Evidence for a clade of nematodes, arthropods and other moulting animals

Recent advances in understanding vertebrate segmentation

Segmentation is the partitioning of the body axis into a series of repeating units or segments. This widespread body plan is found in annelids, arthropods, and chordates, showing it to be a successful developmental strategy for growing and generating diverse morphology and anatomy. Segmentation has been extensively studied over the years. Forty years ago, Cooke and Zeeman published the Clock and Wavefront model, creating a theoretical framework of how developing cells could acquire and keep temporal and spatial information in order to generate a segmented pattern. Twenty years later, in 1997, Palmeirim and co-workers found the first clock gene whose oscillatory expression pattern fitted within Cooke and Zeeman's model. Currently, in 2017, new experimental techniques, such as new ex vivo experimental models, real-time imaging of gene expression, live single cell tracking, and simplified transgenics approaches, are revealing some of the fine details of the molecular processes underlying the inner workings of the segmentation mechanisms, bringing new insights into this fundamental process. Here we review and discuss new emerging views that further our understanding of the vertebrate segmentation clock, with a particular emphasis on recent publications that challenge and/or complement the currently accepted Clock and Wavefront model.

Zoology: War of the Worms

The phylogenetic affinities of Xenacoelomorpha - the phylum comprising Xenoturbella bocki and acoelomorph worms - are debated. Two recent studies conclude they represent the earliest branching bilaterally symmetrical animals, but additional tests may be needed to confirm this notion.

The genomic basis of nematode parasitism

Nematodes are highly abundant animals, and many species have a parasitic lifestyle. Nematode parasites are important pathogens of humans and other animals, and there is considerable interest in understanding their molecular and genomic adaptations to nematode parasitism. This has been approached in three main ways: comparing the genomes of closely related parasitic and free-living taxa, comparing the gene expression of parasitic and free-living life cycle stages of parasitic nematode species, and analysing the molecules that parasitic nematodes excrete and secrete. To date, these studies show that many species of parasitic nematodes have genomes that have large gene families coding for proteases/peptidases, protease inhibitors, SCP/TAPS proteins and acetylcholinesterases, and in many cases there is evidence that these appear to be used by parasitic stages inside hosts, and are often secreted. Many parasitic nematodes have taxa-restricted gene families that also appear to be involved in parasitism, emphasizing that there is still much to be discovered about what it takes to be a parasitic nematode.

Bioinspired self-healing materials: lessons from nature

Healing is an intrinsic ability in the incredibly biodiverse populations of the plant and animal kingdoms created through evolution. Plants and animals approach healing in similar ways but with unique pathways, such as damage containment in plants or clotting in animals. After analyzing the examples of healing and defense mechanisms found in living nature, eight prevalent mechanisms were identified: reversible muscle control, clotting, cellular response, layering, protective surfaces, vascular networks or capsules, exposure, and replenishable functional coatings. Then the relationship between these mechanisms, nature's best (evolutionary) methods of mitigating and healing damage, and existing technology in self-healing materials are described. The goals of this top-level overview are to provide a framework for relating the behavior seen in living nature to bioinspired materials, act as a resource to addressing the limitations/problems with existing materials, and open up new avenues of insight and research into self-healing materials.

Developmental biology and potential use of Alboglossiphonia lata (Annelida: Hirudinea) as an "Evo-Devo" model organism

BACKGROUND

The need for the adaptation of species of annelids as "Evo-Devo" model organisms of the superphylum Lophotrochozoa to refine the understanding of the phylogenetic relationships between bilaterian organisms, has promoted an increase in the studies dealing with embryonic development among related species such as leeches from the Glossiphoniidae family. The present study aims to describe the embryogenesis of Alboglossiphonia lata (Oka, 1910), a freshwater glossiphoniid leech, chiefly distributed in East Asia, and validate standard molecular biology techniques to support the use of this species as an additional model for "Evo-Devo" studies.

RESULTS

A. lata undergoes direct development, and follows the highly conserved clitellate annelid mode of spiral cleavage development; the duration from the egg laying to the juvenile stage is ~7.5 days, and it is iteroparous, indicating that it feeds and deposits eggs again after the first round of brooding, as described in several other glossiphoniid leech species studied to date. The embryos hatch only after complete organ development and proboscis retraction, which has not yet been observed in other glossiphoniid genera. The phylogenetic position of A. lata within the Glossiphoniidae family has been confirmed using cytochrome c oxidase subunit 1 (CO1) sequencing. Lineage tracer injections confirmed the fates of the presumptive meso- and ectodermal precursors, and immunostaining showed the formation of the ventral nerve system during later stages of development. Further, the spatiotemporal expression of an EF-hand calcium-binding protein Calsensin ortholog was characterized, which showed a specific pattern in both the ventral and peripheral nervous systems during the later stages.

CONCLUSIONS

Our description of the embryonic development of A. lata under laboratory conditions provides new data for further comparative studies with other leech and lophotrochozoa model organisms. Moreover, it offers a basis for the establishment of this species as a model for future "Evo-Devo" studies.

Fossils and the Evolution of the Arthropod Brain

The discovery of fossilized brains and ventral nerve cords in lower and mid-Cambrian arthropods has led to crucial insights about the evolution of their central nervous system, the segmental identity of head appendages and the early evolution of eyes and their underlying visual systems. Fundamental ground patterns of lower Cambrian arthropod brains and nervous systems correspond to the ground patterns of brains and nervous systems belonging to three of four major extant panarthropod lineages. These findings demonstrate the evolutionary stability of early neural arrangements over an immense time span. Here, we put these fossil discoveries in the context of evidence from cladistics, as well as developmental and comparative neuroanatomy, which together suggest that despite many evolved modifications of neuropil centers within arthropod brains and ganglia, highly conserved arrangements have been retained. Recent phylogenies of the arthropods, based on fossil and molecular evidence, and estimates of divergence dates, suggest that neural ground patterns characterizing onychophorans, chelicerates and mandibulates are likely to have diverged between the terminal Ediacaran and earliest Cambrian, heralding the exuberant diversification of body forms that account for the Cambrian Explosion.

Rooting phylogenetic trees under the coalescent model using site pattern probabilities

BACKGROUND

Phylogenetic tree inference is a fundamental tool to estimate ancestor-descendant relationships among different species. In phylogenetic studies, identification of the root - the most recent common ancestor of all sampled organisms - is essential for complete understanding of the evolutionary relationships. Rooted trees benefit most downstream application of phylogenies such as species classification or study of adaptation. Often, trees can be rooted by using outgroups, which are species that are known to be more distantly related to the sampled organisms than any other species in the phylogeny. However, outgroups are not always available in evolutionary research.

METHODS

In this study, we develop a new method for rooting species tree under the coalescent model, by developing a series of hypothesis tests for rooting quartet phylogenies using site pattern probabilities. The power of this method is examined by simulation studies and by application to an empirical North American rattlesnake data set.

RESULTS

The method shows high accuracy across the simulation conditions considered, and performs well for the rattlesnake data. Thus, it provides a computationally efficient way to accurately root species-level phylogenies that incorporates the coalescent process. The method is robust to variation in substitution model, but is sensitive to the assumption of a molecular clock.

CONCLUSIONS

Our study establishes a computationally practical method for rooting species trees that is more efficient than traditional methods. The method will benefit numerous evolutionary studies that require rooting a phylogenetic tree without having to specify outgroups.

A phylogenetic classification of gastropod aquaporins

Successful responses to the multifarious challenges of controlling water balance are critical for snails' survival in the great diversity of habitats they occupy. Advances are being made in understanding how such challenges are approached at the molecular level, including through the study of aquaporins, which are proteins functioning to facilitate the passage of water and other small molecules across cellular membranes. Deduced aquaporin amino acid sequences from partial genomic assemblies of three neritimorph species were added to available gastropod data and sequences from other taxa to make a phylogenetic classification of these proteins using maximum likelihood and Bayesian analyses. We identified ten groups, designated as G1 to G10, containing sequences from multiple major gastropod lineages. At least six of the groups appear to be encoded by multiple genes within at least some species. Five weakly-associated sequences from Neritimorpha were not allocated to a group. The designated groups G1, G2, G3, G4, G5 and G7 (previously defined as Malacoglyceroporins) formed clades containing only gastropod sequences and were strongly supported by Bayesian inference. G1, G2, G3 and G5 were also strongly supported by maximum likelihood analyses. Group G6 (previously defined as Malacoaquaporins)was included with sequences from the oyster, Crassostrea gigas in a strongly supported clade. Groups G8 and G9 included only gastropod sequences but were not strongly supported. Groups G8 and G10 were designated to include all the gastropod sequences belonging respectively to strongly-supported clades including human aquaglyceroporins and aquaammoniaporins. Most groups have been found in a wide range of gastropod lineages but all identified representatives of group G7 belong to Apogastropoda whereas G2 is known only from Patellogastropoda and Neritimorpha.

On the evolution of bilaterality

Bilaterality – the possession of two orthogonal body axes – is the name-giving trait of all bilaterian animals. These body axes are established during early embryogenesis and serve as a three-dimensional coordinate system that provides crucial spatial cues for developing cells, tissues, organs and appendages. The emergence of bilaterality was a major evolutionary transition, as it allowed animals to evolve more complex body plans. Therefore, how bilaterality evolved and whether it evolved once or several times independently is a fundamental issue in evolutionary developmental biology. Recent findings from non-bilaterian animals, in particular from Cnidaria, the sister group to Bilateria, have shed new light into the evolutionary origin of bilaterality. Here, we compare the molecular control of body axes in radially and bilaterally symmetric cnidarians and bilaterians, identify the minimal set of traits common for Bilateria, and evaluate whether bilaterality arose once or more than once during evolution.

Antimicrobial effectors in the nematode Caenorhabditis elegans: an outgroup to the Arthropoda

Nematodes and arthropods likely form the taxon Ecdysozoa. Information on antimicrobial effectors from the model nematode Caenorhabditis elegans may thus shed light on the evolutionary origin of these defences in arthropods. This nematode species possesses an extensive armory of putative antimicrobial effector proteins, such as lysozymes, caenopores (or saposin-like proteins), defensin-like peptides, caenacins and neuropeptide-like proteins, in addition to the production of reactive oxygen species and autophagy. As C. elegans is a bacterivore that lives in microbe-rich environments, some of its effector peptides and proteins likely function in both digestion of bacterial food and pathogen elimination. In this review, we provide an overview of C. elegans immune effector proteins and mechanisms. We summarize the experimental evidence of their antimicrobial function and involvement in the response to pathogen infection. We further evaluate the microbe-induced expression of effector genes using WormExp, a recently established database for C. elegans gene expression analysis. We emphasize the need for further analysis at the protein level to demonstrate an antimicrobial activity of these molecules both in vitro and in vivoThis article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'.

ADAR RNA editing below the backbone

ADAR RNA editing enzymes (adenosine deaminases acting on RNA) that convert adenosine bases to inosines were first identified biochemically 30 years ago. Since then, studies on ADARs in genetic model organisms, and evolutionary comparisons between them, continue to reveal a surprising range of pleiotropic biological effects of ADARs. This review focuses on Drosophila melanogaster, which has a single Adar gene encoding a homolog of vertebrate ADAR2 that site-specifically edits hundreds of transcripts to change individual codons in ion channel subunits and membrane and cytoskeletal proteins. Drosophila ADAR is involved in the control of neuronal excitability and neurodegeneration and, intriguingly, in the control of neuronal plasticity and sleep. Drosophila ADAR also interacts strongly with RNA interference, a key antiviral defense mechanism in invertebrates. Recent crystal structures of human ADAR2 deaminase domain-RNA complexes help to interpret available information on Drosophila ADAR isoforms and on the evolution of ADARs from tRNA deaminase ADAT proteins. ADAR RNA editing is a paradigm for the now rapidly expanding range of RNA modifications in mRNAs and ncRNAs. Even with recent progress, much remains to be understood about these groundbreaking ADAR RNA modification systems.

Gene Regulatory Networks, Homology, and the Early Panarthropod Fossil Record

The arthropod body plan is widely believed to have derived from an ancestral form resembling Cambrian-aged fossil lobopodians, and interpretations of morphological and molecular data have long favored this hypothesis. It is possible, however, that appendages and other morphologies observed in extinct and living panarthropods evolved independently. The key to distinguishing between morphological homology and homoplasy lies in the study of developmental gene regulatory networks (GRNs), and specifically, in determining the unique genetic circuits that construct characters. In this study, I discuss character identity and panarthropod appendage evolution within a developmental GRN framework, with a specific focus on potential limb character identity networks ("ChINs"). I summarize recent molecular studies, and argue that current data do not rule out the possibility of independent panarthropod limb evolution. The link between character identity and GRN architecture has broad implications for homology assessment, and this genetic framework offers alternative approaches to fossil character coding, phylogenetic analyses, and future research into the origin of the arthropod body plan.

Can quartet analyses combining maximum likelihood estimation and Hennigian logic overcome long branch attraction in phylogenomic sequence data?

Systematic biases such as long branch attraction can mislead commonly relied upon model-based (i.e. maximum likelihood and Bayesian) phylogenetic methods when, as is usually the case with empirical data, there is model misspecification. We present PhyQuart, a new method for evaluating the three possible binary trees for any quartet of taxa. PhyQuart was developed through a process of reciprocal illumination between a priori considerations and the results of extensive simulations. It is based on identification of site-patterns that can be considered to support a particular quartet tree taking into account the Hennigian distinction between apomorphic and plesiomorphic similarity, and employing corrections to the raw observed frequencies of site-patterns that exploit expectations from maximum likelihood estimation. We demonstrate through extensive simulation experiments that, whereas maximum likeilihood estimation performs well in many cases, it can be outperformed by PhyQuart in cases where it fails due to extreme branch length asymmetries producing long-branch attraction artefacts where there is only very minor model misspecification.

Generation of animal form by the Chordin/Tolloid/BMP gradient: 100 years after D'Arcy Thompson

The classic book "On Growth and Form" by naturalist D'Arcy Thompson was published 100 years ago. To celebrate this landmark, we present experiments in the Xenopus embryo that provide a framework for understanding how simple, quantitative transformations of a morphogen gradient might have affected evolution and morphological diversity of organisms. D'Arcy Thompson proposed that different morphologies might be generated by modifying physical parameters in an underlying system of Cartesian coordinates that pre-existed in Nature and arose during evolutionary history. Chordin is a BMP antagonist secreted by the Spemann organizer located on the dorsal side of the gastrula. Chordin generates a morphogen gradient as first proposed by mathematician Alan Turing. The rate-limiting step of this dorsal-ventral (D-V) morphogen is the degradation of Chordin by the Tolloid metalloproteinase in the ventral side. Chordin is expressed at gastrula on the dorsal side where BMP signaling is low, while at the opposite side peak levels of BMP signaling are reached. In fishes, amphibians, reptiles and birds, high BMP signaling in the ventral region induces transcription of a secreted inhibitor of Tolloid called Sizzled. By depleting Sizzled exclusively in the ventral half of the embryo we were able to expand the ventro-posterior region in an otherwise normal embryo. Conversely, ventral depletion of Tolloid, which stabilizes Chordin, decreased ventral and tail structures, phenocopying the tolloid zebrafish mutation. We explain how historical constraints recorded in the language of DNA become subject to the universal laws of physics when an ancestral reaction-diffusion morphogen gradient dictates form.

The unique uterine structure of the basal monogenean Chimaericola leptogaster (Monogenea: Polyopisthocotylea), an ectoparasite of the relictual holocephalan fish Chimaera monstrosa

Ultrastructural studies of the monogenean uterus are few in number and no non-polystomatid polyopisthocotyleans have been investigated. The uterus of Chimaericola leptogaster, a basal polyopisthocotylean monogenean, has several unusual features, including six reflexed loops comprising four ascending and three descending, longitudinally oriented, linear sections. At the ultrastructural level, three readily distinguishable uterine regions and other distinctive characteristics are apparent. One novel feature occurs in the proximal uterus, where the lining forms a so-called 'single-layered multi-rowed cellular epithelium', which includes two types of cells, tall (ca. 14-19 μm in height) and short (ca. 6-9 μm in height) cells, both lying on the basement membrane. Although known from other bilaterian groups, this is the first record of this type of epithelium in the Neodermata. The lining of the middle uterine region comprises a single regular layer of columnar glandular epithelial cells, which produce numerous rounded, electron-dense granules associated with Golgi complexes. The presence of the uterine glands in the middle region of the uterus is an unusual feature for a monogenean, having previously been described only for basal orders of the Cestoda, i.e. the Gyrocotylidea, Caryophyllidea and Spathebothriidea. Seen in cross-section, the epithelium of the distal uterus contains three areas of tall single-layered columnar epithelium (ca. 30 μm deep) interspersed by three areas of flattened epithelium (ca. 0.2-0.9 μm deep). Such a pattern is quite different from those reported for other monogeneans and, indeed, other neodermatan groups. The investigation has shown that the outer layer of the fully formed eggshell is assembled from epithelial secretions in the middle uterine lumen, but is modified in terms of its shape in the distal uterus. Possible phylogenetic implications arising from the unusual features described are discussed in relation to other neodermatan groups and recent molecular phylogenies of the Bilateria.

Paleobiology of Predators, Parasitoids, and Parasites: Death and Accomodation in the Fossil Record of Continental Invertebrates

Carnivory is the consumption of one animal by another animal; among invertebrates in terrestrial and freshwater ecosystems this type of feeding can take three forms: predation, parasitoidism, and parasitism. Differences among these three functional modes involve (i) whether the duration of feeding on the prey item is quick or there is an accommodation, coevolutionary or otherwise, between the carnivore and the host prey; (ii) whether the prey or host is killed; (iii) whether single or multiple prey or host items are consumed during the carnivore's lifespan, and (iv) the relative sizes of the carnivore and its prey or host. Uniformitarian and nonuniformitarian evidence directly relating to the history of carnivory can be found in exceptionally preserved deposits from the mid-Paleozoic to the Recent, but such evidence is relatively rare because carnivores are the least represented trophic group in ecosystems. Six types of paleobiological data provide evidence for carnivory: taxonomic affiliation, fossil structural and functional attributes, organismic damage, gut contents, coprolites, and indications of mechanisms for predator avoidance.

Only 12 invertebrate phyla have become carnivorous in the continental realm. Six are lophotrochozoans (Acanthocephala, Rotifera, Platyhelminthes, Nemertinea, Mollusca, and Annelida) and six are ecdysozoans (Nematoda, Nematomorpha, Tardigrada, Onychophora, Pentastoma, and Arthropoda). Most of these groups have poor continental fossil records, but the two most diverse—nematodes and arthropods—have comparatively good representation. The record of arthropods documents (i) the presence of predators among primary producers, herbivores, and decomposers in early terrestrial ecosystems; (ii) the addition later in the fossil record of the more accommodationist strategies of parasitoids and parasites interacting with animal hosts; (iii) the occurrence of simpler food-web structures in terrestrial ecosystems prior to parasitoid and parasite diversification; and (iv) a role for mass extinction in the degradation of food-web structure that ultimately affected carnivory. Future research should explore how different modes of carnivory have brought about changes in ecosystem structure through time. Despite numerous caveats and uncertainties, trace fossils left by predators on skeletons of their prey remain one of the most promising research directions in paleoecology and evolutionary paleobiology.

Non-model model organisms

Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future.

Identification of introns harboring functional sequence elements through positional conservation

Many human introns carry out a function, in the sense that they are critical to maintain normal cellular activity. Their identification is fundamental to understanding cellular processes and disease. However, being noncoding elements, such functional introns are poorly predicted based on traditional approaches of sequence and structure conservation. Here, we generated a dataset of human functional introns that carry out different types of functions. We showed that functional introns share common characteristics, such as higher positional conservation along the coding sequence and reduced loss rates, regardless of their specific function. A unique property of the data is that if an intron is unknown to be functional, it still does not mean that it is indeed non-functional. We developed a probabilistic framework that explicitly accounts for this unique property, and predicts which specific human introns are functional. We show that we successfully predict function even when the algorithm is trained on introns with a different type of function. This ability has many implications in studying regulatory networks, gene regulation, the effect of mutations outside exons on human disease, and on our general understanding of intron evolution and their functional exaptation in mammals.

THE AGE AND RELATIONSHIPS OF THE MAJOR ANIMAL PHYLA

Given the uncertainties in the fossil record and the paucity of informative morphological characters, there is still considerable uncertainty as to the phylogenetic affinities and times of origins of essentially all of the phyla of animals. A multilocus analysis of amino-acid sequence data for mitochondrial genes suggests that the major triploblast phyla began diverging approximately 630 million years ago. These results support the hypothesis that the so-called Cambrian radiation of animals actually initiated about 100 million years prior to the Cambrian, as the fossil evidence suggests. In addition, phylogenetic analysis supports the monophyly of animals, an early (~900 million years ago) branching off of the cnidarian lineage, the monophyly of deuterostomes and protostomes, and the inclusion of nematodes in the protostome lineage. The results of this study suggest that, with appropriate levels of taxon sampling and a focus on conserved regions of protein-coding sequence, complete mitochondrial genome analysis may be sufficiently powerful to elucidate the genealogical relationships of many of the animal phyla.

Development of the nervous system in Platynereis dumerilii (Nereididae, Annelida)

Background

The structure and development of the nervous system in Lophotrochozoa has long been recognized as one of the most important subjects for phylogenetic and evolutionary discussion. Many recent papers have presented comprehensive data on the structure and development of catecholaminergic, serotonergic and FMRFamidergic parts of the nervous system. However, relatively few papers contain detailed descriptions of the nervous system in Annelida, one of the largest taxa of Lophotrochozoa. The polychaete species Platynereis dumerilii has recently become one of the more popular model animals in evolutionary and developmental biology. The goal of the present study was to provide a detailed description of its neuronal development. The data obtained will contribute to a better understanding of the basic features of neuronal development in polychaetes.

Results

We have studied the development of the nervous system in P. dumerilii utilizing histo- and immunochemical labelling of catecholamines, serotonin, FMRFamide related peptides, and acetylated tubulin. The first neuron differentiates at the posterior extremity of the protrochophore, reacts to the antibodies against both serotonin and FMRFamide. Then its fibres run forwards along the ventral side. Soon, more neurons appear at the apical extreme, and their basal neurites form the basel structure of the developing brain (cerebral neuropil and circumesophageal connectives). Initial development of the nervous system starts in two rudiments: anterior and posterior. At the nectochaete stage, segmental ganglia start to differentiate in the anterior-to-posterior direction, and the first structures of the stomatogastric and peripheral nervous system appear. All connectives including the unpaired ventral cord develop from initially paired nerves.

Conclusions

We present a detailed description of Platynereis dumerilii neuronal development based on anti-acetylated tubulin, serotonin, and FMRFamide-like immunostaining as well as catecholamine histofluorescence. The development of the nervous system starts from peripheral pioneer neurons at both the posterior and anterior poles of the larva, and their neurites form a scaffold upon which the adult central nervous system develops. The anterior-to-posterior mode of the ventral ganglia development challenges the primary heteronomy concept. Comparison with the development of Mollusca reveals substantial similarities with early neuronal development in larval Solenogastres.

Electronic supplementary material

The online version of this article (doi:10.1186/s12983-017-0211-3) contains supplementary material, which is available to authorized users.

Molting in C. elegans

Molting is an essential developmental process for the majority of animal species on Earth. During the molting process, which is a specialized form of extracellular matrix (ECM) remodeling, the old apical ECM, or cuticle, is replaced with a new one. Many of the genes and pathways identified as important for molting in nematodes are highly conserved in vertebrates and include regulators and components of vesicular trafficking, steroid-hormone signaling, developmental timers, and hedgehog-like signaling. In this review, we discuss what is known about molting, with a focus on studies in Caenorhabditis elegans. We also describe the key structural elements of the cuticle that must be released, newly synthesized, or remodeled for proper molting to occur.

Segmentation in Tardigrada and diversification of segmental patterns in Panarthropoda

The origin and diversification of segmented metazoan body plans has fascinated biologists for over a century. The superphylum Panarthropoda includes three phyla of segmented animals-Euarthropoda, Onychophora, and Tardigrada. This superphylum includes representatives with relatively simple and representatives with relatively complex segmented body plans. At one extreme of this continuum, euarthropods exhibit an incredible diversity of serially homologous segments. Furthermore, distinct tagmosis patterns are exhibited by different classes of euarthropods. At the other extreme, all tardigrades share a simple segmented body plan that consists of a head and four leg-bearing segments. The modular body plans of panarthropods make them a tractable model for understanding diversification of animal body plans more generally. Here we review results of recent morphological and developmental studies of tardigrade segmentation. These results complement investigations of segmentation processes in other panarthropods and paleontological studies to illuminate the earliest steps in the evolution of panarthropod body plans.

Molecular control of gut formation in the spider Parasteatoda tepidariorum

The development of a digestive system is an essential feature of bilaterians. Studies of the molecular control of gut formation in arthropods have been studied in detail in the fruit fly Drosophila melanogaster. However, little is known in other arthropods, especially in noninsect arthropods. To better understand the evolution of arthropod alimentary system, we investigate the molecular control of gut development in the spider Parasteatoda tepidariorum (Pt), the primary chelicerate model species for developmental studies. Orthologs of the ectodermal genes Pt-wingless (Pt-wg) and Pt-hedgehog (Pt-hh), of the endodermal genes, Pt-serpent (Pt-srp) and Pt-hepatocyte-nuclear factor-4 (Pt-hnf4) and of the mesodermal gene Pt-twist (Pt-twi) are expressed in the same germ layers during spider gut development as in D. melanogaster. Thus, our expression data suggest that the downstream molecular components involved in gut development in arthropods are conserved. However, Pt-forkhead (Pt-fkh) expression and function in spiders is considerably different from its D. melanogaster ortholog. Pt-fkh is expressed before gastrulation in a cell population that gives rise to endodermal and mesodermal precursors, suggesting a possible role for this factor in specification of both germ layers. To test this hypothesis, we knocked down Pt-fkh via RNA interference. Pt-fkh RNAi embryos not only fail to develop a proper gut, but also lack the mesodermal Pt-twi expressing cells. Thus, in spiders Pt-fkh specifies endodermal and mesodermal germ layers. We discuss the implications of these findings for the evolution and development of gut formation in Ecdysozoans.

Intra- and interspecific genetic diversity of New Zealand hairworms (Nematomorpha)

Hairworms (Nematomorpha) are a little-known group of parasites, and despite having been represented in the taxonomic literature for over a century, the implementation of molecular genetics in studies of hairworm ecology and evolution lags behind that of other parasitic taxa. In this study, we characterize the genetic diversity of the New Zealand nematomorph fauna and test for genetic structure within the most widespread species found. We provide new mitochondrial and nuclear ribosomal sequence data for three previously described species from New Zealand: Gordius paranensis, Parachordodes diblastus and Euchordodes nigromaculatus. We also present genetic data on a previously reported but undescribed Gordius sp., as well as data from specimens of a new Gordionus sp., a genus new for New Zealand. Phylogenetic analyses of CO1 and nuclear rDNA regions correspond with morphological classification based on scanning electron microscopy, and demonstrate paraphyly of the genus Gordionus and the potential for cryptic species within G. paranensis. Population-level analyses of E. nigromaculatus showed no genetic differentiation among sampling locations across the study area, in contrast to previously observed patterns in known and likely definitive hosts. Taken together, this raises the possibility that factors such as definitive host specificity, intermediate host movement, and passive dispersal of eggs and larvae may influence host-parasite population co-structure in hairworms.

External morphogenesis of the tardigrade Hypsibius dujardini as revealed by scanning electron microscopy

Tardigrada, commonly called water bears, is a taxon of microscopic panarthropods with five-segmented bodies and four pairs of walking legs. Although tardigrades have been known to science for several centuries, questions remain regarding many aspects of their biology, such as embryogenesis. Herein, we used scanning electron microscopy to document the external changes that occur during embryonic development in the tardigrade Hypsibius dujardini (Eutardigrada, Parachela, Hypsibiidae). Our results show an accelerated development of external features, with approximately 30 hrs separating the point at which external structures first become recognizable and a fully formed embryo. All segments appear to arise simultaneously between ∼20 and 25 hrs of development, and no differences in the degree of development could be detected between the limb buds at any stage. Claws emerge shortly after the limb buds and are morphologically similar to those of adults. The origin of the claws is concurrent with that of the sclerotized parts of the mouth, suggesting that all cuticular structures arise simultaneously at ∼30 hrs. The mouth arises as an invagination in the terminal region of the head at ∼25 hrs, closes later in development, and opens again shortly before hatching. The anlagen of the peribuccal lobes arise as one dorsal and one ventral row, each consisting of three lobes, and later form a ring in the late embryo, whereas there is no indication of a labrum anlage at any point during development. Furthermore, we describe limited postembryonic development in the form of cuticular pores that are absent in juveniles but present in adults. This study represents the first scanning electron micrographs of tardigrade embryos, demonstrating the utility of this technique for studying embryogenesis in tardigrades. This work further adds an external morphological perspective to the developmental data already available for H. dujardini, facilitating future comparisons to related panarthropod taxa. J. Morphol. 278:563-573, 2017. © 2017 Wiley Periodicals, Inc.

Gelsolin in Onychophora and Tardigrada with notes on its variability in the Ecdysozoa

Rearrangements of the filamentous actin network involve a broad range of actin binding proteins. Among these, the gelsolin proteins sever actin filaments, cap their fast growing end and nucleate actin assembly in a calcium-dependent manner. Here, we focus on the gelsolin of the onychophoran Peripatoides novaezealandiae and the eutardigrade Hypsibius dujardini. From the cDNA of P. novaezealandiae we obtained the complete coding sequence with an open reading frame of 2178bp. It encodes a protein of 726 amino acids with a calculated molecular mass of 82,610.9Da and a pI of 5.57. This sequence is comprised of six segments (S1-S6). However, analysis of data from TardiBase reveals that the gelsolin of the eutardigrade Hypsibius dujardini has only three segments (S1-S3). The coding sequence consist of 1119bp for 373 amino acids with a calculated molecular mass of 42,440.95Da and a pI of 6.17. The Peripatoides and Hypsibius gelsolin revealed both conserved binding motifs for G-actin, F-actin and phosphatidylinositol 4,5-bisphosphate (PIP₂), along with a full set of type-1 and type-2 Ca²⁺-binding sites which could result in the binding of eight and four calcium ions, respectively. Both gelsolin proteins lack a C-terminal latch-helix indicating a more rapid activation in the submicromolar Ca²⁺ range. We suggest that a gelsolin with three segments was present in the last common ancestor of the ecdysozoan clade Panarthropoda (Onychophora, Tardigrada, Arthropoda), primarily because the gelsolin of all non-Ecdysozoa studied so far (except Chordata) reveals this number of segments. Mapping of our molecular data onto a well-established phylogeny revealed that the number of gelsolin segments does not correlate with the phylogenetic lineage but rather with particular functional demands to alter the kinetics of actin polymerization.

Tardigrada of Ireland: a review of records and an updated checklist of species including a new addition to the Irish fauna

The phylum Tardigrada was not recorded in Ireland until the Clare Island Survey of 1909-1911, with only rare subsequent reports on Irish tardigrade species. In recent decades, significant taxonomic revision has occurred within Tardigrada. This has resulted in the need for a review of all known historical records from Ireland and Northern Ireland in order to produce an updated checklist of valid taxa. The new checklist includes fifty-one tardigrade species and subspecies including a new addition to the Irish fauna reported herein, Echiniscus quadrispinosus quadrispinosus Richters, 1902 from Newtown, Ballyvaughan, Co. Clare.

Onychophoran-like musculature in a phosphatized Cambrian lobopodian

The restricted, exclusively terrestrial distribution of modern Onychophora contrasts strikingly with the rich diversity of onychophoran-like fossils preserved in marine Cambrian Lagerstätten The transition from these early forebears to the modern onychophoran body plan is poorly constrained, in part owing to the absence of fossils preserving details of the soft anatomy. Here, we report muscle tissue in a new early Cambrian (Stage 3) lobopodian, Tritonychus phanerosarkus gen. et sp. nov., preserved in the Orsten fashion by three-dimensional replication in phosphate. This first report of Palaeozoic onychophoran musculature establishes peripheral musculature as a characteristic of the ancestral panarthropod, but documents an unexpected muscular configuration. Phylogenetic analysis reconstructs T. phanerosarkus as one of a few members of the main onychophoran lineage-which was as rare and as cryptic in the Cambrian period as it is today.

Co-evolution of SNF spliceosomal proteins with their RNA targets in trans-splicing nematodes

Although the mechanism of pre-mRNA splicing has been well characterized, the evolution of spliceosomal proteins is poorly understood. The U1A/U2B″/SNF family (hereafter referred to as the SNF family) of RNA binding spliceosomal proteins participates in both the U1 and U2 small interacting nuclear ribonucleoproteins (snRNPs). The highly constrained nature of this system has inhibited an analysis of co-evolutionary trends between the proteins and their RNA binding targets. Here we report accelerated sequence evolution in the SNF protein family in Phylum Nematoda, which has allowed an analysis of protein:RNA co-evolution. In a comparison of SNF genes from ecdysozoan species, we found a correlation between trans-splicing species (nematodes) and increased phylogenetic branch lengths of the SNF protein family, with respect to their sister clade Arthropoda. In particular, we found that nematodes (~70-80 % of pre-mRNAs are trans-spliced) have experienced higher rates of SNF sequence evolution than arthropods (predominantly cis-spliced) at both the nucleotide and amino acid levels. Interestingly, this increased evolutionary rate correlates with the reliance on trans-splicing by nematodes, which would alter the role of the SNF family of spliceosomal proteins. We mapped amino acid substitutions to functionally important regions of the SNF protein, specifically to sites that are predicted to disrupt protein:RNA and protein:protein interactions. Finally, we investigated SNF's RNA targets: the U1 and U2 snRNAs. Both are more divergent in nematodes than arthropods, suggesting the RNAs have co-evolved with SNF in order to maintain the necessarily high affinity interaction that has been characterized in other species.

Phylogenomic Insights into Animal Evolution

Animals make up only a small fraction of the eukaryotic tree of life, yet, from our vantage point as members of the animal kingdom, the evolution of the bewildering diversity of animal forms is endlessly fascinating. In the century following the publication of Darwin's Origin of Species, hypotheses regarding the evolution of the major branches of the animal kingdom - their relationships to each other and the evolution of their body plans - was based on a consideration of the morphological and developmental characteristics of the different animal groups. This morphology-based approach had many successes but important aspects of the evolutionary tree remained disputed. In the past three decades, molecular data, most obviously primary sequences of DNA and proteins, have provided an estimate of animal phylogeny largely independent of the morphological evolution we would ultimately like to understand. The molecular tree that has evolved over the past three decades has drastically altered our view of animal phylogeny and many aspects of the tree are no longer contentious. The focus of molecular studies on relationships between animal groups means, however, that the discipline has become somewhat divorced from the underlying biology and from the morphological characteristics whose evolution we aim to understand. Here, we consider what we currently know of animal phylogeny; what aspects we are still uncertain about and what our improved understanding of animal phylogeny can tell us about the evolution of the great diversity of animal life.

Recent Duplication and Functional Divergence in Parasitic Nematode Levamisole-Sensitive Acetylcholine Receptors

Helminth parasites rely on fast-synaptic transmission in their neuromusculature to experience the outside world and respond to it. Acetylcholine plays a pivotal role in this and its receptors are targeted by a wide variety of both natural and synthetic compounds used in human health and for the control of parasitic disease. The model, Caenorhabditis elegans is characterized by a large number of acetylcholine receptor subunit genes, a feature shared across the nematodes. This dynamic family is characterized by both gene duplication and loss between species. The pentameric levamisole-sensitive acetylcholine receptor has been characterized from C. elegans, comprised of five different subunits. More recently, cognate receptors have been reconstituted from multiple parasitic nematodes that are found to vary in subunit composition. In order to understand the implications of receptor composition change and the origins of potentially novel drug targets, we investigated a specific example of subunit duplication based on analysis of genome data for 25 species from the 50 helminth genome initiative. We found multiple independent duplications of the unc-29, acetylcholine receptor subunit, where codon substitution rate analysis identified positive, directional selection acting on amino acid positions associated with subunit assembly. Characterization of four gene copies from a model parasitic nematode, Haemonchus contortus, demonstrated that each copy has acquired unique functional characteristics based on phenotype rescue of transgenic C. elegans and electrophysiology of receptors reconstituted in Xenopus oocytes. We found evidence that a specific incompatibility has evolved for two subunits co-expressed in muscle. We demonstrated that functional divergence of acetylcholine receptors, driven by directional selection, can occur more rapidly than previously thought and may be mediated by alteration of receptor assembly. This phenomenon is common among the clade V parasitic nematodes and this work provides a foundation for understanding the broader context of changing anthelmintic drug targets across the parasitic nematodes.

Early developmental stages of Ascaris lumbricoides featured by high-resolution mass spectrometry

Ascaris lumbricoides is responsible for a highly disseminated helminth parasitic disease, ascariosis, a relevant parasitosis that responds for great financial burden on the public health system of developing countries. In this work, metabolic fingerprinting using high-resolution mass spectrometry (HRMS) was employed to identify marker molecules from A. lumbricoides in different development stages. We have identified nine biomarkers, such as pheromones and steroidal prohormones in early stages, among other molecules in late development stages, making up four molecules for fertilized eggs, four marker molecules for first larvae (L1) and one marker molecule for third larvae (L3). Therefore, our findings indicate that this approach is suitable for biochemical characterization of A. lumbricoides development stages. Moreover, the straightforward analytical method employed, with almost no sample preparation from a complex matrix (feces) using high-resolution mass spectrometry, suggests that it is possible to seek for an easier and faster way to study animal molding processes.

Rising levels of atmospheric oxygen and evolution of Nrf2

In mammals, the master transcription regulator of antioxidant defences is provided by the Nrf2 protein. Phylogenetic analyses of Nrf2 sequences are used here to derive a molecular clock that manifests persuasive evidence that Nrf2 orthologues emerged, and then diverged, at two time points that correlate with well-established geochemical and palaeobiological chronologies during progression of the 'Great Oxygenation Event'. We demonstrate that orthologues of Nrf2 first appeared in fungi around 1.5 Ga during the Paleoproterozoic when photosynthetic oxygen was being absorbed into the oceans. A subsequent significant divergence in Nrf2 is seen during the split between fungi and the Metazoa approximately 1.0-1.2 Ga, at a time when oceanic ventilation released free oxygen to the atmosphere, but with most being absorbed by methane oxidation and oxidative weathering of land surfaces until approximately 800 Ma. Atmospheric oxygen levels thereafter accumulated giving rise to metazoan success known as the Cambrian explosion commencing at ~541 Ma. Atmospheric O2 levels then rose in the mid Paleozoic (359-252 Ma), and Nrf2 diverged once again at the division between mammals and non-mammalian vertebrates during the Permian-Triassic boundary (~252 Ma). Understanding Nrf2 evolution as an effective antioxidant response may have repercussions for improved human health.

Eukaryotic origins

The origin of the eukaryotes is a fundamental scientific question that for over 30 years has generated a spirited debate between the competing Archaea (or three domains) tree and the eocyte tree. As eukaryotes ourselves, humans have a personal interest in our origins. Eukaryotes contain their defining organelle, the nucleus, after which they are named. They have a complex evolutionary history, over time acquiring multiple organelles, including mitochondria, chloroplasts, smooth and rough endoplasmic reticula, and other organelles all of which may hint at their origins. It is the evolutionary history of the nucleus and their other organelles that have intrigued molecular evolutionists, myself included, for the past 30 years and which continues to hold our interest as increasingly compelling evidence favours the eocyte tree. As with any orthodoxy, it takes time to embrace new concepts and techniques.

Rooting the tree of life: the phylogenetic jury is still out

This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue. First, we briefly review the difficulties plaguing phylogenetic inference and the ways to improve the modelling of the substitution process, which is highly heterogeneous, both across sites and over time. We further observe that enriched taxon samplings, better gene samplings and clever data removal strategies have led to numerous revisions of the ToL, and that these improved shallow phylogenies nearly always relocate simple organisms higher in the ToL provided that long-branch attraction artefacts are kept at bay. Then, we note that, despite the flood of genomic data available since 2000, there has been a surprisingly low interest in inferring the root of the ToL. Furthermore, the rare studies dealing with this question were almost always based on methods dating from the 1990s that have been shown to be inaccurate for much more shallow issues! This leads us to argue that the current consensus about a bacterial root for the ToL can be traced back to the prejudice of Aristotle's Great Chain of Beings, in which simple organisms are ancestors of more complex life forms. Finally, we demonstrate that even the best models cannot yet handle the complexity of the evolutionary process encountered both at shallow depth, when the outgroup is too distant, and at the level of the inter-domain relationships. Altogether, we conclude that the commonly accepted bacterial root is still unproven and that the root of the ToL should be revisited using phylogenomic supermatrices to ensure that new evidence for eukaryogenesis, such as the recently described Lokiarcheota, is interpreted in a sound phylogenetic framework.

LS³: A Method for Improving Phylogenomic Inferences When Evolutionary Rates Are Heterogeneous among Taxa

Phylogenetic inference artifacts can occur when sequence evolution deviates from assumptions made by the models used to analyze them. The combination of strong model assumption violations and highly heterogeneous lineage evolutionary rates can become problematic in phylogenetic inference, and lead to the well-described long-branch attraction (LBA) artifact. Here, we define an objective criterion for assessing lineage evolutionary rate heterogeneity among predefined lineages: the result of a likelihood ratio test between a model in which the lineages evolve at the same rate (homogeneous model) and a model in which different lineage rates are allowed (heterogeneous model). We implement this criterion in the algorithm Locus Specific Sequence Subsampling (LS³), aimed at reducing the effects of LBA in multi-gene datasets. For each gene, LS³ sequentially removes the fastest-evolving taxon of the ingroup and tests for lineage rate homogeneity until all lineages have uniform evolutionary rates. The sequences excluded from the homogeneously evolving taxon subset are flagged as potentially problematic. The software implementation provides the user with the possibility to remove the flagged sequences for generating a new concatenated alignment. We tested LS³ with simulations and two real datasets containing LBA artifacts: a nucleotide dataset regarding the position of Glires within mammals and an amino-acid dataset concerning the position of nematodes within bilaterians. The initially incorrect phylogenies were corrected in all cases upon removing data flagged by LS³.

Animal Evolution: When Small Worms Cast Long Phylogenetic Shadows

New phylogenetic studies of minuscule worms reveal interesting perspectives about animal body plan evolution, but were early bilaterian animals large or small?

Holding it together: rapid evolution and positive selection in the synaptonemal complex of Drosophila

Background

The synaptonemal complex (SC) is a highly conserved meiotic structure that functions to pair homologs and facilitate meiotic recombination in most eukaryotes. Five Drosophila SC proteins have been identified and localized within the complex: C(3)G, C(2)M, CONA, ORD, and the newly identified Corolla. The SC is required for meiotic recombination in Drosophila and absence of these proteins leads to reduced crossing over and chromosomal nondisjunction. Despite the conserved nature of the SC and the key role that these five proteins have in meiosis in D. melanogaster, they display little apparent sequence conservation outside the genus. To identify factors that explain this lack of apparent conservation, we performed a molecular evolutionary analysis of these genes across the Drosophila genus.

Results

For the five SC components, gene sequence similarity declines rapidly with increasing phylogenetic distance and only ORD and C(2)M are identifiable outside of the Drosophila genus. SC gene sequences have a higher dN/dS (ω) rate ratio than the genome wide average and this can in part be explained by the action of positive selection in almost every SC component. Across the genus, there is significant variation in ω for each protein. It further appears that ω estimates for the five SC components are in accordance with their physical position within the SC. Components interacting with chromatin evolve slowest and components comprising the central elements evolve the most rapidly. Finally, using population genetic approaches, we demonstrate that positive selection on SC components is ongoing.

Conclusions

SC components within Drosophila show little apparent sequence homology to those identified in other model organisms due to their rapid evolution. We propose that the Drosophila SC is evolving rapidly due to two combined effects. First, we propose that a high rate of evolution can be partly explained by low purifying selection on protein components whose function is to simply hold chromosomes together. We also propose that positive selection in the SC is driven by its sex-specificity combined with its role in facilitating both recombination and centromere clustering in the face of recurrent bouts of drive in female meiosis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0670-8) contains supplementary material, which is available to authorized users.

A Novel Extracellular Gut Symbiont in the Marine Worm Priapulus caudatus (Priapulida) Reveals an Alphaproteobacterial Symbiont Clade of the Ecdysozoa

Priapulus caudatus (phylum Priapulida) is a benthic marine predatory worm with a cosmopolitan distribution. In its digestive tract we detected symbiotic bacteria that were consistently present in specimens collected over 8 years from three sites at the Swedish west coast. Based on their 16S rRNA gene sequence, these symbionts comprise a novel genus of the order Rickettsiales (Alphaproteobacteria). Electron microscopy and fluorescence in situ hybridization (FISH) identified them as extracellular, elongate bacteria closely associated with the microvilli, for which we propose the name “Candidatus Tenuibacter priapulorum”. Within Rickettsiales, they form a phylogenetically well-defined, family-level clade with uncultured symbionts of marine, terrestrial, and freshwater arthropods. Cand. Tenuibacter priapulorum expands the host range of this candidate family from Arthropoda to the entire Ecdysozoa, which may indicate an evolutionary adaptation of this bacterial group to the microvilli-lined guts of the Ecdysozoa.

Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes

Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83–99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25–22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20–17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity.

Lymphatic filariasis and loiasis are diseases caused by insect-borne filarial nematodes. Here, Suh et al. identify a retrotransposon that is present in the genomes of these nematodes and seven tropical bird lineages, indicating two waves of horizontal gene transfer around 17–25 million years ago.