Higher-level metazoan relationships: recent progress and remaining questions

Developmental and genomic insight into the origin of the tardigrade body plan

Tardigrada is an ancient lineage of miniaturized animals. As an outgroup of the well-studied Arthropoda and Onychophora, studies of tardigrades hold the potential to reveal important insights into body plan evolution in Panarthropoda. Previous studies have revealed interesting facets of tardigrade development and genomics that suggest that a highly compact body plan is a derived condition of this lineage, rather than it representing an ancestral state of Panarthropoda. This conclusion was based on studies of several species from Eutardigrada. We review these studies and expand on them by analyzing the publicly available genome and transcriptome assemblies of Echiniscus testudo, a representative of Heterotardigrada. These new analyses allow us to phylogenetically reconstruct important features of genome evolution in Tardigrada. We use available data from tardigrades to interrogate several recent models of body plan evolution in Panarthropoda. Although anterior segments of panarthropods are highly diverse in terms of anatomy and development, both within individuals and between species, we conclude that a simple one-to-one alignment of anterior segments across Panarthropoda is the best available model of segmental homology. In addition to providing important insight into body plan diversification within Panarthropoda, we speculate that studies of tardigrades may reveal generalizable pathways to miniaturization.

A single-cell RNA-seq analysis of early larval cell-types of the starfish, Patiria pectinifera: Insights into evolution of the chordate body plan

Ambulacrarians (echinoderms and hemichordates) are a sister group to chordates; thus, their larval cell-types may provide clues about evolution of chordate body plans. Although most genic information accumulated to date pertains to sea urchin embryogenesis, starfish embryogenesis represents a more ancestral mode than that of sea urchins. We performed single-cell RNA-seq analysis of cell-types from gastrulae and bipinnarial larvae of the starfish, Patiria pectinifera, and categorized them into 22 clusters, each of which is composed of cells with specific, shared profiles of development-relevant gene expression. Oral and aboral ectoderm, apical plate, hindgut or archenteron, midgut or intestine, pharynx, endomesoderm, stomodeum, and mesenchyme of the gastrulae, and neurons, ciliary bands, enterocoel and muscle of larvae were characterized by expression profiles of at least two relevant transcription factor genes and signaling molecular genes. Expression of Hox2, Hox7, Hox9/10, and Hox11/13b was detected in cells of clusters that form the larval enterocoel. By comparing homologous gene expression profiles in chordate embryos, we discuss and propose how the chordate body plan evolved from a deuterostome ancestor, from which the echinoderm body plan also evolved.

The Cambrian cirratuliform Iotuba denotes an early annelid radiation

The principal animal lineages (phyla) diverged in the Cambrian, but most diversity at lower taxonomic ranks arose more gradually over the subsequent 500 Myr. Annelid worms seem to exemplify this pattern, based on molecular analyses and the fossil record: Cambrian Burgess Shale-type deposits host a single, early-diverging crown-group annelid alongside a morphologically and taxonomically conservative stem group; the polychaete sub-classes diverge in the Ordovician; and many orders and families are first documented in Carboniferous Lagerstätten. Fifteen new fossils of the 'phoronid' Iotuba (=Eophoronis) chengjiangensis from the early Cambrian Chengjiang Lagerstätte challenge this picture. A chaetal cephalic cage surrounds a retractile head with branchial plates, affiliating Iotuba with the derived polychaete families 'Flabelligeridae' and Acrocirridae. Unless this similarity represents profound convergent evolution, this relationship would pull back the origin of the nested crown groups of Cirratuliformia, Sedentaria and Pleistoannelida by tens of millions of years-indicating a dramatic unseen origin of modern annelid diversity in the heat of the Cambrian 'explosion'.

Humans, fish, spiders and bees inherited working memory and attention from their last common ancestor

All brain processes that generate behaviour, apart from reflexes, operate with information that is in an "activated" state. This activated information, which is known as working memory (WM), is generated by the effect of attentional processes on incoming information or information previously stored in short-term or long-term memory (STM or LTM). Information in WM tends to remain the focus of attention; and WM, attention and STM together enable information to be available to mental processes and the behaviours that follow on from them. WM and attention underpin all flexible mental processes, such as solving problems, making choices, preparing for opportunities or threats that could be nearby, or simply finding the way home. Neither WM nor attention are necessarily conscious, and both may have evolved long before consciousness. WM and attention, with similar properties, are possessed by humans, archerfish, and other vertebrates; jumping spiders, honey bees, and other arthropods; and members of other clades, whose last common ancestor (LCA) is believed to have lived more than 600 million years ago. It has been reported that very similar genes control the development of vertebrate and arthropod brains, and were likely inherited from their LCA. Genes that control brain development are conserved because brains generate adaptive behaviour. However, the neural processes that generate behaviour operate with the activated information in WM, so WM and attention must have existed prior to the evolution of brains. It is proposed that WM and attention are widespread amongst animal species because they are phylogenetically conserved mechanisms that are essential to all mental processing, and were inherited from the LCA of vertebrates, arthropods, and some other animal clades.

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.

C. elegans: out on an evolutionary limb

The natural environment of the free-living nematode Caenorhabditis elegans is rich in pathogenic microbes. There is now ample evidence to indicate that these pathogens exert a strong selection pressure on C. elegans, and have shaped its genome, physiology, and behaviour. In this short review, we concentrate on how C. elegans stands out from other animals in terms of its immune repertoire and innate immune signalling pathways. We discuss how C. elegans often detects pathogens because of their effects on essential cellular processes, or organelle integrity, in addition to direct microbial recognition. We illustrate the extensive molecular plasticity that is characteristic of immune defences in C. elegans and highlight some remarkable instances of lineage-specific innovation in innate immune mechanisms.

Revisiting kinorhynch segmentation: variation of segmental patterns in the nervous system of three aberrant species

BACKGROUND

Kinorhynch segmentation differs from the patterns found in Chordata, Arthropoda and Annelida which have coeloms and circulatory systems. Due to these differences and their obsolete status as 'Aschelminthes', the microscopic kinorhynchs are often not acknowledged as segmented bilaterians. Yet, morphological studies have shown a conserved segmental arrangement of ectodermal and mesodermal organ systems with spatial correspondence along the anterior-posterior axis. However, a few aberrant kinorhynch lineages present a worm-like body plan with thin cuticle and less distinct segmentation, and thus their study may aid to shed new light on the evolution of segmental patterns within Kinorhyncha.

RESULTS

Here we found the nervous system in the aberrant Cateria styx and Franciscideres kalenesos to be clearly segmental, and similar to those of non-aberrant kinorhynchs; hereby not mirroring their otherwise aberrant and posteriorly shifted myoanatomy. In Zelinkaderes yong, however, the segmental arrangement of the nervous system is also shifted posteriorly and misaligned with respect to the cuticular segmentation.

CONCLUSIONS

The morphological disparity together with the distant phylogenetic positions of F. kalenesos, C. styx and Z. yong support a convergent origin of aberrant appearances and segmental mismatches within Kinorhyncha.

Geographical sampling bias on the assessment of endemism areas for marine meiobenthic fauna

Species distribution patterns are constrained by historical and ecological processes in space and time, but very often the species range sizes are geographical sampling biases resulting from unequal sampling effort. One of the most common definitions of endemism is based on the "congruence of distributional areas" criterion, when two or more species have the same distributional limits. By acknowledging that available data of marine meiobenthic species are prone to geographical sampling bias and that can affect the accuracy of the biogeographical signals, the present study combines analyses of inventory incompleteness and recognition of spatial congruence of Gastrotricha, Kinorhyncha, meiobenthic Annelida and Tardigrada in order to better understand the large-scale distribution of these organisms in coastal and shelf areas of the world. We used the marine bioregionalization framework for geographical operative units to quantify the inventory incompleteness effect (by modelling spatial predictions of species richness) and to recognize areas of endemism. Our models showed that the difference between observed and expected species richness in the Southern Hemisphere is much higher than in the Northern Hemisphere. Parsimony Analysis of Endemicity delimited 20 areas of endemism, most found in the Northern Hemisphere. Distribution patterns of meiobenthic species are shown to respond to events of geographical barriers and abiotic features, and their distribution is far from homogeneous throughout the world. Also, our data show that ecoregions with distinct biotas have at least some cohesion over evolutionary time. However, we found that inventory incompleteness may significantly affect the explanatory power of areas of endemism delimitation in both hemispheres. Yet, whereas future increases in sampling efforts are likely to change the spatial congruence ranges in the Southern Hemisphere, patterns for the Northern Hemisphere may prove to be relatively more resilient.

Nemertean, brachiopod and phoronid neuropeptidomics reveals ancestral spiralian signalling systems

Neuropeptides are diverse signaling molecules in animals commonly acting through G-protein coupled receptors (GPCRs). Neuropeptides and their receptors underwent extensive diversification in bilaterians and the relationships of many peptide–receptor systems have been clarified. However, we lack a detailed picture of neuropeptide evolution in lophotrochozoans as in-depth studies only exist for mollusks and annelids. Here, we analyze peptidergic systems in Nemertea, Brachiopoda, and Phoronida. We screened transcriptomes from 13 nemertean, 6 brachiopod, and 4 phoronid species for proneuropeptides and neuropeptide GPCRs. With mass spectrometry from the nemertean Lineus longissimus, we validated several predicted peptides and identified novel ones. Molecular phylogeny combined with peptide-sequence and gene-structure comparisons allowed us to comprehensively map spiralian neuropeptide evolution. We found most mollusk and annelid peptidergic systems also in nemerteans, brachiopods, and phoronids. We uncovered previously hidden relationships including the orthologies of spiralian CCWamides to arthropod agatoxin-like peptides and of mollusk APGWamides to RGWamides from annelids, with ortholog systems in nemerteans, brachiopods, and phoronids. We found that pleurin neuropeptides previously only found in mollusks are also present in nemerteans and brachiopods. We also identified cases of gene family duplications and losses. These include a protostome-specific expansion of RFamide/Wamide signaling, a spiralian expansion of GnRH-related peptides, and duplications of vasopressin/oxytocin before the divergence of brachiopods, phoronids, and nemerteans. This analysis expands our knowledge of peptidergic signaling in spiralians and other protostomes. Our annotated data set of nearly 1,300 proneuropeptide sequences and 600 GPCRs presents a useful resource for further studies of neuropeptide signaling.

Diversity in the Development of the Neuromuscular System of Nemertean Larvae (Nemertea, Spiralia)

In studies on the development of nervous systems and musculature, fluorescent labeling of neuroactive substances and filamentous actin (f-actin) of muscle cells and the subsequent analysis with confocal laser scanning microscopy (CLSM), has led to a broad comparative data set for the majority of the clades of the superphylum Spiralia. However, a number of clades remain understudied, which results in gaps in our knowledge that drastically hamper the formulation of broad-scale hypotheses on the evolutionary developmental biology (EvoDevo) of the structures in question. Regarding comparative data on the development of the peptidergic nervous system and the musculature of species belonging to the spiralian clade Nemertea (ribbon worms), such considerable knowledge gaps are manifest. This paper presents first findings on fluorescent labeling of the FMRFamide-like component of the nervous system and contributes additional data on the muscle development in the presently still underrepresented larvae of palaeo- and hoplonemertean species. Whereas the architecture of the FMRFamide-like nervous system is comparably uniform between the studied representatives, the formation of the musculature differs considerably, exhibiting developmental modes yet undescribed for any spiralian species. The presented results fill a significant gap in the spiralian EvoDevo data set and thus allow for further elaboration of hypotheses on the ancestral pattern of the musculature and a prominent component of the nervous system in Nemertea. However, with respect to the variety observed, it is expected that the true diversity of the developmental pathways is still to be discovered when more detailed data on other nemertean species will be available.

activin-2 is required for regeneration of polarity on the planarian anterior-posterior axis

Planarians are flatworms and can perform whole-body regeneration. This ability involves a mechanism to distinguish between anterior-facing wounds that require head regeneration and posterior-facing wounds that require tail regeneration. How this head-tail regeneration polarity decision is made is studied to identify principles underlying tissue-identity specification in regeneration. We report that inhibition of activin-2, which encodes an Activin-like signaling ligand, resulted in the regeneration of ectopic posterior-facing heads following amputation. During tissue turnover in uninjured planarians, positional information is constitutively expressed in muscle to maintain proper patterning. Positional information includes Wnts expressed in the posterior and Wnt antagonists expressed in the anterior. Upon amputation, several wound-induced genes promote re-establishment of positional information. The head-versus-tail regeneration decision involves preferential wound induction of the Wnt antagonist notum at anterior-facing over posterior-facing wounds. Asymmetric activation of notum represents the earliest known molecular distinction between head and tail regeneration, yet how it occurs is unknown. activin-2 RNAi animals displayed symmetric wound-induced activation of notum at anterior- and posterior-facing wounds, providing a molecular explanation for their ectopic posterior-head phenotype. activin-2 RNAi animals also displayed anterior-posterior (AP) axis splitting, with two heads appearing in anterior blastemas, and various combinations of heads and tails appearing in posterior blastemas. This was associated with ectopic nucleation of anterior poles, which are head-tip muscle cells that facilitate AP and medial-lateral (ML) pattern at posterior-facing wounds. These findings reveal a role for Activin signaling in determining the outcome of AP-axis-patterning events that are specific to regeneration.

A central problem in animal regeneration is how animals determine what body part to regenerate. Planarians are flatworms that can regenerate any missing body region, and are studied to identify mechanisms underlying regeneration. At transverse amputation planes, a poorly understood mechanism specifies regeneration of either a head or a tail. This head-versus-tail regeneration decision-making process is referred to as regeneration polarity and has been studied for over a century to identify mechanisms that specify what to regenerate. The gene notum, which encodes a Wnt antagonist, is induced within hours after injury preferentially at anterior-facing wounds, where it specifies head regeneration. We report that Activin signaling is required for regeneration polarity, and the underlying asymmetric activation of notum at anterior- over posterior-facing wounds. We propose that Activin signaling is involved in regeneration-specific responses broadly in the animal kingdom.

Cancer and the breakdown of multicellularity: What Dictyostelium discoideum, a social amoeba, can teach us

Ancient pathways promoting unicellularity and multicellularity are associated with cancer, the former being pro-oncogenic and the latter acting to suppress oncogenesis. However, there are only a limited number of non-vertebrate models for studying these pathways. Here, we review Dictyostelium discoideum and describe how it can be used to understand these gene networks. D. discoideum has a unicellular and multicellular life cycle, making it possible to study orthologs of cancer-associated genes in both phases. During development, differentiated amoebae form a fruiting body composed of a mass of spores that are supported atop a stalk. A portion of the cells sacrifice themselves to become non-reproductive stalk cells. Cheating disrupts the principles of multicellularity, as cheater cells alter their cell fate to preferentially become spores. Importantly, D. discoideum has gene networks and several strategies for maintaining multicellularity. Therefore, D. discoideum can help us better understand how conserved genes and pathways involved in multicellularity also influence cancer development, potentially identifying new therapeutic avenues.

Prospective enzymes for omega-3 PUFA biosynthesis found in endoparasitic classes within the phylum Platyhelminthes

The free-living infectious stages of macroparasites, specifically, the cercariae of trematodes (flatworms), are likely to be significant (albeit underappreciated) vectors of nutritionally important polyunsaturated fatty acids (PUFA) to consumers within aquatic food webs, and other macroparasites could serve similar roles. In the context of de novo omega-3 (n-3) PUFA biosynthesis, it was thought that most animals lack the fatty acid (FA) desaturase enzymes that convert stearic acid (18:0) into ɑ-linolenic acid (ALA; 18:3n-3), the main FA precursor for n-3 long-chain PUFA. Recently, novel sequences of these enzymes were recovered from 80 species from six invertebrate phyla, with experimental confirmation of gene function in five phyla. Given this wide distribution, and the unusual attributes of flatworm genomes, we conducted an additional search for genes for de novo n-3 PUFA in the phylum Platyhelminthes. Searches with experimentally confirmed sequences from Rotifera recovered nine relevant FA desaturase sequences from eight species in four genera in the two exclusively endoparasite classes (Trematoda and Cestoda). These results could indicate adaptations of these particular parasite species, or may reflect the uneven taxonomic coverage of sequence databases. Although additional genomic data and, particularly, experimental study of gene functionality are important future validation steps, our results indicate endoparasitic platyhelminths may have enzymes for de novo n-3 PUFA biosynthesis, thereby contributing to global PUFA production, but also representing a potential target for clinical antihelmintic applications.

Rho Family of Ras-Like GTPases in Early-Branching Animals

Non-bilaterian animals consist of four phyla; Porifera, Cnidaria, Ctenophora, and Placozoa. These early-diverging animals are crucial for understanding the evolution of the entire animal lineage. The Rho family of proteins make up a major branch of the Ras superfamily of small GTPases, which function as key molecular switches that play important roles in converting and amplifying external signals into cellular responses. This review represents a compilation of the current knowledge on Rho-family GTPases in non-bilaterian animals, the available experimental data about their biochemical characteristics and functions, as well as original bioinformatics analysis, in order to gain a general insight into the evolutionary history of Rho-family GTPases in simple animals.

Neural architecture and regeneration in the acoel Hofstenia miamia

The origin of bilateral symmetry, a major transition in animal evolution, coincided with the evolution of organized nervous systems that show regionalization along major body axes. Studies of Xenacoelomorpha, the likely outgroup lineage to all other animals with bilateral symmetry, can inform the evolutionary history of animal nervous systems. Here, we characterized the neural anatomy of the acoel Hofstenia miamia. Our analysis of transcriptomic data uncovered orthologues of enzymes for all major neurotransmitter synthesis pathways. Expression patterns of these enzymes revealed the presence of a nerve net and an anterior condensation of neural cells. The anterior condensation was layered, containing several cell types with distinct molecular identities organized in spatially distinct territories. Using these anterior cell types and structures as landmarks, we obtained a detailed timeline for regeneration of the H. miamia nervous system, showing that the anterior condensation is restored by eight days after amputation. Our work detailing neural anatomy in H. miamia will enable mechanistic studies of neural cell type diversity and regeneration and provide insight into the evolution of these processes.

Dicyemid Mesozoans: A Unique Parasitic Lifestyle and a Reduced Genome

Dicyemids, previously called “mesozoans” (intermediates between unicellular protozoans and multicellular metazoans), are an enigmatic animal group. They have a highly simplified adult body, comprising only ∼30 cells, and they have a unique parasitic lifestyle. Recently, dicyemids were shown to be spiralians, with affinities to the Platyhelminthes. In order to understand molecular mechanisms involved in evolution of this odd animal, we sequenced the genome of Dicyema japonicum and a reference transcriptome assembly using mixed-stage samples. The D. japonicum genome features a high proportion of repetitive sequences that account for 49% of the genome. The dicyemid genome is reduced to ∼67.5 Mb with 5,012 protein-coding genes. Only four Hox genes exist in the genome, with no clustering. Gene distribution in KEGG pathways shows that D. japonicum has fewer genes in most pathways. Instead of eliminating entire critical metabolic pathways, parasitic lineages likely simplify pathways by eliminating pathway-specific genes, while genes with fundamental functions may be retained in multiple pathways. In principle, parasites can stand to lose genes that are unnecessary, in order to conserve energy. However, whether retained genes in incomplete pathways serve intermediate functions and how parasites overcome the physiological needs served by lost genes, remain to be investigated in future studies.

NCBI Taxonomy: a comprehensive update on curation, resources and tools

The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration. Since the last review of this resource in 2012, it has undergone several improvements. Most notable is the shift from a single SQL database to a series of linked databases tied to a framework of data called NameBank. This means that relations among data elements can be adjusted in more detail, resulting in expanded annotation of synonyms, the ability to flag names with specific nomenclatural properties, enhanced tracking of publications tied to names and improved annotation of scientific authorities and types. Additionally, practices utilized by NCBI Taxonomy curators specific to major taxonomic groups are described, terms peculiar to NCBI Taxonomy are explained, external resources are acknowledged and updates to tools and other resources are documented. Database URL: https://www.ncbi.nlm.nih.gov/taxonomy.

Gene expression profiles of dicyemid life-cycle stages may explain how dispersing larvae locate new hosts

Metazoans have evolved a great variety of life histories in response to environmental conditions. A unique example is encountered in dicyemid mesozoans. In addition to a highly simplified adult body comprising only ~ 30 cells, dicyemids exhibit a parasitic lifestyle that includes nematogens (asexual reproductive adults), rhombogens (sexual reproductive adults), vermiform larvae generated by nematogens, and infusoriform larvae generated by rhombogens. However, due to the difficulties of observing microscopic endoparasites, the complex life cycle and biological functions of life-cycle stages of dicyemids have remained mysterious. Taking advantage of the recently decoded genome of Dicyema japonicum, we examined genes that undergird this lifestyle. Using stage-specific gene expression profiles, we found that biological processes associated with molecular transport, developmental regulation, and sensory response are specified at different stages. Together with the expression of potential neurotransmitters, we further suggest that apical cells in infusoriform larva probably serve sensory functions, although dicyemids have no nervous system. Gene expression profiles show that more genes are expressed in free-living infusoriform larvae than in the other three stages, and that some of these genes are likely involved in locating new hosts. These data provide molecular information about the unique lifestyle of dicyemids and illustrate how an extremely simplified endoparasite adapted and retained gene sets and morphological characters to complete its life cycle.

SUPPLEMENTARY INFORMATION

Supplementary information accompanies this paper at 10.1186/s40851-019-0146-y.

A nemertean excitatory peptide/CCHamide regulates ciliary swimming in the larvae of Lineus longissimus

Background

The trochozoan excitatory peptide (EP) and its ortholog, the arthropod CCHamide, are neuropeptides that are only investigated in very few animal species. Previous studies on different trochozoan species focused on their physiological effect in adult specimens, demonstrating a myo-excitatory effect, often on tissues of the digestive system. The function of EP in the planktonic larvae of trochozoans has not yet been studied.

Results

We surveyed transcriptomes from species of various spiralian (Orthonectida, Nemertea, Brachiopoda, Entoprocta, Rotifera) and ecdysozoan taxa (Tardigrada, Onychophora, Priapulida, Loricifera, Nematomorpha) to investigate the evolution of EPs/CCHamides in protostomes. We found that the EPs of several pilidiophoran nemerteans show a characteristic difference in their C-terminus. Deorphanization of a pilidiophoran EP receptor showed, that the two splice variants of the nemertean Lineus longissimus EP activate a single receptor. We investigated the expression of EP in L. longissimus larvae and juveniles with customized antibodies and found that EP positive nerves in larvae project from the apical organ to the ciliary band and that EP is expressed more broadly in juveniles in the neuropil and the prominent longitudinal nerve cords. While exposing juvenile L. longissimus specimens to synthetic excitatory peptides did not show any obvious effect, exposure of larvae to either of the two EPs increased the beat frequency of their locomotory cilia and shifted their vertical swimming distribution in a water column upwards.

Conclusion

Our results show that EP/CCHamide peptides are broadly conserved in protostomes. We show that the EP increases the ciliary beat frequency of L. longissimus larvae, which shifts their vertical distribution in a water column upwards. Endogenous EP may be released at the ciliary band from the projections of apical organ EP positive neurons to regulate ciliary beating. This locomotory function of EP in L. longissimus larvae stands in contrast to the repeated association of EP/CCHamides with its myo-excitatory effect in adult trochozoans and the general association with the digestive system in many protostomes.

Electronic supplementary material

The online version of this article (10.1186/s12983-019-0326-9) contains supplementary material, which is available to authorized users.

OMA standalone: orthology inference among public and custom genomes and transcriptomes

Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many analyses lies in identifying orthologs—corresponding genes across multiple species—but this is far from trivial. The Orthologous MAtrix (OMA) database is a leading resource for identifying orthologs among publicly available, complete genomes. Here, we describe the OMA pipeline available as a standalone program for Linux and Mac. When run on a cluster, it has native support for the LSF, SGE, PBS Pro, and Slurm job schedulers and can scale up to thousands of parallel processes. Another key feature of OMA standalone is that users can combine their own data with existing public data by exporting genomes and precomputed alignments from the OMA database, which currently contains over 2100 complete genomes. We compare OMA standalone to other methods in the context of phylogenetic tree inference, by inferring a phylogeny of Lophotrochozoa, a challenging clade within the protostomes. We also discuss other potential applications of OMA standalone, including identifying gene families having undergone duplications/losses in specific clades, and identifying potential drug targets in nonmodel organisms. OMA standalone is available under the permissive open source Mozilla Public License Version 2.0.

Diurodrilus kunii sp. nov. (Annelida: Diurodrilidae) and a Molecular Phylogeny of the Genus

A new species of stygobiontic interstitial annelid, Diurodrilus kunii sp. nov., is described based on material collected from medium sand sediment (ϕ = 1.2-1.7) at groundwater level (40-100 cm in depth; 5-15 m inland from splash zone) in the intertidal beach slope on Ishikari Beach, facing the Sea of Japan, Hokkaido, Japan. The new species differs from six known congeners in the arrangement of the anterior-head ventral ciliophores, the degree of development in the primary and secondary toes, and the shape of the spermatozoa. We inferred the phylogenetic position of the new species among other congeners for which 18S rRNA, 28S rRNA, and COI gene sequences were available in public databases. This is the first representative of the genus from the Northwest Pacific.

Evolutionary Implications of the microRNA- and piRNA Complement of Lepidodermella squamata (Gastrotricha)

Gastrotrichs-'hairy bellies'-are microscopic free-living animals inhabiting marine and freshwater habitats. Based on morphological and early molecular analyses, gastrotrichs were placed close to nematodes, but recent phylogenomic analyses have suggested their close relationship to flatworms (Platyhelminthes) within Spiralia. Small non-coding RNA data on e.g., microRNAs (miRNAs) and PIWI-interacting RNAs (piRNA) may help to resolve this long-standing question. MiRNAs are short post-transcriptional gene regulators that together with piRNAs play key roles in development. In a 'multi-omics' approach we here used small-RNA sequencing, available transcriptome and genomic data to unravel the miRNA- and piRNA complements along with the RNAi (RNA interference) protein machinery of Lepidodermella squamata (Gastrotricha, Chaetonotida). We identified 52 miRNA genes representing 35 highly conserved miRNA families specific to Eumetazoa, Bilateria, Protostomia, and Spiralia, respectively, with overall high similarities to platyhelminth miRNA complements. In addition, we found four large piRNA clusters that also resemble flatworm piRNAs but not those earlier described for nematodes. Congruently, transcriptomic annotation revealed that the Lepidodermella protein machinery is highly similar to flatworms, too. Taken together, miRNA, piRNA, and protein data support a close relationship of gastrotrichs and flatworms.

Homologs of Human Dengue-Resistance Genes, FKBP1B and ATCAY, Confer Antiviral Resistance in Aedes aegypti Mosquitoes

Dengue virus (DENV) is transmitted by mosquitoes and is a major public health concern. The study of innate mosquito defense mechanisms against DENV have revealed crucial roles for the Toll, Imd, JAK-STAT, and RNAi pathways in mediating DENV in the mosquito. Often overlooked in such studies is the role of intrinsic cellular defense mechanisms that we hypothesize to work in concert with the classical immune pathways to affect organismal defense. Our understanding of the molecular interaction of DENV with mosquito host cells is limited, and we propose to expand upon the recent results from a genome-scale, small interfering RNA (siRNA)-based study that identified mammalian host proteins associated with resistance to dengue/West Nile virus (DENV/WNV) infection. The study identified 22 human DENV/WNV resistance genes (DVR), and we hypothesized that a subset would be functionally conserved in Aedes aegypti mosquitoes, imparting cellular defense against flaviviruses in this species. We identified 12 homologs of 22 human DVR genes in the Ae. aegypti genome. To evaluate their possible role in cellular resistance/antiviral defense against DENV, we used siRNA silencing targeted against each of the 12 homologs in an Ae. aegypti cell line (Aag2) infected with DENV2 and identified that silencing of the two candidates, AeFKBP1 and AeATCAY, homologs of human FKBP1B and ATCAY, were associated with a viral increase. We then used dsRNA to silence each of the two genes in adult mosquitoes to validate the observed antiviral functions in vivo. Depletion of AeFKBP1 or AeATCAY increased viral dissemination through the mosquito at 14 days post-infection. Our results demonstrated that AeFKBP1 and AeATCAY mediate resistance to DENV akin to what has been described for their homologs in humans. AeFKBP1 and AeATCAY provide a rare opportunity to elucidate a DENV-resistance mechanism that may be evolutionarily conserved between humans and Ae. aegypti.

Long-distance passive dispersal in microscopic aquatic animals

Given their dormancy capability (long-term resistant stages) and their ability to colonise and reproduce, microscopic aquatic animals have been suggested having cosmopolitan distribution. Their dormant stages may be continuously moved by mobile elements through the entire planet to any suitable habitat, preventing the formation of biogeographical patterns. In this review, I will go through the evidence we have on the most common microscopic aquatic animals, namely nematodes, rotifers, and tardigrades, for each of the assumptions allowing long-distance dispersal (dormancy, viability, and reproduction) and all the evidence we have for transportation, directly from surveys of dispersing stages, and indirectly from the outcome of successful dispersal in biogeographical and phylogeographical studies. The current knowledge reveals biogeographical patterns also for microscopic organisms, with species-specific differences in ecological features that make some taxa indeed cosmopolitan with the potential for long-distance dispersal, but others with restricted geographic distributions.

Evolutionary dynamics of origin and loss in the deep history of phospholipase D toxin genes

Background

Venom-expressed sphingomyelinase D/phospholipase D (SMase D/PLD) enzymes evolved from the ubiquitous glycerophosphoryl diester phosphodiesterases (GDPD). Expression of GDPD-like SMaseD/PLD toxins in both arachnids and bacteria has inspired consideration of the relative contributions of lateral gene transfer and convergent recruitment in the evolutionary history of this lineage. Previous work recognized two distinct lineages, a SicTox-like (ST-like) clade including the arachnid toxins, and an Actinobacterial-toxin like (AT-like) clade including the bacterial toxins and numerous fungal homologs.

Results

Here we expand taxon sampling by homology detection to discover new GDPD-like SMase D/PLD homologs. The ST-like clade now includes homologs in a wider variety of arthropods along with a sister group in Cnidaria; the AT-like clade now includes additional fungal phyla and proteobacterial homologs; and we report a third clade expressed in diverse aquatic metazoan taxa, a few single-celled eukaryotes, and a few aquatic proteobacteria. GDPD-like SMaseD/PLDs have an ancient presence in chelicerates within the ST-like family and ctenophores within the Aquatic family. A rooted phylogenetic tree shows that the three clades derived from a basal paraphyletic group of proteobacterial GDPD-like SMase D/PLDs, some of which are on mobile genetic elements. GDPD-like SMase D/PLDs share a signature C-terminal motif and a shortened βα1 loop, features that distinguish them from GDPDs. The three major clades also have active site loop signatures that distinguish them from GDPDs and from each other. Analysis of molecular phylogenies with respect to organismal relationships reveals a dynamic evolutionary history including both lateral gene transfer and gene duplication/loss.

Conclusions

The GDPD-like SMaseD/PLD enzymes derive from a single ancient ancestor, likely proteobacterial, and radiated into diverse organismal lineages at least in part through lateral gene transfer.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1302-2) contains supplementary material, which is available to authorized users.

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.

A general theory of genital homologies for the Hexapoda (Pancrustacea) derived from skeletomuscular correspondences, with emphasis on the Endopterygota

No consensus exists for the homology and terminology of the male genitalia of the Hexapoda despite over a century of debate. Based on dissections and the literature, genital skeletomusculature was compared across the Hexapoda and contrasted with the Remipedia, the closest pancrustacean outgroup. The pattern of origin and insertion for extrinsic and intrinsic genitalic musculature was found to be consistent among the Ectognatha, Protura, and the Remipedia, allowing for the inference of homologies given recent phylogenomic studies. The penis of the Hexapoda is inferred to be derived from medially-fused primary gonopods (gonopore-bearing limbs), while the genitalia of the Ectognatha are inferred to include both the tenth-segmental penis and the ninth-segmental secondary gonopods, similar to the genitalia of female insects which comprise gonopods of the eighth and ninth segments. A new nomenclatural system for hexapodan genitalic musculature is presented and applied, and a general list of anatomical concepts is provided. Novel and refined homologies are proposed for all hexapodan orders, and a series of groundplans are postulated. Emphasis is placed on the Endopterygota, for which fine-grained transition series are hypothesized given observed skeletomuscular correspondences.

Genome-wide identification of the entire 90 glutathione S-transferase (GST) subfamily genes in four rotifer Brachionus species and transcriptional modulation in response to endocrine disrupting chemicals

Genome-wide identification of glutathione S-transferase (GST), a major phase II detoxification enzyme, was investigated in four different aquatic model rotifer species Brachionus koreanus, B. plicatilis, B. rotundiformis, and B. calyciflorus. GSTs are ubiquitous antioxidant enzymes that play versatile function including cellular detoxification, stress alleviation, and production of the radical conjugates. Among the four rotifers, B. rotundiformis was found with the least number of GST genes (total 19 GST genes), whereas the other three species shared 23 to 24 GST genes. Among the identified GST genes, belonging to the cytosolic GST superfamily, the expansion of GST sigma classes mainly occurs through tandem duplication, resulting in tandem-arrayed gene clusters on the chromosomes. Overall, the number of genes discovered in this study was highest in the sigma class, zeta, alpha, and omega in descending order. With integration of phylogenetic analysis and xenobiotic-mediated GST mRNA expression patterns along with previous enzymatic activities, the functional divergence among species-specific GST genes was clearly observed. This study covers full identification of GST classes in three marine rotifer and one fresh-water rotifer species and their important role in marine environmental ecotoxicology.

Evolution of the bilaterian mouth and anus

It is widely held that the bilaterian tubular gut with mouth and anus evolved from a simple gut with one major gastric opening. However, there is no consensus on how this happened. Did the single gastric opening evolve into a mouth, with the anus forming elsewhere in the body (protostomy), or did it evolve into an anus, with the mouth forming elsewhere (deuterostomy), or did it evolve into both mouth and anus (amphistomy)? These questions are addressed by the comparison of developmental fates of the blastopore, the opening of the embryonic gut, in diverse animals that live today. Here we review comparative data on the identity and fate of blastoporal tissue, investigate how the formation of the through-gut relates to the major body axes, and discuss to what extent evolutionary scenarios are consistent with these data. Available evidence indicates that stem bilaterians had a slit-like gastric opening that was partially closed in subsequent evolution, leaving open the anus and most likely also the mouth, which would favour amphistomy. We discuss remaining difficulties, and outline directions for future research.

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.].

The Ecology of Freshwater Planarians

Planarians are on the rise as a model system for regeneration and stem cell dynamics. Almost in parallel the interest in planarian field biology has declined. Besides representing an independent research discipline in its own right, understanding of the natural habitat is also directly relevant to optimizing culture conditions in the laboratory. Moreover, the current laboratory models are but few of hundreds of planarian species worldwide. Their adaptation to a wide range of ecological niches has resulted in a fascinating diversity of regenerative abilities, body size, reproduction strategies, and life expectancy, to name just a few. With the currently ongoing establishment of large planarian species collections, such phenotypic diversity becomes accessible to comparative mechanistic analysis in the laboratory. Overall, we hope that this chapter inspires an integral view of the planarian model system that not only includes the molecular and cellular processes under investigation but also the evolutionary forces that shaped them in the first place.

A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella

BACKGROUND

Xenoturbella is a group of marine benthic animals lacking an anus and a centralized nervous system. Molecular phylogenetic analyses group the animal together with the Acoelomorpha, forming the Xenacoelomorpha. This group has been suggested to be either a sister group to the Nephrozoa or a deuterostome, and therefore it may provide important insights into origins of bilaterian traits such as an anus, the nephron, feeding larvae and centralized nervous systems. However, only five Xenoturbella species have been reported and the evolutionary history of xenoturbellids and Xenacoelomorpha remains obscure.

RESULTS

Here we describe a new Xenoturbella species from the western Pacific Ocean, and report a new xenoturbellid structure - the frontal pore. Non-destructive microCT was used to investigate the internal morphology of this soft-bodied animal. This revealed the presence of a frontal pore that is continuous with the ventral glandular network and which exhibits similarities with the frontal organ in acoelomorphs.

CONCLUSIONS

Our results suggest that large size, oval mouth, frontal pore and ventral glandular network may be ancestral features for Xenoturbella. Further studies will clarify the evolutionary relationship of the frontal pore and ventral glandular network of xenoturbellids and the acoelomorph frontal organ. One of the habitats of the newly identified species is easily accessible from a marine station and so this species promises to be valuable for research on bilaterian and deuterostome evolution.

Independent origins of parasitism in Animalia

Nearly half of all animals may have a parasitic lifestyle, yet the number of transitions to parasitism and their potential for species diversification remain unresolved. Based on a comprehensive survey of the animal kingdom, we find that parasitism has independently evolved at least 223 times in just 15 phyla, with the majority of identified independent parasitic groups occurring in the Arthropoda, at or below the level of Family. Metazoan parasitology is dominated by the study of helminthes; however, only 20% of independently derived parasite taxa belong to those groups, with numerous transitions also seen in Mollusca, Rotifera, Annelida and Cnidaria. Parasitism is almost entirely absent from deuterostomes, and although worm-like morphology and host associations are widespread across Animalia, the dual symbiotic and trophic interactions required for parasitism may constrain its evolution from antecedent consumer strategies such as generalist predators and filter feeders. In general, parasitic groups do not differ from their free-living relatives in their potential for speciation. However, the 10 largest parasitic clades contain 90% of described parasitic species, or perhaps 40% of all animal species. Hence, a substantial fraction of animal diversity on the Earth arose following these few transitions to a parasitic trophic strategy.

Nodal signalling and asymmetry of the nervous system

The role of Nodal signalling in nervous system asymmetry is still poorly understood. Here, we review and discuss how asymmetric Nodal signalling controls the ontogeny of nervous system asymmetry using a comparative developmental perspective. A detailed analysis of asymmetry in ascidians and fishes reveals a critical context-dependency of Nodal function and emphasizes that bilaterally paired and midline-unpaired structures/organs behave as different entities. We propose a conceptual framework to dissect the developmental function of Nodal as asymmetry inducer and laterality modulator in the nervous system, which can be used to study other types of body and visceral organ asymmetries. Using insights from developmental biology, we also present novel evolutionary hypotheses on how Nodal led the evolution of directional asymmetry in the brain, with a particular focus on the epithalamus. We intend this paper to provide a synthesis on how Nodal signalling controls left-right asymmetry of the nervous system.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.

Annelids shed light on the evolution of spiralian development

Spiralian development is characterized by stereotypic cell geometry and spindle orientation in early cleavage stage embryos, as well as conservation of ultimate fates of descendent clones. Diverse taxa such as molluscs, annelids, flatworms, and nemerteans exhibit spiralian development, but it is a mystery how such a conserved developmental program gives rise to such diverse body plans. This review highlights examples of variation during early development among spiralians, emphasizing recent experimental studies in the annelid Capitella teleta Blake, Grassle and Eckelbarger, 2009. Intracellular fate mapping studies in C. teleta reveal that many of its cells’ fates are shared among spiralians, but it also has a novel origin for trunk mesoderm (3c and 3d micromeres). Studies have identified an inductive signal in spiralians that has “organizing activity” and that influences cell fates in the surrounding embryo. Capitella teleta also has an organizing activity; however, surprisingly, it is localized to a different cell, it signals at a different developmental stage, and likely utilizes a distinct molecular signaling pathway compared with that in molluscs. A model is presented to provide a mechanistic explanation of evolutionary changes in the cellular identity of the organizer. Detailed experimental investigations in spiralian embryos demonstrate variation in developmental features that may influence the evolution of novel forms.

Evolution of Myeloid Cells

In 1882, Elie Metchnikoff identified myeloid-like cells from starfish larvae responding to the invasion by a foreign body (rose thorn). This marked the origins for the study of innate immunity, and an appreciation that cellular immunity was well established even in these "primitive" organisms. This chapter focuses on these myeloid cells as well as the newest members of this family, the dendritic cells, and explores their evolutionary origins. Our goal is to provide evolutionary context for the development of the multilayered immune system of mammals, where myeloid cells now serve as central effectors of innate immunity and regulators of adaptive immunity. Overall, we find that core contributions of myeloid cells to the regulation of inflammation are based on mechanisms that have been honed over hundreds of millions of years of evolution. Using phagocytosis as a platform, we show how fairly simple beginnings have offered a robust foundation onto which additional control features have been integrated, resulting in central regulatory nodes that now manage multifactorial aspects of homeostasis and immunity.

Increased taxon sampling reveals thousands of hidden orthologs in flatworms

Gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the gene complement of an organism consists of hidden orthologs, i.e., those with no apparent homology to sequenced animal lineages—mistakenly considered new genes—but actually representing rapidly evolving orthologs or undetected paralogs. Here, we describe Leapfrog, a simple automated BLAST pipeline that leverages increased taxon sampling to overcome long evolutionary distances and identify putative hidden orthologs in large transcriptomic databases by transitive homology. As a case study, we used 35 transcriptomes of 29 flatworm lineages to recover 3427 putative hidden orthologs, some unidentified by OrthoFinder and HaMStR, two common orthogroup inference algorithms. Unexpectedly, we do not observe a correlation between the number of putative hidden orthologs in a lineage and its “average” evolutionary rate. Hidden orthologs do not show unusual sequence composition biases that might account for systematic errors in sequence similarity searches. Instead, gene duplication with divergence of one paralog and weak positive selection appear to underlie hidden orthology in Platyhelminthes. By using Leapfrog, we identify key centrosome-related genes and homeodomain classes previously reported as absent in free-living flatworms, e.g., planarians. Altogether, our findings demonstrate that hidden orthologs comprise a significant proportion of the gene repertoire in flatworms, qualifying the impact of gene losses and gains in gene complement evolution.

Conservation of estrogen receptor function in invertebrate reproduction

Background

Rotifers are microscopic aquatic invertebrates that reproduce both sexually and asexually. Though rotifers are phylogenetically distant from humans, and have specialized reproductive physiology, this work identifies a surprising conservation in the control of reproduction between humans and rotifers through the estrogen receptor. Until recently, steroid signaling has been observed in only a few invertebrate taxa and its role in regulating invertebrate reproduction has not been clearly demonstrated. Insights into the evolution of sex signaling pathways can be gained by clarifying how receptors function in invertebrate reproduction.

Results

In this paper, we show that a ligand-activated estrogen-like receptor in rotifers binds human estradiol and regulates reproductive output in females. In other invertebrates characterized thus far, ER ligand binding domains have occluded ligand-binding sites and the ERs are not ligand activated. We have used a suite of computational, biochemical and biological techniques to determine that the rotifer ER binding site is not occluded and can bind human estradiol.

Conclusions

Our results demonstrate that this mammalian hormone receptor plays a key role in reproduction of the ancient microinvertebrate Brachinous manjavacas. The presence and activity of the ER within the phylum Rotifera indicates that the ER structure and function is highly conserved throughout animal evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0909-z) contains supplementary material, which is available to authorized users.

Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system

Background

Understanding gene expression changes over lifespan in diverse animal species will lead to insights to conserved processes in the biology of aging and allow development of interventions to improve health. Rotifers are small aquatic invertebrates that have been used in aging studies for nearly 100 years and are now re-emerging as a modern model system. To provide a baseline to evaluate genetic responses to interventions that change health throughout lifespan and a framework for new hypotheses about the molecular genetic mechanisms of aging, we examined the transcriptome of an asexual female lineage of the rotifer Brachionus manjavacas at five life stages: eggs, neonates, and early-, late-, and post-reproductive adults.

Results

There are widespread shifts in gene expression over the lifespan of B. manjavacas; the largest change occurs between neonates and early reproductive adults and is characterized by down-regulation of developmental genes and up-regulation of genes involved in reproduction. The expression profile of post-reproductive adults was distinct from that of other life stages. While few genes were significantly differentially expressed in the late- to post-reproductive transition, gene set enrichment analysis revealed multiple down-regulated pathways in metabolism, maintenance and repair, and proteostasis, united by genes involved in mitochondrial function and oxidative phosphorylation.

Conclusions

This study provides the first examination of changes in gene expression over lifespan in rotifers. We detected differential expression of many genes with human orthologs that are absent in Drosophila and C. elegans, highlighting the potential of the rotifer model in aging studies. Our findings suggest that small but coordinated changes in expression of many genes in pathways that integrate diverse functions drive the aging process. The observation of simultaneous declines in expression of genes in multiple pathways may have consequences for health and longevity not detected by single- or multi-gene knockdown in otherwise healthy animals. Investigation of subtle but genome-wide change in these pathways during aging is an important area for future study.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3540-x) contains supplementary material, which is available to authorized users.

Evolutionary dynamics of triosephosphate isomerase gene intron location pattern in Metazoa: A new perspective on intron evolution in animals

Intron evolution, including its dynamics in the evolutionary transitions and diversification of eukaryotes, remains elusive. Inadequate taxon sampling due to data shortage, unclear phylogenetic framework, and inappropriate outgroup application might be among the causes. Besides, the integrity of all the introns within a gene was often neglected previously. Taking advantage of the ancient conserved triosephosphate isomerase gene (tim), the relatively robust phylogeny of Metazoa, and choanoflagellates as outgroup, the evolutionary dynamics of tim intron location pattern (ILP) in Metazoa was investigated. From 133 representative species of ten phyla, 30 types of ILPs were identified. A most common one, which harbors the maximum six intron positions, is deduced to be the common ancestral tim ILP of Metazoa, which almost had formed in their protozoan ancestor and was surprisingly retained and passed down till to each ancestors of metazoan phyla. In the subsequent animal diversification, it underwent different evolutionary trajectories: within Deuterostomia, it was almost completely retained only with changes in a few species with relatively recently fast-evolving histories, while within the rapidly radiating Protostomia, besides few but remarkable retention, it usually displayed extensive intron losses and a few gains. Therefore, a common ancestral exon-intron arrangement pattern of an animal gene is definitely discovered; besides the 'intron-rich view' of early animal genes being confirmed, the novel insight that high exon-intron re-arrangements of genes seem to be associated with the relatively recently rapid evolution of lineages/species/genomes but have no correlation with the ancient major evolutionary transitions in animal evolution, is revealed.

Comparison of neuromuscular development in two dinophilid species (Annelida) suggests progenetic origin of Dinophilus gyrociliatus

BACKGROUND

Several independent meiofaunal lineages are suggested to have originated through progenesis, however, morphological support for this heterochronous process is still lacking. Progenesis is defined as an arrest of somatic development (synchronously in various organ systems) due to early maturation, resulting in adults resembling larvae or juveniles of the ancestors. Accordingly, we established a detailed neuromuscular developmental atlas of two closely related Dinophilidae using immunohistochemistry and CLSM. This allows us to test for progenesis, questioning whether i) the adult smaller, dimorphic Dinophilus gyrociliatus resembles a younger developmental stage of the larger, monomorphic D. taeniatus and whether ii) dwarf males of D. gyrociliatus resemble an early developmental stage of D. gyrociliatus females.

RESULTS

Both species form longitudinal muscle bundles first, followed by circular muscles, creating a grid of body wall musculature, which is the densest in adult D. taeniatus, while the architecture in adult female D. gyrociliatus resembles that of prehatching D. taeniatus. Both species display a subepidermal ganglionated nervous system with an anterior dorsal brain and five longitudinal ventral nerve bundles with six sets of segmental commissures (associated with paired ganglia). Neural differentiation of D. taeniatus and female D. gyrociliatus commissures occurs before hatching: both species start out forming one transverse neurite bundle per segment, which are thereafter joined by additional thin bundles. Whereas D. gyrociliatus arrests its development at this stage, adult D. taeniatus condenses the thin commissures again into one thick commissural bundle per segment. Generally, D. taeniatus adults demonstrate a seemingly more organized (= segmental) pattern of serotonin-like and FMRFamide-like immunoreactive elements. The dwarf male of D. gyrociliatus displays a highly aberrant neuromuscular system, showing no close resemblance to any early developmental stage of female Dinophilus, although the onset of muscular development mirrors the early myogenesis in females.

CONCLUSION

The apparent synchronous arrest of nervous and muscular development in adult female D. gyrociliatus, resembling the prehatching stage of D. taeniatus, suggests that D. gyrociliatus have originated through progenesis. The synchrony in arrest of three organ systems, which show opposing reduction and addition of elements, presents one of the morphologically best-argued cases of progenesis within Spiralia.

Molecular Evolution of MDM1, a "Duplication-Resistant" Gene in Vertebrates

BACKGROUND

The mouse double minute 1 (Mdm1) gene was first reported and cloned in mouse tumor cell lines as an oncogene candidate. Later, it was found that mutation of Mdm1 might cause age-related retinal degeneration 2 in mice by genetic linkage analysis. Additionally, the MDM1 protein was found to be expressed in the centrosomes, cilia, and the nucleus of multiciliated tracheal epithelial cells in mice. These observations suggest that MDM1 may have some basal functions in cell physiology. However, the evolutionary history of this gene and its expression during embryonic development remain largely unexplored.

RESULTS

Using molecular phylogenetic analysis, we found that the MDM1 gene encoded an evolutionarily conserved protein across all metazoans. We also found that the MDM1 gene was in a conserved synteny in vertebrates. In almost all the species that were analyzed, there was only one MDM1 gene based on current genome annotations. Since vertebrate genomes underwent two to three rounds of whole-genome duplications around the origin of the vertebrates, it is interesting that only one MDM1 ohnolog was retained. This observation implies that other MDM1 ohnologs were lost after the whole-genome duplications. Furthermore, using whole-mount in situ hybridization, we found that mdm1 was expressed in the forebrain, nephric ducts, and tail buds during zebrafish early embryonic development.

CONCLUSION

MDM1 is an evolutionary conserved gene, and its homologous genes can be traced back to basal metazoan lineages. In vertebrates, the MDM1 gene is in a conserved synteny and there is only one MDM1 ohnolog suggesting it is a "duplication-resistant" gene. Its expression patterns in early zebrafish embryos indicate that mdm1 may play important roles in the development of the central nervous system, kidneys, and hematopoietic system.

Neuromuscular study of early branching Diuronotus aspetos (Paucitubulatina) yields insights into the evolution of organs systems in Gastrotricha

BACKGROUND

Diuronotus is one of the most recently described genera of Paucitubulatina, one of the three major clades in Gastrotricha. Its morphology suggests that Diuronotus is an early branch of Paucitubulatina, making it a key taxon for understanding the evolution of this morphologically understudied group. Here we test its phylogenetic position employing molecular data, and provide detailed descriptions of the muscular, nervous, and ciliary systems of Diuronotus aspetos, using immunohistochemistry and confocal laser scanning microscopy.

RESULTS

We confirm the proposed position of D. aspetos within Muselliferidae, and find this family to be the sister group to Xenotrichulidae. The muscular system, revealed by F-actin staining, shows a simple, but unique organization of the trunk musculature with a reduction to three pairs of longitudinal muscles and addition of up to five pairs of dorso-ventral muscles, versus the six longitudinal and two dorso-ventral pairs found in most Paucitubulatina. Using acetylated α-tubulin immunoreactivity, we describe the pharynx in detail, including new nervous structures, two pairs of sensory cilia, and a unique canal system. The central nervous system, as revealed by immunohistochemistry, shows the general pattern of Gastrotricha having a bilobed brain and a pair of ventro-longitudinal nerve cords. However, in addition are found an anterior nerve ring, several anterior longitudinal nerves, and four ventral commissures (pharyngeal, trunk, pre-anal, and terminal). Two pairs of protonephridia are documented, while other Paucitubulatina have one. Moreover, the precise arrangement of multiciliated cells is unraveled, yielding a pattern of possibly systematic importance.

CONCLUSION

Several neural structures of Diuronotus resemble those found in Xenotrichula (Xenotrichulidae) and may constitute new apomorphies of Paucitubulatina, or even Gastrotricha. In order to test these new evolutionary hypotheses, comparable morphological data from other understudied gastrotrich branches and a better resolution of the basal nodes of the gastrotrich phylogeny are warranted. Nonetheless, the present study offers new insights into the evolution of organ systems and systematic importance of so-far neglected characters in Gastrotricha.

Matrotrophy and placentation in invertebrates: a new paradigm

Matrotrophy, the continuous extra-vitelline supply of nutrients from the parent to the progeny during gestation, is one of the masterpieces of nature, contributing to offspring fitness and often correlated with evolutionary diversification. The most elaborate form of matrotrophy-placentotrophy-is well known for its broad occurrence among vertebrates, but the comparative distribution and structural diversity of matrotrophic expression among invertebrates is wanting. In the first comprehensive analysis of matrotrophy across the animal kingdom, we report that regardless of the degree of expression, it is established or inferred in at least 21 of 34 animal phyla, significantly exceeding previous accounts and changing the old paradigm that these phenomena are infrequent among invertebrates. In 10 phyla, matrotrophy is represented by only one or a few species, whereas in 11 it is either not uncommon or widespread and even pervasive. Among invertebrate phyla, Platyhelminthes, Arthropoda and Bryozoa dominate, with 162, 83 and 53 partly or wholly matrotrophic families, respectively. In comparison, Chordata has more than 220 families that include or consist entirely of matrotrophic species. We analysed the distribution of reproductive patterns among and within invertebrate phyla using recently published molecular phylogenies: matrotrophy has seemingly evolved at least 140 times in all major superclades: Parazoa and Eumetazoa, Radiata and Bilateria, Protostomia and Deuterostomia, Lophotrochozoa and Ecdysozoa. In Cycliophora and some Digenea, it may have evolved twice in the same life cycle. The provisioning of developing young is associated with almost all known types of incubation chambers, with matrotrophic viviparity more widespread (20 phyla) than brooding (10 phyla). In nine phyla, both matrotrophic incubation types are present. Matrotrophy is expressed in five nutritive modes, of which histotrophy and placentotrophy are most prevalent. Oophagy, embryophagy and histophagy are rarer, plausibly evolving through heterochronous development of the embryonic mouthparts and digestive system. During gestation, matrotrophic modes can shift, intergrade, and be performed simultaneously. Invertebrate matrotrophic adaptations are less complex structurally than in chordates, but they are more diverse, being formed either by a parent, embryo, or both. In a broad and still preliminary sense, there are indications of trends or grades of evolutionarily increasing complexity of nutritive structures: formation of (i) local zones of enhanced nutritional transport (placental analogues), including specialized parent-offspring cell complexes and various appendages increasing the entire secreting and absorbing surfaces as well as the contact surface between embryo and parent, (ii) compartmentalization of the common incubatory space into more compact and 'isolated' chambers with presumably more effective nutritional relationships, and (iii) internal secretory ('milk') glands. Some placental analogues in onychophorans and arthropods mimic the simplest placental variants in vertebrates, comprising striking examples of convergent evolution acting at all levels-positional, structural and physiological.