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

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 new, simplified, drying protocol to prepare tardigrades for scanning electron microscopy

A new protocol for preparation of tardigrades for scanning electron microscope (SEM) analysis is proposed. The more conventional protocols require various steps and a long time to obtain good drying of water bears, together with specific and uncommon instruments (i.e., critical point dryer) or highly volatile toxic compounds (i.e., hexametildisilazane). The new protocol can be performed using few and simple instruments and materials, all easily accessible, and produces a high yield in terms of dried animals in excellent condition for the observation of external morphological structures with SEM. The acquired data exhibit considerable promise, and the proposed methodology shows potential for application to other meiofaunal groups, including small arthropods, nematodes, and rotifers. RESEARCH HIGHLIGHTS: Cheap, safe, and fast new method for Tardigrada preparation for SEM. With the new protocol, the number of animals required for SEM studies is minimized. New protocol is potentially applicable to the study of other meiofaunal soft-bodied taxa.

A multiscale approach reveals elaborate circulatory system and intermittent heartbeat in velvet worms (Onychophora)

An antagonistic hemolymph-muscular system is essential for soft-bodied invertebrates. Many ecdysozoans (molting animals) possess neither a heart nor a vascular or circulatory system, whereas most arthropods exhibit a well-developed circulatory system. How did this system evolve and how was it subsequently modified in panarthropod lineages? As the closest relatives of arthropods and tardigrades, onychophorans (velvet worms) represent a key group for addressing this question. We therefore analyzed the entire circulatory system of the peripatopsid Euperipatoides rowelli and discovered a surprisingly elaborate organization. Our findings suggest that the last common ancestor of Onychophora and Arthropoda most likely possessed an open vascular system, a posteriorly closed heart with segmental ostia, a pericardial sinus filled with nephrocytes and an impermeable pericardial septum, whereas the evolutionary origin of plical and pericardial channels is unclear. Our study further revealed an intermittent heartbeat-regular breaks of rhythmic, peristaltic contractions of the heart-in velvet worms, which might stimulate similar investigations in arthropods.

Review of extra-embryonic tissues in the closest arthropod relatives, onychophorans and tardigrades

The so-called extra-embryonic tissues are important for embryonic development in many animals, although they are not considered to be part of the germ band or the embryo proper. They can serve a variety of functions, such as nutrient uptake and waste removal, protection of the embryo against mechanical stress, immune response and morphogenesis. In insects, a subgroup of arthropods, extra-embryonic tissues have been studied extensively and there is increasing evidence that they might contribute more to embryonic development than previously thought. In this review, we provide an assessment of the occurrence and possible functions of extra-embryonic tissues in the closest arthropod relatives, onychophorans (velvet worms) and tardigrades (water bears). While there is no evidence for their existence in tardigrades, these tissues show a remarkable diversity across the onychophoran subgroups. A comparison of extra-embryonic tissues of onychophorans to those of arthropods suggests shared functions in embryonic nutrition and morphogenesis. Apparent contribution to the final form of the embryo in onychophorans and at least some arthropods supports the hypothesis that extra-embryonic tissues are involved in organogenesis. In order to account for this role, the commonly used definition of these tissues as 'extra-embryonic' should be reconsidered. This article is part of the theme issue 'Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom'.

A three-eyed radiodont with fossilized neuroanatomy informs the origin of the arthropod head and segmentation

In addition to being among the most iconic and bizarre-looking Cambrian animals, radiodonts are a group that offers key insight into the acquisition of the arthropod body plan by virtue of their phylogenetic divergence prior to all living members of the phylum. Nonetheless, radiodont fossils are rare and often fragmentary, and contentions over their interpretation have hindered resolution of important evolutionary conundrums. Here, we describe 268 specimens of Stanleycaris hirpex from the Cambrian Burgess Shale, including many exceptionally preserved whole-body specimens, informing the most complete reconstruction of a radiodont to date. The trunk region of Stanleycaris has up to 17 segments plus two pairs of filiform caudal blades. The recognition of dorsal sclerotic segmentation of the trunk cuticle and putative unganglionated nerve cords provides new insight into the relative timing of acquisition of segmental traits, the epitome of the arthropod body plan. In addition to the pair of stalked lateral eyes, the short head unexpectedly bears a large median eye situated behind a preocular sclerite on an anteriorly projecting head lobe. Upon re-evaluation, similar median eyes can be identified in other Cambrian panarthropods demonstrating a deep evolutionary continuity. The exquisitely preserved brain of Stanleycaris is consistent with the hypothesized deutocerebral innervation of the frontal appendages, reconciling neuroanatomical evidence with external morphology in support of an ancestrally bipartite head and brain for arthropods. We propose that the integration of this bipartite head prior to the acquisition of most segmental characters exclusively in the arthropod trunk may help explain its developmental differentiation.

Tardigrades and their emergence as model organisms

Experimentally tractable organisms like C. elegans, Drosophila, zebrafish, and mouse are popular models for addressing diverse questions in biology. In 1997, two of the most valuable invertebrate model organisms to date-C. elegans and Drosophila-were found to be much more closely related to each other than expected. C. elegans and Drosophila belong to the nematodes and arthropods, respectively, and these two phyla and six other phyla make up a clade of molting animals referred to as the Ecdysozoa. The other ecdysozoan phyla could be valuable models for comparative biology, taking advantage of the rich and continual sources of research findings as well as tools from both C. elegans and Drosophila. But when the Ecdysozoa was first recognized, few tools were available for laboratory studies in any of these six other ecdysozoan phyla. In 1999 I began an effort to develop tools for studying one such phylum, the tardigrades. Here, I describe how the tardigrade species Hypsibius exemplaris and tardigrades more generally have emerged over the past two decades as valuable new models for answering diverse questions. To date, these questions have included how animal body plans evolve and how biological materials can survive some remarkably extreme conditions.

Extensive loss of Wnt genes in Tardigrada

Background

Wnt genes code for ligands that activate signaling pathways during development in Metazoa. Through the canonical Wnt (cWnt) signaling pathway, these genes regulate important processes in bilaterian development, such as establishing the anteroposterior axis and posterior growth. In Arthropoda, Wnt ligands also regulate segment polarity, and outgrowth and patterning of developing appendages. Arthropods are part of a lineage called Panarthropoda that includes Onychophora and Tardigrada. Previous studies revealed potential roles of Wnt genes in regulating posterior growth, segment polarity, and growth and patterning of legs in Onychophora. Unlike most other panarthropods, tardigrades lack posterior growth, but retain segmentation and appendages. Here, we investigated Wnt genes in tardigrades to gain insight into potential roles that these genes play during development of the highly compact and miniaturized tardigrade body plan.

Results

We analyzed published genomes for two representatives of Tardigrada, Hypsibius exemplaris and Ramazzottius varieornatus. We identified single orthologs of Wnt4, Wnt5, Wnt9, Wnt11, and WntA, as well as two Wnt16 paralogs in both tardigrade genomes. We only found a Wnt2 ortholog in H. exemplaris. We could not identify orthologs of Wnt1, Wnt6, Wnt7, Wnt8, or Wnt10. We identified most other components of cWnt signaling in both tardigrade genomes. However, we were unable to identify an ortholog of arrow/Lrp5/6, a gene that codes for a Frizzled co-receptor of Wnt ligands. Additionally, we found that some other animals that have lost several Wnt genes and are secondarily miniaturized, like tardigrades, are also missing an ortholog of arrow/Lrp5/6. We analyzed the embryonic expression patterns of Wnt genes in H. exemplaris during developmental stages that span the establishment of the AP axis through segmentation and leg development. We detected expression of all Wnt genes in H. exemplaris besides one of the Wnt16 paralogs. During embryo elongation, expression of several Wnt genes was restricted to the posterior pole or a region between the anterior and posterior poles. Wnt genes were expressed in distinct patterns during segmentation and development of legs in H. exemplaris, rather than in broadly overlapping patterns.

Conclusions

Our results indicate that Wnt signaling has been highly modified in Tardigrada. While most components of cWnt signaling are conserved in tardigrades, we conclude that tardigrades have lost Wnt1, Wnt6, Wnt7, Wnt8, and Wnt10, along with arrow/Lrp5/6. Our expression data may indicate a conserved role of Wnt genes in specifying posterior identities during establishment of the AP axis. However, the loss of several Wnt genes and the distinct expression patterns of Wnt genes during segmentation and leg development may indicate that combinatorial interactions among Wnt genes are less important during tardigrade development compared to many other animals. Based on our results, and comparisons to previous studies, we speculate that the loss of several Wnt genes in Tardigrada may be related to a reduced number of cells and simplified development that accompanied miniaturization and anatomical simplification in this lineage.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01954-y.

Loss of intermediate regions of perpendicular body axes contributed to miniaturization of tardigrades

Tardigrades have a miniaturized body plan. Miniaturization in tardigrades is associated with the loss of several organ systems and an intermediate region of their anteroposterior (AP) axis. However, how miniaturization has affected tardigrade legs is unclear. In arthropods and in onychophorans, the leg gap genes are expressed in regionalized proximodistal (PD) patterns in the legs. Functional studies indicate that these genes regulate growth in their respective expression domains and establish PD identities, partly through mutually antagonistic regulatory interactions. Here, we investigated the expression patterns of tardigrade orthologs of the leg gap genes. Rather than being restricted to a proximal leg region, as in arthropods and onychophorans, we detected coexpression of orthologues of homothorax and extradenticle broadly across the legs of the first three trunk segments in the tardigrade Hypsibius exemplaris. We could not identify a dachshund orthologue in tardigrade genomes, a gene that is expressed in an intermediate region of developing legs in arthropods and onychophorans, suggesting that this gene was lost in the tardigrade lineage. We detected Distal-less expression broadly across all developing leg buds in H. exemplaris embryos, unlike in arthropods and onychophorans, in which it exhibits a distally restricted expression domain. The broad expression patterns of the remaining leg gap genes in H. exemplaris legs may reflect the loss of dachshund and the accompanying loss of an intermediate region of the legs in the tardigrade lineage. We propose that the loss of intermediate regions of both the AP and PD body axes contributed to miniaturization of Tardigrada.

Comparison of the transcriptomes of two tardigrades with different hatching coordination

BACKGROUND

Tardigrades are microscopic organisms, famous for their tolerance against extreme environments. The establishment of rearing systems of multiple species has allowed for comparison of tardigrade physiology, in particular in embryogenesis. Interestingly, in-lab cultures of limnic species showed smaller variation in hatching timing than terrestrial species, suggesting a hatching regulation mechanism acquired by adaptation to their habitat.

RESULTS

To this end, we screened for coordinated gene expression during the development of two species of tardigrades, Hypsibius exemplaris and Ramazzottius varieornatus, and observed induction of the arthropod molting pathway. Exposure of ecdysteroids and juvenile hormone analog affected egg hatching but not embryonic development in only the limnic H. exemplaris.

CONCLUSION

These observations suggest a hatching regulation mechanism by the molting pathway in H. exemplaris.

Acoustomicrofluidic separation of tardigrades from raw cultures for sample preparation

Tardigrades are microscopic animals widely known for their ability to survive in extreme conditions. They are the focus of current research in the fields of taxonomy, biogeography, genomics, proteomics, development, space biology, evolution and ecology. Tardigrades, such as Hypsibius exemplaris, are being advocated as a next-generation model organism for genomic and developmental studies. The raw culture of H. exemplaris usually contains tardigrades themselves, their eggs, faeces and algal food. Experimentation with tardigrades often requires the demanding and laborious separation of tardigrades from raw samples to prepare pure and contamination-free tardigrade samples. In this paper, we propose a two-step acoustomicrofluidic separation method to isolate tardigrades from raw samples. In the first step, a passive microfluidic filter composed of an array of traps is used to remove large algal clusters in the raw sample. In the second step, a surface acoustic wave-based active microfluidic separation device is used to deflect tardigrades continuously from their original streamlines inside the microchannel and thus isolate them selectively from algae and eggs. The experimental results demonstrated the efficient separation of tardigrades, with a recovery rate of 96% and an impurity of 4% algae on average in a continuous, contactless, automated, rapid and biocompatible manner.

Cellular morphology of leg musculature in the water bear Hypsibius exemplaris (Tardigrada) unravels serial homologies

Tardigrades (water bears) are microscopic, segmented ecdysozoans with four pairs of legs. Lobopodous limbs that are similar to those seen in tardigrades are hypothesized to represent the ancestral state of Panarthropoda (Tardigrada + Onychophora + Arthropoda), and their evolutionary history is important to our understanding of ecdysozoan evolution. Equally important is our understanding of the functional morphology of these legs, which requires knowledge of their musculature. Tardigrade musculature is well documented but open questions remain. For example, while the muscular organization of each trunk segment and its legs is unique, three of the four trunk segments are nevertheless relatively homonomous. To what extent, then, do leg muscles show segmental patterns? Specifically, which leg muscles are serially repeated and which are unique? The present study addresses these questions using a combination of techniques intended to visualize both the overall layout and fine structure of leg muscles in the eutardigrade Hypsibius exemplaris. In doing so, we propose serial homologies for all leg muscles in each of the four legs and reveal new details of their cellular structure and attachment sites. We compare our results to those of previous studies and address the functional implications of specialized muscle cell morphologies.

Expression of NK genes that are not part of the NK cluster in the onychophoran Euperipatoides rowelli (Peripatopsidae)

Background

NK genes are a group of homeobox transcription factors that are involved in various molecular pathways across bilaterians. They are typically divided into two subgroups, the NK cluster (NKC) and NK-linked genes (NKL). While the NKC genes have been studied in various bilaterians, corresponding data of many NKL genes are missing to date. To further investigate the ancestral roles of NK family genes, we analyzed the expression patterns of NKL genes in the onychophoran Euperipatoides rowelli.

Results

The NKL gene complement of E. rowelli comprises eight genes, including BarH, Bari, Emx, Hhex, Nedx, NK2.1, vax and NK2.2, of which only NK2.2 was studied previously. Our data for the remaining seven NKL genes revealed expression in different structures associated with the developing nervous system in embryos of E. rowelli. While NK2.1 and vax are expressed in distinct medial regions of the developing protocerebrum early in development, BarH, Bari, Emx, Hhex and Nedx are expressed in late developmental stages, after all major structures of the nervous system have been established. Furthermore, BarH and Nedx are expressed in distinct mesodermal domains in the developing limbs.

Conclusions

Comparison of our expression data to those of other bilaterians revealed similar patterns of NK2.1, vax, BarH and Emx in various aspects of neural development, such as the formation of anterior neurosecretory cells mediated by a conserved molecular mechanism including NK2.1 and vax, and the development of the central and peripheral nervous system involving BarH and Emx. A conserved role in neural development has also been reported from NK2.2, suggesting that the NKL genes might have been primarily involved in neural development in the last common ancestor of bilaterians or at least nephrozoans (all bilaterians excluding xenacoelomorphs). The lack of comparative data for many of the remaining NKL genes, including Bari, Hhex and Nedx currently hampers further evolutionary conclusions. Hence, future studies should focus on the expression of these genes in other bilaterians, which would provide a basis for comparative studies and might help to better understand the role of NK genes in the diversification of bilaterians.

Electronic supplementary material

The online version of this article (10.1186/s12861-019-0185-9) contains supplementary material, which is available to authorized users.

Miniaturization of tardigrades (water bears): Morphological and genomic perspectives

Tardigrades form a monophyletic group of microscopic ecdysozoans best known for surviving extreme environmental conditions. Due to their key phylogenetic position as a subgroup of the Panarthropoda, understanding tardigrade biology is important for comparative studies with related groups like Arthropoda. Panarthropods - and Ecdysozoa as a whole - likely evolved from macroscopic ancestors, with several taxa becoming secondarily miniaturized. Morphological and genomic evidence likewise points to a miniaturized tardigrade ancestor. The five-segmented tardigrade body typically measures less than 1 mm in length and consists of only about 1000 cells. Most organs comprise a relatively small number of cells, with the highest proportion belonging to the central nervous system, while muscles are reduced to a single cell each. Similarly, fully sequenced genomes of three tardigrade species - together with Hox gene expression data - point to extensive modifications, rearrangements, and major losses of genes and even a large body region. Parallels are evident with related ecdysozoans that may have also undergone genomic reductions, such as the nematode Caenorhabditis elegans. We interpret these data together as evidence of miniaturization in the tardigrade lineage, while cautioning that the effects of miniaturization may manifest in different ways depending on the organ or organ system under examination.

The Emergence of the Tardigrade Hypsibius exemplaris as a Model System

The success of scientists in revealing biological mechanisms has depended in large part on choosing tractable model systems. In 1997, molecular phylogenetics revealed that two of biology's most tractable models-Caenorhabditis elegans and Drosophila-are much more closely related to each other than had been thought previously. I began to explore whether any of the little-studied members of this branch of the tree of life might serve as a new model for comparative biology that could make use of the rich and ongoing sources of information flowing from C. elegans and Drosophila research. Tardigrades, also known as water bears, make up a phylum of microscopic animals. The tardigrade Hypsibius exemplaris (recently disambiguated from a closely related species, Hypsibius dujardini) can be maintained in laboratories and has a generation time of <2 wk at room temperature. Stocks of animals can be stored frozen and revived. The animals and their embryos are optically clear, and embryos are laid in groups, with each synchronous clutch of embryos laid in a clear molt. We have developed techniques for laboratory study of this system, including methods for microinjection of animals, immunolocalization, in situ hybridization, RNA interference, transcriptomics, and methods for identifying proteins that mediate tolerance to extreme environments. Here, I review the development of this animal as an emerging model system, as well as recent molecular studies aimed at understanding the evolution of developmental mechanisms that underpin the evolution of animal form and at understanding how biological materials can survive extreme environments.

Halloween genes in panarthropods and the evolution of the early moulting pathway in Ecdysozoa

Moulting is a characteristic feature of Ecdysozoa-the clade of moulting animals that includes the hyperdiverse arthropods and less speciose groups, such as onychophorans, tardigrades and nematodes. Moulting has been best analysed in arthropods, specifically in insects and crustaceans, in which a complex neuroendocrine system acts at the genomic level and initiates the transcription of genes responsible for moulting. The key moulting hormones, ecdysone and 20-hydroxyecdysone, are subsequently synthesized from cholesterol ingested with food. Their biosynthesis is regulated by the Rieske-domain protein Neverland and cytochrome P450 enzymes encoded by the so-called 'Halloween' genes. Ecdysone is then released into the haemolymph and modified into 20-hydroxyecdysone, which binds to the nuclear receptor EcR/USP and initiates transcription of the Early genes. As little is known about the moulting pathway of other ecdysozoans, we examined the occurrence of genes involved in ecdysteroid biosynthesis and the early moulting cascade across ecdysozoan subgroups. Genomic and transcriptomic searches revealed no Halloween genes in cycloneuralians, whereas only shadow (CYP315A1) is present in onychophorans and tardigrades, suggesting that the Halloween genes evolved stepwise in panarthropods. These findings imply that the genes which were responsible for the ecdysteroid biosynthesis in the last common ancestor of Ecdysozoa are currently unknown.

Expression of NK cluster genes in the onychophoran Euperipatoides rowelli: implications for the evolution of NK family genes in nephrozoans

Background

Understanding the evolution and development of morphological traits of the last common bilaterian ancestor is a major goal of the evo-devo discipline. The reconstruction of this "urbilaterian" is mainly based on comparative studies of common molecular patterning mechanisms in recent model organisms. The NK homeobox genes are key players in many of these molecular pathways, including processes regulating mesoderm, heart and neural development. Shared features seen in the expression patterns of NK genes have been used to determine the ancestral bilaterian characters. However, the commonly used model organisms provide only a limited view on the evolution of these molecular pathways. To further investigate the ancestral roles of NK cluster genes, we analyzed their expression patterns in the onychophoran Euperipatoides rowelli.

Results

We identified nine transcripts of NK cluster genes in E. rowelli, including single copies of NK1, NK3, NK4, NK5, Msx, Lbx and Tlx, and two copies of NK6. All of these genes except for NK6.1 and NK6.2 are expressed in different mesodermal organs and tissues in embryos of E. rowelli, including the anlagen of somatic musculature and the heart. Furthermore, we found distinct expression patterns of NK3, NK5, NK6, Lbx and Msx in the developing nervous system. The same holds true for the NKL gene NK2.2, which does not belong to the NK cluster but is a related gene playing a role in neural patterning. Surprisingly, NK1, Msx and Lbx are additionally expressed in a segment polarity-like pattern early in development-a feature that has been otherwise reported only from annelids.

Conclusion

Our results indicate that the NK cluster genes were involved in mesoderm and neural development in the last common ancestor of bilaterians or at least nephrozoans (i.e., bilaterians to the exclusion of xenacoelomorphs). By comparing our data from an onychophoran to those from other bilaterians, we critically review the hypothesis of a complex "urbilaterian" with a segmented body, a pulsatile organ or heart, and a condensed mediolaterally patterned nerve cord.