at frequencies >350 Hz, the ostium showed a flattened ovoid shape, and the cauda increased its length; (3) the species that do not produce sounds, did not show any modifications, relative to the form of consensus. Despite finding sister species that presented similar sulcus shapes in the phylogeny, the results did not confirm that this can be used as a phylogenetic character. This work discusses whether the combined effects of phylogenetic legacy and natural functional selection have led to convergent evolution for the sulcus form. The differences presented by the sulcus of species that occupy the same clade, could indicate that there is a displacement of characters. The sagittal otolith and the sensory macula associated with the sulcus acusticus are highly plastic structures that are subject to strong evolutionary pressure in relation to environmental and behavioral factors, resulting in great variability in shapes that can be associated with a specific character. The variation in the shape of the sulcus would allow the analysed species to coexist in the same coastal soundscapes, without losing their particular hearing needs, even in case of overlapping their spatial and temporal distribution areas.

Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny

There is conflicting evidence as to whether Porifera (sponges) or Ctenophora (comb jellies) comprise the root of the animal phylogeny. Support for either a Porifera-sister or Ctenophore-sister tree has been extensively examined in the context of model selection, taxon sampling, and outgroup selection. The influence of dataset construction is comparatively understudied. We re-examine five animal phylogeny datasets that have supported either root hypothesis using an approach designed to enrich orthologous signal in phylogenomic datasets. We find that many component orthogroups in animal datasets fail to recover major lineages as monophyletic with the exception of Ctenophora, regardless of the supported root. Enriching these datasets to retain orthogroups recovering ≥3 major lineages reduces dataset size by up to 50% while retaining underlying phylogenetic information and taxon sampling. Site-heterogeneous phylogenomic analysis of these enriched datasets recovers both Porifera-sister and Ctenophora-sister positions, even with additional constraints on outgroup sampling. Two datasets which previously supported Ctenophora-sister support Porifera-sister upon enrichment. All enriched datasets display improved model fitness under posterior predictive analysis. While not conclusively rooting animals at either Porifera or Ctenophora, we do see an increase in signal for Porifera-sister and a decrease in signal for Ctenophore-sister when data are filtered for orthologous signal. Our results indicate that dataset size and construction as well as model fit influence animal root inference.

A novel, conserved and possibly functional motif "WHWGHTW" in mitochondrial transcription across Bilateria

The animal mitogenomes which undergone a reductive evolution has an obvious loss of coding capacity compared to their known closest relatives, but it has not yet been fully investigated why and how the intergenic regions do not encode protein and have no known functions, are stably maintained, replicated, and transmitted by the genome. These relatively small intergenic regions may not be under neutral evolution and they may have functional and/or regulatory roles that have yet to be identified. Here, the distribution pattern, sequence content and location of a novel sequence motif of 'WWWGHTW' were bioinformatically investigated and characterised by constructing a sampling mitogenome dataset of 1889 species from 14 phyla representing the clade of Bilateria. This motif is reverse complementary of the previously described DmTTF binding sequence and found in the nd4L- (X) -trnT gene cluster. This cluster commonly exhibits a strand displacement region and an intergenic region among the bilaterian superphylums, particularly in Ecdysozoa. This motif may be accepted as a substrate providing binding sites for the specific interaction with transcription factors because of (i) its reverse complementarity of previously described DmTTF binding sequence, and (ii) the possession of G and T nucleotides in the fourth and sixth positions, (iii) the bias on T and G nucleotides instead of C and A in the degenerated positions. This suggestion is also supported by the presence of a strand displacement region in the nd4L- (X) -trnT gene cluster, particularly in Ecdysozoa consisting of the most rearranged mitogenomes among the bilaterian superphylums.

The discovery of new Chilean taxa revolutionizes the systematics of Geoplaninae Neotropical land planarians (Platyhelminthes: Tricladida)

Two subfamilies of land planarians (Geoplanidae) are endemic to the Neotropical region, namely Geoplaninae (with 29 genera and 346 nominal species, most of which are from Brazil) and its sister-group Timyminae, with only two Chilean species. The systematics of these groups through morphology and molecular data (COI and 28S rDNA genes), including nine new Chilean species, is re-assessed in this study. The great morphological diversity of the Chilean species is congruent with the molecular trees and, accordingly, five new genera (Adinoplana, Harana, Myoplana, Sarcoplana and Transandiplana) are proposed, each characterized by putative synapomorphies. Seven new tribes are also erected (Adinoplanini, Gusanini, Haranini, Inakayaliini, Myoplanini, Polycladini and Sarcoplanini), each one monogeneric, except Geoplanini (which includes all genera under the current concept of Geoplaninae plus the Chilean Transandiplana) and Sarcoplanini (with Sarcoplana and the already known Mapuplana, Pichidamas and Wallamapuplana). Re-diagnoses of Geoplaninae, Timymini, Gusana, Inakayalia, Polycladus and Pichidamas are proposed and biogeographic remarks on Transandiplana are provided

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.

Coelomic System of the Sea Urchin Strongylocentrotus pallidus (Echinodermata, Echinoidea) and the Issue of Coelomic Metamery in Echinoderms

The representatives of the main phylogenetic clades of Bilateria are characterized by metamery. In Deuterostomia, metamery is presented in hemichordates and chordates. Sea urchins have 7 metameric coelomic rings located along the oral-aboral axis of the body. A similar coelomic metamery is also a sign of representatives of other classes of echinoderms. We hypothesize that the metameric coelomic rings in echinoderms are inherent of the common ancestor of Deuterostomia. Asymmetry in the structure of echinoderm coeloms is the result of ancestral forms lying on the right side of the body, which led to a reduction of the coeloms on the right side. During the sedentary lifestyle, the left-side coeloms formed metameric coelomic rings.

Who's who in Magelona: phylogenetic hypotheses under Magelonidae Cunningham & Ramage, 1888 (Annelida: Polychaeta)

Known as shovel head worms, members of Magelonidae comprise a group of polychaetes readily recognised by the uniquely shaped, dorso-ventrally flattened prostomium and paired ventro-laterally inserted papillated palps. The present study is the first published account of inferences of phylogenetic hypotheses within Magelonidae. Members of 72 species of Magelona and two species of Octomagelona were included, with outgroups including members of one species of Chaetopteridae and four of Spionidae. The phylogenetic inferences were performed to causally account for 176 characters distributed among 79 subjects, and produced 2,417,600 cladograms, each with 404 steps. A formal definition of Magelonidae is provided, represented by a composite phylogenetic hypothesis explaining seven synapomorphies: shovel-shaped prostomium, prostomial ridges, absence of nuchal organs, ventral insertion of palps and their papillation, presence of a burrowing organ, and unique body regionation. Octomagelona is synonymised with Magelona due to the latter being paraphyletic relative to the former. The consequence is that Magelonidae is monotypic, such that Magelona cannot be formally defined as associated with any phylogenetic hypotheses. As such, the latter name is an empirically empty placeholder, but because of the binomial name requirement mandated by the International Code of Zoological Nomenclature, the definition is identical to that of Magelonidae. Several key features for future descriptions are suggested: prostomial dimensions, presence/absence of prostomial horns, morphology of anterior lamellae, presence/absence of specialised chaetae, and lateral abdominal pouches. Additionally, great care must be taken to fully describe and illustrate all thoracic chaetigers in descriptions.

A Novel Approach to Investigate the Effect of Tree Reconstruction Artifacts in Single-Gene Analysis Clarifies Opsin Evolution in Nonbilaterian Metazoans

Our ability to correctly reconstruct a phylogenetic tree is strongly affected by both systematic errors and the amount of phylogenetic signal in the data. Current approaches to tackle tree reconstruction artifacts, such as the use of parameter-rich models, do not translate readily to single-gene alignments. This, coupled with the limited amount of phylogenetic information contained in single-gene alignments, makes gene trees particularly difficult to reconstruct. Opsin phylogeny illustrates this problem clearly. Opsins are G-protein coupled receptors utilized in photoreceptive processes across Metazoa and their protein sequences are roughly 300 amino acids long. A number of incongruent opsin phylogenies have been published and opsin evolution remains poorly understood. Here, we present a novel approach, the canary sequence approach, to investigate and potentially circumvent errors in single-gene phylogenies. First, we demonstrate our approach using two well-understood cases of long-branch attraction in single-gene data sets, and simulations. After that, we apply our approach to a large collection of well-characterized opsins to clarify the relationships of the three main opsin subfamilies.

Comparative and Evolutionary Physiology of Vasopressin/ Oxytocin-Type Neuropeptide Signaling in Invertebrates

The identification of structurally related hypothalamic hormones that regulate blood pressure and diuresis (vasopressin, VP; CYFQNCPRG-NH2) or lactation and uterine contraction (oxytocin, OT; CYIQNCPLG-NH2) was a major advance in neuroendocrinology, recognized in the award of the Nobel Prize for Chemistry in 1955. Furthermore, the discovery of central actions of VP and OT as regulators of reproductive and social behavior in humans and other mammals has broadened interest in these neuropeptides beyond physiology into psychology. VP/OT-type neuropeptides and their G-protein coupled receptors originated in a common ancestor of the Bilateria (Urbilateria), with invertebrates typically having a single VP/OT-type neuropeptide and cognate receptor. Gene/genome duplications followed by gene loss gave rise to variety in the number of VP/OT-type neuropeptides and receptors in different vertebrate lineages. Recent advances in comparative transcriptomics/genomics have enabled discovery of VP/OT-type neuropeptides in an ever-growing diversity of invertebrate taxa, providing new opportunities to gain insights into the evolution of VP/OT-type neuropeptide function in the Bilateria. Here we review the comparative physiology of VP/OT-type neuropeptides in invertebrates, with roles in regulation of reproduction, feeding, and water/salt homeostasis emerging as common themes. For example, we highlight recent reports of roles in regulation of oocyte maturation in the sea-squirt Ciona intestinalis, extraoral feeding behavior in the starfish Asterias rubens and energy status and dessication resistance in ants. Thus, VP/OT-type neuropeptides are pleiotropic regulators of physiological processes, with evolutionarily conserved roles that can be traced back to Urbilateria. To gain a deeper understanding of the evolution of VP/OT-type neuropeptide function it may be necessary to not only determine the actions of the peptides but also to characterize the transcriptomic/proteomic/metabolomic profiles of cells expressing VP/OT-type precursors and/or VP/OT-type receptors within the framework of anatomically and functionally identified neuronal networks. Furthermore, investigation of VP/OT-type neuropeptide function in a wider range of invertebrate species is now needed if we are to determine how and when this ancient signaling system was recruited to regulate diverse physiological and behavioral processes in different branches of animal phylogeny and in contrasting environmental contexts.

Muscular Development in Urechis unicinctus (Echiura, Annelida)

Echiura is one of the most intriguing major subgroups of phylum Annelida because, unlike most other annelids, echiuran adults lack metameric body segmentation. Urechis unicinctus lives in U-shape burrows of soft sediments. Little is known about the molecular mechanisms underlying the development of U. unicinctus. Herein, we overviewed the developmental process from zygote to juvenile U. unicinctus using immunohistochemistry and F-actin staining for the nervous and muscular systems, respectively. Through F-actin staining, we found that muscle fibers began to form in the trochophore phase and that muscles for feeding were produced first. Subsequently, in the segmentation larval stage, the transversal muscle was formed in the shape of a ring in an anterior-to-posterior direction with segment formation, as well as a ventromedian muscle for the formation of a ventral nerve cord. After that, many muscle fibers were produced along the entire body and formed the worm-shaped larva. Finally, we investigated the spatiotemporal expression of Uun_st-mhc, Uun_troponin I, Uun_calponin, and Uun_twist genes found in U. unicinctus. During embryonic development, the striated and smooth muscle genes were co-expressed in the same region. However, the adult body wall muscles showed differential gene expression of each muscle layer. The results of this study will provide the basis for the understanding of muscle differentiation in Echiura.

Widespread patterns of gene loss in the evolution of the animal kingdom

The animal kingdom shows an astonishing diversity, the product of over 550 million years of animal evolution. The current wealth of genome sequence data offers an opportunity to better understand the genomic basis of this diversity. Here we analyse a sampling of 102 whole genomes including >2.6 million protein sequences. We infer major genomic patterns associated with the variety of animal forms from the superphylum to phylum level. We show that a remarkable amount of gene loss occurred during the evolution of two major groups of bilaterian animals, Ecdysozoa and Deuterostomia, and further loss in several deuterostome lineages. Deuterostomes and protostomes also show large genome novelties. At the phylum level, flatworms, nematodes and tardigrades show the largest reduction of gene complement, alongside gene novelty. These findings paint a picture of evolution in the animal kingdom in which reductive evolution at the protein-coding level played a major role in shaping genome composition.

Ancient origins of arthropod moulting pathway components

Ecdysis (moulting) is the defining character of Ecdysoza (arthropods, nematodes and related phyla). Despite superficial similarities, the signalling cascade underlying moulting differs between Panarthropoda and the remaining ecdysozoans. Here, we reconstruct the evolution of major components of the ecdysis pathway. Its key elements evolved much earlier than previously thought and are present in non-moulting lophotrochozoans and deuterostomes. Eclosion hormone (EH) and bursicon originated prior to the cnidarian-bilaterian split, whereas ecdysis-triggering hormone (ETH) and crustacean cardioactive peptide (CCAP) evolved in the bilaterian last common ancestor (LCA). Identification of EH, CCAP and bursicon in Onychophora and EH, ETH and CCAP in Tardigrada suggests that the pathway was present in the panarthropod LCA. Trunk, an ancient extracellular signalling molecule and a well-established paralog of the insect peptide prothoracicotropic hormone (PTTH), is present in the non-bilaterian ctenophore Mnemiopsis leidyi. This constitutes the first case of a ctenophore signalling peptide with homology to a neuropeptide.

Animals such as insects, crabs and spiders belong to one of the most species-rich animal groups, called the arthropods. These animals have exoskeletons, which are hard, external coverings that support their bodies. Arthropods shed their exoskeletons as they grow, a process called ecdysis or moulting, and this behaviour is controlled by a set of hormones and small protein-like molecules called neuropeptides that allow communication between neurons.

Other animals, such as roundworms, also moult; and together with arthropods they are classified into a group called the Ecdysozoa. Since moulting is a common behaviour in ecdysozoans, it was previously assumed that its signalling components had evolved in the common ancestor of roundworms and arthropods, although differences in the moulting machinery between both groups exist.

Here, De Oliveira et al. investigate the evolutionary origins of the arthropod moulting machinery and find that some of the hormones and neuropeptides involved appeared long before the arthropods themselves.

Database searches showed that important hormones and neuropeptides involved in arthropod moulting can be found in diverse animal groups, such as jellyfish, molluscs and starfish, confirming that these molecules evolved before the last common ancestor of roundworms and arthropods. These animals must therefore use the hormones and neuropeptides in many processes unrelated to moulting. De Oliveira et al. also found that roundworms have lost most of these molecules, and that moulting in these animals must be driven by a different complement of hormones and neuropeptides.

These results invite research into the role of moulting hormones and neuropeptides in animals outside the Ecdysozoa. They also show that signalling pathways and the processes they regulate are highly adaptable: two animals can use the same hormone in entirely different processes, but conversely, the same behaviour may be regulated by different molecules depending on the animal. This means that the evolution of a process and the evolution of its regulation can be decoupled, a finding that has important implications for the study of signalling pathways and their evolution.

Integrating morphology and in vivo skeletal mobility with digital models to infer function in brittle star arms

Brittle stars (Phylum Echinodermata, Class Ophiuroidea) have evolved rapid locomotion employing muscle and skeletal elements within their (usually) five arms to apply forces in a manner analogous to that of vertebrates. Inferring the inner workings of the arm has been difficult as the skeleton is internal and many of the ossicles are sub-millimeter in size. Advances in 3D visualization and technology have made the study of movement in ophiuroids possible. We developed six virtual 3D skeletal models to demonstrate the potential range of motion of the main arm ossicles, known as vertebrae, and six virtual 3D skeletal models of non-vertebral ossicles. These models revealed the joint center and relative position of the arm ossicles during near-maximal range of motion. The models also provide a platform for the comparative evaluation of functional capabilities between disparate ophiuroid arm morphologies. We made observations on specimens of Ophioderma brevispina and Ophiothrix angulata. As these two taxa exemplify two major morphological categories of ophiuroid vertebrae, they provide a basis for an initial assessment of the functional consequences of these disparate vertebral morphologies. These models suggest potential differences in the structure of the intervertebral articulations in these two species, implying disparities in arm flexion mechanics. We also evaluated the differences in the range of motion between segments in the proximal and distal halves of the arm length in a specimen of O. brevispina, and found that the morphology of vertebrae in the distal portion of the arm allows for higher mobility than in the proximal portion. Our models of non-vertebral ossicles show that they rotate further in the direction of movement than the vertebrae themselves in order to accommodate arm flexion. These findings raise doubts over previous hypotheses regarding the functional consequences of ophiuroid arm disparity. Our study demonstrates the value of integrating experimental data and visualization of articulated structures when making functional interpretations instead of relying on observations of vertebral or segmental morphology alone. This methodological framework can be applied to other ophiuroid taxa to enable comparative functional analyses. It will also facilitate biomechanical analyses of other invertebrate groups to illuminate how appendage or locomotor function evolved.

CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes

Motivation

Codon reassignments have been reported across all domains of life. With the increasing number of sequenced genomes, the development of systematic approaches for genetic code detection is essential for accurate downstream analyses. Three automated prediction tools exist so far: FACIL, GenDecoder and Bagheera; the last two respectively restricted to metazoan mitochondrial genomes and CUG reassignments in yeast nuclear genomes. These tools can only analyze a single genome at a time and are often not followed by a validation procedure, resulting in a high rate of false positives.

Results

We present CoreTracker, a new algorithm for the inference of sense-to-sense codon reassignments. CoreTracker identifies potential codon reassignments in a set of related genomes, then uses statistical evaluations and a random forest classifier to predict those that are the most likely to be correct. Predicted reassignments are then validated through a phylogeny-aware step that evaluates the impact of the new genetic code on the protein alignment. Handling simultaneously a set of genomes in a phylogenetic framework, allows tracing back the evolution of each reassignment, which provides information on its underlying mechanism. Applied to metazoan and yeast genomes, CoreTracker significantly outperforms existing methods on both precision and sensitivity.

Availability and implementation

CoreTracker is written in Python and available at https://github.com/UdeM-LBIT/CoreTracker.

Contact

mabrouk@iro.umontreal.ca.

Supplementary information

Supplementary data are available at Bioinformatics online.

Revealing Mytilus galloprovincialis transcriptomic profiles during ontogeny

Mediterranean mussels are a worldwide spread bivalve species with extraordinary biological success. One of the reasons of this success could be the reproduction strategy of bivalves, characterized by the presence of trochophore larvae. Larval development in bivalves has been a topic of raising interest in the scientific community but it deserves much more attention. The principal objective of this work was to study the transcriptomic profile of the ontogeny of Mytilus galloprovincialis analyzing the gene expression in different developmental stages, from oocytes to juveniles. For this purpose, after conducting a 454 sequencing of the transcriptomes of mussel hemocytes, adult tissues and larvae, a new DNA microarray was designed and developed. The studied developmental stages: unfertilized oocytes, veliger, pediveliger, settled larvae and juveniles, showed very different transcriptomic profiles and clustered in groups defining their characteristic gene expression along ontogeny. Our results show that oocytes present a distinct and characteristic transcriptome. After metamorphosis, both settled larvae and juveniles showed a very similar transcriptome, with no enriched GO terms found between these two stages. This suggests: 1.- the progressive loss of RNA of maternal origin through larval development and 2.- the stabilization of the gene expression after settlement. On the other hand during metamorphosis a specific profile of differentially expressed genes was found. These genes were related to processes such as differentiation and biosynthesis. Processes related to the immune response were strongly down regulated. These suggest a development commitment at the expense of other non-essential functions, which are temporary set aside. Immune genes such as antimicrobial peptides suffer a decreased expression during metamorphosis. In fact, we found that the oocytes which express a higher quantity of genes such as myticins are more likely to reach success of the offspring, compared to oocytes poor in such mRNAs, whose progeny died before reaching metamorphosis.

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.].

An evolutionary perspective on the role of mesencephalic astrocyte-derived neurotrophic factor (MANF): At the crossroads of poriferan innate immune and apoptotic pathways

The mesencephalic astrocyte-derived neurotrophic factor (MANF) belongs to a recently discovered family of neurotrophic factors. MANF can be secreted but is generally resident within the endoplasmic reticulum (ER) in neuronal and non-neuronal cells, where it is involved in the ER stress response with pro-survival effects. Here we report the discovery of the MANF homolog SDMANF in the sponge Suberites domuncula. The basal positioning of sponges (phylum Porifera) in the animal tree of life offers a unique vantage point on the early evolution of the metazoan-specific genetic toolkit and molecular pathways. Since sponges lack a conventional nervous system, SDMANF presents an enticing opportunity to investigate the evolutionary ancient role of these neurotrophic factors. SDMANF shares considerable sequence similarity with its metazoan homologs. It also comprises a putative protein binding domain with sequence similarities to the Bcl-2 family of apoptotic regulators. In Suberites, SDMANF is expressed in the vicinity of bacteriocytes, where it co-localizes with the toll-like receptor SDTLR. In transfected human cells, SDMANF was detected in both the organelle protein fraction and the cell culture medium. The intracellular SDMANF protein level was up-regulated in response to both a Golgi/ER transport inhibitor and bacterial lipopolysaccharides (LPS). Upon LPS challenge, transfected cells revealed a decreased caspase-3 activity and increased cell viability with no inducible Bax expression compared to the wild type. These results suggest a deep evolutionary original cytoprotective role of MANF, at the crossroads of innate immune and apoptotic pathways, of which a neurotrophic function might have arisen later in metazoan evolution.

Characterization of Drosophila Saposin-related mutants as a model for lysosomal sphingolipid storage diseases

Sphingolipidoses are inherited diseases belonging to the class of lysosomal storage diseases (LSDs), which are characterized by the accumulation of indigestible material in the lysosome caused by specific defects in the lysosomal degradation machinery. While some LSDs can be efficiently treated by enzyme replacement therapy (ERT), this is not possible if the nervous system is affected due to the presence of the blood-brain barrier. Sphingolipidoses in particular often present as severe, untreatable forms of LSDs with massive sphingolipid and membrane accumulation in lysosomes, neurodegeneration and very short life expectancy. The digestion of intralumenal membranes within lysosomes is facilitated by lysosomal sphingolipid activator proteins (saposins), which are cleaved from a prosaposin precursor. Prosaposin mutations cause some of the severest forms of sphingolipidoses, and are associated with perinatal lethality in mice, hampering studies on disease progression. We identify the Drosophila prosaposin orthologue Saposin-related (Sap-r) as a key regulator of lysosomal lipid homeostasis in the fly. Its mutation leads to a typical spingolipidosis phenotype with an enlarged endolysosomal compartment and sphingolipid accumulation as shown by mass spectrometry and thin layer chromatography. Sap-r mutants show reduced viability with ∼50% survival to adulthood, allowing us to study progressive neurodegeneration and analyze their lipid profile in young and aged flies. Additionally, we observe a defect in sterol homeostasis with local sterol depletion at the plasma membrane. Furthermore, we find that autophagy is increased, resulting in the accumulation of mitochondria in lysosomes, concomitant with increased oxidative stress. Together, we establish Drosophila Sap-r mutants as a lysosomal storage disease model suitable for studying the age-dependent progression of lysosomal dysfunction associated with lipid accumulation and the resulting pathological signaling events.

Phylogenetic analysis of ionotropic L-glutamate receptor genes in the Bilateria, with special notes on Aplysia californica

Background

The neurotransmitter L-Glutamate (L-Glu) acting at ionotropic L-Glu receptors (iGluR) conveys fast excitatory signal transmission in the nervous systems of all animals. iGluR-dependent neurotransmission is a key component of the synaptic plasticity that underlies learning and memory. During learning, two subtypes of iGluR, α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPAR) and N-methyl-D-aspartate receptors (NMDAR), are dynamically regulated postsynaptically in vertebrates. Invertebrate organisms such as Aplysia californica (Aplysia) are well-studied models for iGluR-mediated function, yet no studies to date have analyzed the evolutionary relationships between iGluR genes in these species and those in vertebrates, to identify genes that may mediate plasticity. We conducted a thorough phylogenetic analysis spanning Bilateria to elucidate these relationships. The expression status of iGluR genes in the Aplysia nervous system was also examined.

Results

Our analysis shows that ancestral genes for both NMDAR and AMPAR subtypes were present in the common bilaterian ancestor. NMDAR genes show very high conservation in motifs responsible for forming the conductance pore of the ion channel. The number of NMDAR subunits is greater in vertebrates due to an increased number of splice variants and an increased number of genes, likely due to gene duplication events. AMPAR subunits form an orthologous group, and there is high variability in the number of AMPAR genes in each species due to extensive taxon specific gene gain and loss. qPCR results show that all 12 Aplysia iGluR subunits are expressed in all nervous system ganglia.

Conclusions

Orthologous NMDAR subunits in all species studied suggests conserved function across Bilateria, and potentially a conserved mechanism of neuroplasticity and learning. Vertebrates display an increased number of NMDAR genes and splice variants, which may play a role in their greater diversity of physiological responses. Extensive gene gain and loss of AMPAR genes may result in different physiological properties that are taxon specific. Our results suggest a significant role for L-Glu mediated responses throughout the Aplysia nervous system, consistent with L-Glu’s role as the primary excitatory neurotransmitter.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0871-1) contains supplementary material, which is available to authorized users.

The life of the freshwater bryozoan Stephanella hina (Bryozoa, Phylactolaemata)-a crucial key to elucidating bryozoan evolution

BACKGROUND

Phylactolaemata is the earliest branch and the sister group to all extant bryozoans. It is considered a small relict group that, perhaps due to the invasion of freshwater, has retained ancestral features. Reconstruction of the ground pattern of Phylactolaemata is thus essential for reconstructing the ground pattern of all Bryozoa, and for inferring phylogenetic relationships to possible sister taxa. It is well known that Stephanella hina, the sole member of the family Stephanelllidae, is probably one of the earliest offshoots among the Phylactolaemata and shows some morphological peculiarities. However, key aspects of its biology are largely unknown. The aim of the present study was to analyze live specimens of this species, in order to both document its behavior and describe its colony morphology.

RESULTS

The colony morphology of Stephanella hina consists of zooidal arrangements with lateral budding sites reminiscent of other bryozoan taxa, i.e., Steno- and Gymnolaemata. Zooids protrude vertically from the substrate and are covered in a non-rigid jelly-like ectocyst. The latter is a transparent, sticky hull that for the most part shows no distinct connection to the endocyst. Interestingly, individual zooids can be readily separated from the rest of the colony. The loose tube-like ectocyst can be removed from the animals that produces individuals that are unable to retract their lophophore, but merely shorten their trunk by contraction of the retractor muscles.

CONCLUSIONS

These observations indicate that S. hina is unique among Phylactolaemata and support the notion that bryozoans evolved from worm-like ancestors. In addition, we raise several arguments for its placement into a separate family, Stephanellidae, rather than among the Plumatellidae, as previously suggested.

Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks

BACKGROUND

Mollusks display a striking morphological disparity, including, among others, worm-like animals (the aplacophorans), snails and slugs, bivalves, and cephalopods. This phenotypic diversity renders them ideal for studies into animal evolution. Despite being one of the most species-rich phyla, molecular and in silico studies concerning specific key developmental gene families are still scarce, thus hampering deeper insights into the molecular machinery that governs the development and evolution of the various molluscan class-level taxa.

RESULTS

Next-generation sequencing was used to retrieve transcriptomes of representatives of seven out of the eight recent class-level taxa of mollusks. Similarity searches, phylogenetic inferences, and a detailed manual curation were used to identify and confirm the orthology of numerous molluscan Hox and ParaHox genes, which resulted in a comprehensive catalog that highlights the evolution of these genes in Mollusca and other metazoans. The identification of a specific molluscan motif in the Hox paralog group 5 and a lophotrochozoan ParaHox motif in the Gsx gene is described. Functional analyses using KEGG and GO tools enabled a detailed description of key developmental genes expressed in important pathways such as Hedgehog, Wnt, and Notch during development of the respective species. The KEGG analysis revealed Wnt8, Wnt11, and Wnt16 as Wnt genes hitherto not reported for mollusks, thereby enlarging the known Wnt complement of the phylum. In addition, novel Hedgehog (Hh)-related genes were identified in the gastropod Lottia cf. kogamogai, demonstrating a more complex gene content in this species than in other mollusks.

CONCLUSIONS

The use of de novo transcriptome assembly and well-designed in silico protocols proved to be a robust approach for surveying and mining large sequence data in a wide range of non-model mollusks. The data presented herein constitute only a small fraction of the information retrieved from the analysed molluscan transcriptomes, which can be promptly employed in the identification of novel genes and gene families, phylogenetic inferences, and other studies using molecular tools. As such, our study provides an important framework for understanding some of the underlying molecular mechanisms involved in molluscan body plan diversification and hints towards functions of key developmental genes in molluscan morphogenesis.

An Isochore-Like Structure in the Genome of the Flatworm Schistosoma mansoni

Eukaryotic genomes are compositionally heterogeneous, that is, composed by regions that differ in guanine-cytosine (GC) content (isochores). The most well documented case is that of vertebrates (mainly mammals) although it has been also noted among unicellular eukaryotes and invertebrates. In the human genome, regarded as a typical mammal, this heterogeneity is associated with several features. Specifically, genes located in GC-richest regions are the GC3-richest, display CpG islands and have shorter introns. Furthermore, these genes are more heavily expressed and tend to be located at the extremes of the chromosomes. Although the compositional heterogeneity seems to be widespread among eukaryotes, the associated properties noted in the human genome and other mammals have not been investigated in depth in other taxa Here we provide evidence that the genome of the parasitic flatworm Schistosoma mansoni is compositionally heterogeneous and exhibits an isochore-like structure, displaying some features associated, until now, only with the human and other vertebrate genomes, with the exception of gene concentration.

Nanoporous Structures Similar to Those Reported from Squid Sucker Teeth are also Present in Egg Shells of a Terrestrial Flatworm (Platyhelminthes; Rhabditophora; Geoplanidae) from Hachijojima (Izu Islands, Japan)

Shells of the egg cocoon of a terrestrial planarian (Diversibipalium sp.) from Hachijojima were found to be composed of a lattice of parallel nanotubes of ca. 120 nm diameter oriented perpendicular to the shell's surface. The arrangement of the porous proteinaceous tubes closely resembles that has recently been reported from the sucker teeth of squid and to date is the only other example of this kind of structure. Although the array of nanotubes undoubtedly contributes to the stiffness of the shell and helps protecting the embryo, questions such as to how the planary worm produces the array of nanotubes and what exactly their chemical and physical properties are versus those of the squid sucker tooth still remain to be answered.

Developmental Transcriptome Analysis and Identification of Genes Involved in Larval Metamorphosis of the Razor Clam, Sinonovacula constricta

The razor clam Sinonovacula constricta is an important commercial species. The deficiency of developmental transcriptomic data is becoming the bottleneck of further researches on the mechanisms underlying settlement and metamorphosis in early development. In this study, de novo transcriptome sequencing was performed for S. constricta at different early developmental stages by using Illumina HiSeq 2000 paired-end (PE) sequencing technology. A total of 112,209,077 PE clean reads were generated. De novo assembly generated 249,795 contigs with an average length of 585 bp. Gene annotation resulted in the identification of 22,870 unigene hits against the NCBI database. Eight unique sequences related to metamorphosis were identified and analyzed using real-time PCR. The razor clam reference transcriptome would provide useful information on early developmental and metamorphosis mechanisms and could be used in the genetic breeding of shellfish.

Histories of molecules: Reconciling the past

Molecular data and methods have become centrally important to evolutionary analysis, largely because they have enabled global phylogenetic reconstructions of the relationships between organisms in the tree of life. Often, however, molecular stories conflict dramatically with morphology-based histories of lineages. The evolutionary origin of animal groups provides one such case. In other instances, different molecular analyses have so far proved irreconcilable. The ancient and major divergence of eukaryotes from prokaryotic ancestors is an example of this sort of problem. Efforts to overcome these conflicts highlight the role models play in phylogenetic reconstruction. One crucial model is the molecular clock; another is that of 'simple-to-complex' modification. I will examine animal and eukaryote evolution against a backdrop of increasing methodological sophistication in molecular phylogeny, and conclude with some reflections on the nature of historical science in the molecular era of phylogeny.

Embracing the comparative approach: how robust phylogenies and broader developmental sampling impacts the understanding of nervous system evolution

Molecular biology has provided a rich dataset to develop hypotheses of nervous system evolution. The startling patterning similarities between distantly related animals during the development of their central nervous system (CNS) have resulted in the hypothesis that a CNS with a single centralized medullary cord and a partitioned brain is homologous across bilaterians. However, the ability to precisely reconstruct ancestral neural architectures from molecular genetic information requires that these gene networks specifically map with particular neural anatomies. A growing body of literature representing the development of a wider range of metazoan neural architectures demonstrates that patterning gene network complexity is maintained in animals with more modest levels of neural complexity. Furthermore, a robust phylogenetic framework that provides the basis for testing the congruence of these homology hypotheses has been lacking since the advent of the field of 'evo-devo'. Recent progress in molecular phylogenetics is refining the necessary framework to test previous homology statements that span large evolutionary distances. In this review, we describe recent advances in animal phylogeny and exemplify for two neural characters-the partitioned brain of arthropods and the ventral centralized nerve cords of annelids-a test for congruence using this framework. The sequential sister taxa at the base of Ecdysozoa and Spiralia comprise small, interstitial groups. This topology is not consistent with the hypothesis of homology of tripartitioned brain of arthropods and vertebrates as well as the ventral arthropod and rope-like ladder nervous system of annelids. There can be exquisite conservation of gene regulatory networks between distantly related groups with contrasting levels of nervous system centralization and complexity. Consequently, the utility of molecular characters to reconstruct ancestral neural organization in deep time is limited.

The ctenophore lineage is older than sponges? That cannot be right! Or can it?

Recent phylogenetic analyses resulting from collection of whole genome data suggest that ctenophores, or comb jellies, are sister to all other animals. Even before publication, this result prompted discussion among researchers. Here, I counter common criticisms raised about this result and show that assumptions placing sponges as the basal-most extant animal lineage are based on limited evidence and questionable premises. For example, the idea that sponges are simple and the reported similarity of sponge choanocytes to Choanflagellata do not provide useful characters for determining the positions of sponges within the animal tree. Intertwined with discussion of basal metazoan phylogeny is consideration of the evolution of neuronal systems. Recent data show that neural systems of ctenophores are vastly different from those of other animals and use different sets of cellular and genetic mechanisms. Thus, neural systems appear to have at least two independent origins regardless of whether ctenophores or sponges are the earliest branching extant animal lineage.

Metamorphic remodeling of morphology and the body cavity in Phoronopsis harmeri (Lophotrochozoa, Phoronida): the evolution of the phoronid body plan and life cycle

BACKGROUND

Phoronids undergo a remarkable metamorphosis, in which some parts of the larval body are consumed by the juvenile and the body plan completely changes. According to the only previous hypothesis concerning the evolution of the phoronid body plan, a hypothetical ancestor of phoronids inhabited a U-shaped burrow in soft sediment, where it drew the anterior and posterior parts of the body together and eventually fused them. In the current study, we investigated the metamorphosis of Phoronopsis harmeri with light, electron, and laser confocal microscopy.

RESULTS

During metamorphosis, the larval hood is engulfed by the juvenile; the epidermis of the postroral ciliated band is squeezed from the tentacular epidermis and then engulfed; the larval telotroch undergoes cell death and disappears; and the juvenile body forms from the metasomal sack of the larva. The dorsal side of the larva becomes very short, whereas the ventral side becomes very long. The terminal portion of the juvenile body is the ampulla, which can repeatedly increase and decrease in diameter. This flexibility of the ampulla enables the juvenile to dig into the sediment. The large blastocoel of the larval collar gives rise to the lophophoral blood vessels of the juvenile. The dorsal blood vessel of the larva becomes the definitive median blood vessel. The juvenile inherits the larval protocoel, mesocoel, and metacoel. Late in metamorphosis, however, the protocoel loses its epithelial structure: the desmosomes between cells and the basal lamina under the cells disappear. This loss may reflect a reduction of the protocoel, which is a characteristic of some recent phoronids.

CONCLUSIONS

Based on our investigation of P. harmeri metamorphosis, we hypothesize that the phoronid ancestor was worm-like animal that possessed preoral, tentacular, and trunk coeloms. It lived on the soft sediment and collected food with its tentacles. When threatened, this worm-like ancestor buried itself in the soft sediment by means of the ventral protrusion into which the loop of the intestine and the blood vessels were drawn. We propose that this behavior gave rise to the body plan of all recent phoronids. The evolution of phoronid life cycle seems having more in common with"intercalation" than "terminal addition" theories.

Origin and higher-level diversification of acariform mites - evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment

BACKGROUND

Acariformes is the most species-rich and morphologically diverse radiation of chelicerate arthropods, known from the oldest terrestrial ecosystems. It is also a key lineage in understanding the evolution of this group, with the most vexing question whether mites, or Acari (Parasitiformes and Acariformes) is monophyletic. Previous molecular studies recovered Acari either as monophyletic or non-monophyletic, albeit with a limited taxon sampling. Similarly, relationships between basal acariform groups (include little-known, deep-soil 'endeostigmatan' mites) and major lineages of Acariformes (Sarcoptiformes, Prostigmata) are virtually unknown. We infer phylogeny of chelicerate arthropods, using a large and representative dataset, comprising all main in- and outgroups (228 taxa). Basal diversity of Acariformes is particularly well sampled. With this dataset, we conduct a series of phylogenetically explicit tests of chelicerate and acariform relationships and present a phylogenetic framework for internal relationships of acariform mites.

RESULTS

Our molecular data strongly support a diphyletic Acari, with Acariformes as the sister group to Solifugae (PP =1.0; BP = 100), the so called Poecilophysidea. Among Acariformes, some representatives of the basal group Endeostigmata (mainly deep-soil mites) were recovered as sister-groups to the remaining Acariformes (i. e., Trombidiformes + and most of Sarcoptiformes). Desmonomatan oribatid mites (soil and litter mites) were recovered as the monophyletic sister group of Astigmata (e. g., stored product mites, house dust mites, mange mites, feather and fur mites). Trombidiformes (Sphaerolichida + Prostigmata) is strongly supported (PP =1.0; BP = 98-100). Labidostommatina was inferred as the basal lineage of Prostigmata. Eleutherengona (e. g., spider mites) and Parasitengona (e. g., chiggers, fresh water mites) were recovered as monophyletic. By contrast, Eupodina (e. g., snout mites and relatives) was not. Marine mites (Halacaridae) were traditionally regarded as the sister-group to Bdelloidea (Eupodina), but our analyses show their close relationships to Parasitengona.

CONCLUSIONS

Non-trivial relationships recovered by our analyses with high support (i.e., basal arrangement of endeostigmatid lineages, the position of marine mites, polyphyly of Eupodina) had been proposed by previous underappreciated morphological studies. Thus, we update currently the accepted taxonomic classification to reflect these results: the superfamily Halacaroidea Murray, 1877 is moved from the infraorder Eupodina Krantz, 1978 to Anystina van der Hammen, 1972; and the subfamily Erythracarinae Oudemans, 1936 (formerly in Anystidae Oudemans, 1902) is elevated to family rank, Erythracaridae stat. ressur., leaving Anystidae only with the nominal subfamily. Our study also shows that a clade comprising early derivative Endeostigmata (Alycidae, Nanorchestidae, Nematalycidae, and maybe Alicorhagiidae) should be treated as a taxon with the same rank as Sarcoptiformes and Trombidiformes, and the scope of the superfamily Bdelloidea should be changed. Before turning those findings into nomenclatural changes, however, we consider that our study calls for (i) finding shared apomorphies of the early derivative Endeostigmata clade and the clade including the remaining Acariformes; (ii) a well-supported hypothesis for Alicorhagiidae placement; (iii) sampling the families Proterorhagiidae, Proteonematalycidae and Grandjeanicidae not yet included in molecular analyses; (iv) undertake a denser sampling of clades traditionally placed in Eupodina, Anystina (Trombidiformes) and Palaeosomata (Sarcoptiformes), since consensus networks and Internode certainty (IC) and IC All (ICA) indices indicate high levels of conflict in these tree regions. Our study shows that regions of ambiguous alignment may provide useful phylogenetic signal when secondary structure information is used to guide the alignment procedure and provides an R implementation to the Bayesian Relative Rates test.

Biodiversity Meets Neuroscience: From the Sequencing Ship (Ship-Seq) to Deciphering Parallel Evolution of Neural Systems in Omic's Era

The origins of neural systems and centralized brains are one of the major transitions in evolution. These events might occur more than once over 570-600 million years. The convergent evolution of neural circuits is evident from a diversity of unique adaptive strategies implemented by ctenophores, cnidarians, acoels, molluscs, and basal deuterostomes. But, further integration of biodiversity research and neuroscience is required to decipher critical events leading to development of complex integrative and cognitive functions. Here, we outline reference species and interdisciplinary approaches in reconstructing the evolution of nervous systems. In the "omic" era, it is now possible to establish fully functional genomics laboratories aboard of oceanic ships and perform sequencing and real-time analyses of data at any oceanic location (named here as Ship-Seq). In doing so, fragile, rare, cryptic, and planktonic organisms, or even entire marine ecosystems, are becoming accessible directly to experimental and physiological analyses by modern analytical tools. Thus, we are now in a position to take full advantages from countless "experiments" Nature performed for us in the course of 3.5 billion years of biological evolution. Together with progress in computational and comparative genomics, evolutionary neuroscience, proteomic and developmental biology, a new surprising picture is emerging that reveals many ways of how nervous systems evolved. As a result, this symposium provides a unique opportunity to revisit old questions about the origins of biological complexity.

Scenarios for the making of vertebrates

Over the past 200 years, almost every invertebrate phylum has been proposed as a starting point for evolving vertebrates. Most of these scenarios are outdated, but several are still seriously considered. The short-range transition from ancestral invertebrate chordates (similar to amphioxus and tunicates) to vertebrates is well accepted. However, longer-range transitions leading up to the invertebrate chordates themselves are more controversial. Opinion is divided between the annelid and the enteropneust scenarios, predicting, respectively, a complex or a simple ancestor for bilaterian animals. Deciding between these ideas will be facilitated by further comparative studies of multicellular animals, including enigmatic taxa such as xenacoelomorphs.

A higher level classification of all living organisms

We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists' expert opinions in a unified and coherent, hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collaborative effort is to provide a hierarchical classification serving not only the needs of the CoL's database providers but also the diverse public-domain user community, most of whom are familiar with the Linnaean conceptual system of ordering taxon relationships. This classification is neither phylogenetic nor evolutionary but instead represents a consensus view that accommodates taxonomic choices and practical compromises among diverse expert opinions, public usages, and conflicting evidence about the boundaries between taxa and the ranks of major taxa, including kingdoms. Certain key issues, some not fully resolved, are addressed in particular. Beyond its immediate use as a management tool for the CoL and ITIS (Integrated Taxonomic Information System), it is immediately valuable as a reference for taxonomic and biodiversity research, as a tool for societal communication, and as a classificatory "backbone" for biodiversity databases, museum collections, libraries, and textbooks. Such a modern comprehensive hierarchy has not previously existed at this level of specificity.

Evolutionary aspects in intermediate filament proteins

Intermediate filament (IF) proteins, together with tubulins and actins, constitute the majority of cytoskeletal proteins in metazoans. Proteins of the IF family fulfil increasingly diverse functions but share common structural features. Phylogenetic analysis within the metazoan lineage traces back their origin to a common lamin-like ancestor. Major steps in lamin evolution occurred at the base of the vertebrate radiation, while cytoplasmic IF protein subfamilies evolved independently in the major metazoan lineages.

Predation and the origin of neurones

The core design of spiking neurones is remarkably similar throughout the animal kingdom. Their basic function as fast-signalling thresholding cells might have been established very early in their evolutionary history. Identifying the selection pressures that drove animals to evolve spiking neurones could help us interpret their design and function today. We review fossil, ecological and molecular evidence to investigate when and why animals evolved spiking neurones. Fossils suggest that animals evolved nervous systems soon after the advent of animal-on-animal predation, 550 million years ago (MYa). Between 550 and 525 MYa, we see the first fossil appearances of many animal innovations, including eyes. Animal behavioural complexity increased during this period as well, as evidenced by their traces, suggesting that nervous systems were an innovation of that time. Fossils further suggest that, before 550 MYa, animals were either filter feeders or microbial mat grazers. Extant sponges and Trichoplax perform these tasks using energetically cheaper alternatives than spiking neurones. Genetic evidence testifies that nervous systems evolved before the protostome-deuterostome split. It is less clear whether nervous systems evolved before the cnidarian-bilaterian split, so cnidarians and bilaterians might have evolved their nervous systems independently. The fossil record indicates that the advent of predation could fit into the window of time between those two splits, though molecular clock studies dispute this claim. Collectively, these lines of evidence indicate that animals evolved spiking neurones soon after they started eating each other. The first sensory neurones could have been threshold detectors that spiked in response to other animals in their proximity, alerting them to perform precisely timed actions, such as striking or fleeing.

Adhesive proteins of stalked and acorn barnacles display homology with low sequence similarities

Barnacle adhesion underwater is an important phenomenon to understand for the prevention of biofouling and potential biotechnological innovations, yet so far, identifying what makes barnacle glue proteins ‘sticky’ has proved elusive. Examination of a broad range of species within the barnacles may be instructive to identify conserved adhesive domains. We add to extensive information from the acorn barnacles (order Sessilia) by providing the first protein analysis of a stalked barnacle adhesive, Lepas anatifera (order Lepadiformes). It was possible to separate the L. anatifera adhesive into at least 10 protein bands using SDS-PAGE. Intense bands were present at approximately 30, 70, 90 and 110 kilodaltons (kDa). Mass spectrometry for protein identification was followed by de novo sequencing which detected 52 peptides of 7–16 amino acids in length. None of the peptides matched published or unpublished transcriptome sequences, but some amino acid sequence similarity was apparent between L. anatifera and closely-related Dosima fascicularis. Antibodies against two acorn barnacle proteins (ab-cp-52k and ab-cp-68k) showed cross-reactivity in the adhesive glands of L. anatifera. We also analysed the similarity of adhesive proteins across several barnacle taxa, including Pollicipes pollicipes (a stalked barnacle in the order Scalpelliformes). Sequence alignment of published expressed sequence tags clearly indicated that P. pollicipes possesses homologues for the 19 kDa and 100 kDa proteins in acorn barnacles. Homology aside, sequence similarity in amino acid and gene sequences tended to decline as taxonomic distance increased, with minimum similarities of 18–26%, depending on the gene. The results indicate that some adhesive proteins (e.g. 100 kDa) are more conserved within barnacles than others (20 kDa).

Repurposed transcriptomic data facilitate discovery of innate immunity toll-like receptor (TLR) Genes across Lophotrochozoa

The growing volume of genomic data from across life represents opportunities for deriving valuable biological information from data that were initially collected for another purpose. Here, we use transcriptomes collected for phylogenomic studies to search for toll-like receptor (TLR) genes in poorly sampled lophotrochozoan clades (Annelida, Mollusca, Brachiopoda, Phoronida, and Entoprocta) and one ecdysozoan clade (Priapulida). TLR genes are involved in innate immunity across animals by recognizing potential microbial infection. They have an extracellular leucine-rich repeat (LRR) domain connected to a transmembrane domain and an intracellular toll/interleukin-1 receptor (TIR) domain. Consequently, these genes are important in initiating a signaling pathway to trigger defense. We found at least one TLR ortholog in all but two taxa examined, suggesting that a broad array of lophotrochozoans may have innate immune systems similar to those observed in vertebrates and arthropods. Comparison to the SMART database confirmed the presence of both the LRR and the TIR protein motifs characteristic of TLR genes. Because we looked at only one transcriptome per species, discovery of TLR genes was limited for most taxa. However, several TRL-like genes that vary in the number and placement of LRR domains were found in phoronids. Additionally, several contigs contained LRR domains but lacked TIR domains, suggesting they were not TLRs. Many of these LRR-containing contigs had other domains (e.g., immunoglobin) and are likely involved in innate immunity.