Arthropod phylogeny: an overview from the perspectives of morphology, molecular data and the fossil record

The venom and telopodal defence systems of the centipede Lithobius forficatus are functionally convergent serial homologues

BACKGROUND

Evolution of novelty is a central theme in evolutionary biology, yet studying the origins of traits with an apparently discontinuous origin remains a major challenge. Venom systems are a well-suited model for the study of this phenomenon because they capture several aspects of novelty across multiple levels of biological complexity. However, while there is some knowledge on the evolution of individual toxins, not much is known about the evolution of venom systems as a whole. One way of shedding light on the evolution of new traits is to investigate less specialised serial homologues, i.e. repeated traits in an organism that share a developmental origin. This approach can be particularly informative in animals with repetitive body segments, such as centipedes.

RESULTS

Here, we investigate morphological and biochemical aspects of the defensive telopodal glandular organs borne on the posterior legs of venomous stone centipedes (Lithobiomorpha), using a multimethod approach, including behavioural observations, comparative morphology, proteomics, comparative transcriptomics and molecular phylogenetics. We show that the anterior venom system and posterior telopodal defence system are functionally convergent serial homologues, where one (telopodal defence) represents a model for the putative early evolutionary state of the other (venom). Venom glands and telopodal glandular organs appear to have evolved from the same type of epidermal gland (four-cell recto-canal type) and while the telopodal defensive secretion shares a great degree of compositional overlap with centipede venoms in general, these similarities arose predominantly through convergent recruitment of distantly related toxin-like components. Both systems are composed of elements predisposed to functional innovation across levels of biological complexity that range from proteins to glands, demonstrating clear parallels between molecular and morphological traits in the properties that facilitate the evolution of novelty.

CONCLUSIONS

The evolution of the lithobiomorph telopodal defence system provides indirect empirical support for the plausibility of the hypothesised evolutionary origin of the centipede venom system, which occurred through functional innovation and gradual specialisation of existing epidermal glands. Our results thus exemplify how continuous transformation and functional innovation can drive the apparent discontinuous emergence of novelties on higher levels of biological complexity.

Uniquely preserved gut contents illuminate trilobite palaeophysiology

Trilobites are among the most iconic of fossils and formed a prominent component of marine ecosystems during most of their 270-million-year-long history from the early Cambrian period to the end Permian period1. More than 20,000 species have been described to date, with presumed lifestyles ranging from infaunal burrowing to a planktonic life in the water column2. Inferred trophic roles range from detritivores to predators, but all are based on indirect evidence such as body and gut morphology, modes of preservation and attributed feeding traces; no trilobite specimen with internal gut contents has been described3,4. Here we present the complete and fully itemized gut contents of an Ordovician trilobite, Bohemolichas incola, preserved three-dimensionally in a siliceous nodule and visualized by synchrotron microtomography. The tightly packed, almost continuous gut fill comprises partly fragmented calcareous shells indicating high feeding intensity. The lack of dissolution of the shells implies a neutral or alkaline environment along the entire length of the intestine supporting digestive enzymes comparable to those in modern crustaceans or chelicerates. Scavengers burrowing into the trilobite carcase targeted soft tissues below the glabella but avoided the gut, suggesting noxious conditions and possibly ongoing enzymatic activity.

Was There a Cambrian Explosion on Land? The Case of Arthropod Terrestrialization

Arthropods, the most diverse form of macroscopic life in the history of the Earth, originated in the sea. Since the early Cambrian, at least ~518 million years ago, these animals have dominated the oceans of the world. By the Silurian-Devonian, the fossil record attests to arthropods becoming the first animals to colonize land, However, a growing body of molecular dating and palaeontological evidence suggests that the three major terrestrial arthropod groups (myriapods, hexapods, and arachnids), as well as vascular plants, may have invaded land as early as the Cambrian-Ordovician. These dates precede the oldest fossil evidence of those groups and suggest an unrecorded continental "Cambrian explosion" a hundred million years prior to the formation of early complex terrestrial ecosystems in the Silurian-Devonian. We review the palaeontological, phylogenomic, and molecular clock evidence pertaining to the proposed Cambrian terrestrialization of the arthropods. We argue that despite the challenges posed by incomplete preservation and the scarcity of early Palaeozoic terrestrial deposits, the discrepancy between molecular clock estimates and the fossil record is narrower than is often claimed. We discuss strategies for closing the gap between molecular clock estimates and fossil data in the evolution of early ecosystems on land.

The Birth of the Mammalian Sleep

Simple Summary

Mammals evolved from reptiles as a consequence of an evolutionary bottleneck. Some diurnal reptiles extended their activity, first to twilight and then to the entire dark time. This forced the change of the visual system. Pursuing maximal sensitivity, they abandoned the filters protecting the eyes against the dangerous diurnal light, which, in turn, forced immobility in lightproof burrows during light time. This was the birth of the mammalian sleep. Then, the Cretacic-Paleogene extinction of dinosaurs leaved free the diurnal niche and allowed the expansion of a few early mammals to diurnal life and the high variability of sleep traits. On the other hand, we propose that the idling rest is a state showing homeostatic regulation. Therefore, the difference between behavioral rest and wakeful idling is rather low: both show quiescence, raised sensory thresholds, reversibility, specific sleeping-resting sites and body positions, it is a pleasing state, and both are dependent of circadian and homeostatic regulation. Indeed, the most important difference is the unconsciousness of sleep and the consciousness of wakeful idling. Thus, we propose that sleep is a mere upgrade of the wakeful rest, and both may have the same function: guaranteeing rest during a part of the daily cycle.

Abstract

Mammals evolved from small-sized reptiles that developed endothermic metabolism. This allowed filling the nocturnal niche. They traded-off visual acuity for sensitivity but became defenseless against the dangerous daylight. To avoid such danger, they rested with closed eyes in lightproof burrows during light-time. This was the birth of the mammalian sleep, the main finding of this report. Improved audition and olfaction counterweighed the visual impairments and facilitated the cortical development. This process is called “The Nocturnal Evolutionary Bottleneck”. Pre-mammals were nocturnal until the Cretacic-Paleogene extinction of dinosaurs. Some early mammals returned to diurnal activity, and this allowed the high variability in sleeping patterns observed today. The traits of Waking Idleness are almost identical to those of behavioral sleep, including homeostatic regulation. This is another important finding of this report. In summary, behavioral sleep seems to be an upgrade of Waking Idleness Indeed, the trait that never fails to show is quiescence. We conclude that the main function of sleep consists in guaranteeing it during a part of the daily cycle.

Torsion-Resistant Structures: A Nature Addressed Solution

The complexity of torsional load, its three-dimensional nature, its combination with other stresses, and its disruptive impact make torsional failure prevention an ambitious goal. However, even if the problem has been addressed for decades, a deep and organized treatment is still lacking in the actual research landscape. For this reason, this review aims at presenting a methodical approach to address torsional issues starting from a punctual problem definition. Accidents and breaks due to torsion, which often occur in different engineering fields such as mechanical, biomedical, and civil industry are considered and critically compared. More in depth, the limitations of common-designed torsion-resistant structures (i.e., high complexity and increased weight) are highlighted, and emerge as a crucial point for a deeper nature-driven analysis of novel solutions. In this context, an accurate screening of torsion-resistant bio-inspired unit cells is presented, taking inspiration specifically from plants, that are often subjected to the torsional effect of winds. As future insights, the actual state of technology suggests an innovative transposition to the industry: these unit cells could be prominently implied to develop novel metamaterials that could be able to address the torsional issue with a multi-scale and tailored arrangement.

Evolution of Toll, Spatzle and MyD88 in insects: the problem of the Diptera bias

BACKGROUND

Arthropoda, the most numerous and diverse metazoan phylum, has species in many habitats where they encounter various microorganisms and, as a result, mechanisms for pathogen recognition and elimination have evolved. The Toll pathway, involved in the innate immune system, was first described as part of the developmental pathway for dorsal-ventral differentiation in Drosophila. Its later discovery in vertebrates suggested that this system was extremely conserved. However, there is variation in presence/absence, copy number and sequence divergence in various genes along the pathway. As most studies have only focused on Diptera, for a comprehensive and accurate homology-based approach it is important to understand gene function in a number of different species and, in a group as diverse as insects, the use of species belonging to different taxonomic groups is essential.

RESULTS

We evaluated the diversity of Toll pathway gene families in 39 Arthropod genomes, encompassing 13 different Insect Orders. Through computational methods, we shed some light into the evolution and functional annotation of protein families involved in the Toll pathway innate immune response. Our data indicates that: 1) intracellular proteins of the Toll pathway show mostly species-specific expansions; 2) the different Toll subfamilies seem to have distinct evolutionary backgrounds; 3) patterns of gene expansion observed in the Toll phylogenetic tree indicate that homology based methods of functional inference might not be accurate for some subfamilies; 4) Spatzle subfamilies are highly divergent and also pose a problem for homology based inference; 5) Spatzle subfamilies should not be analyzed together in the same phylogenetic framework; 6) network analyses seem to be a good first step in inferring functional groups in these cases. We specifically show that understanding Drosophila's Toll functions might not indicate the same function in other species.

CONCLUSIONS

Our results show the importance of using species representing the different orders to better understand insect gene content, origin and evolution. More specifically, in intracellular Toll pathway gene families the presence of orthologues has important implications for homology based functional inference. Also, the different evolutionary backgrounds of Toll gene subfamilies should be taken into consideration when functional studies are performed, especially for TOLL9, TOLL, TOLL2_7, and the new TOLL10 clade. The presence of Diptera specific clades or the ones lacking Diptera species show the importance of overcoming the Diptera bias when performing functional characterization of Toll pathways.

Visual metamorphoses in insects and malacostracans: Transitions between an aquatic and terrestrial life

Arthropods operate in an outrageous diversity of environments. From the deep sea to dense tropical forests, to wide open arctic tundra, they have colonized almost every possible habitat. Within these environments, the presence of light is nearly ubiquitous, varying in intensity, wavelength, and polarization. Light provides critical information about the environment, such as time of day or where food sources may be located. Animals take advantage of this prevalent and informative cue to make behavioral choices. However, the types of choices animals face depend greatly on their environments and needs at any given time. In particular, animals that undergo metamorphosis, with arthropods being the prime example, experience dramatic changes in both behavior and ecology, which in turn may require altering the structure and function of sensory systems such as vision. Amphibiotic organisms maintain aquatic lifestyles as juveniles before transitioning to terrestrial lifestyles as adults. However, light behaves differently in water than in air, resulting in distinct aquatic and terrestrial optical environments. Visual changes in response to these optical differences can occur on multiple levels, from corneal structure down to neural organization. In this review, we summarize examples of alterations in the visual systems of amphibiotic larval and adult insects and malacostracan crustaceans, specifically those attributed to environmental differences between metamorphic phases.

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.

Functional morphology of a lobopod: case study of an onychophoran leg

Segmental, paired locomotory appendages are a characteristic feature of Panarthropoda-a diversified clade of moulting animals that includes onychophorans (velvet worms), tardigrades (water bears) and arthropods. While arthropods acquired a sclerotized exoskeleton and articulated limbs, onychophorans and tardigrades possess a soft body and unjointed limbs called lobopods, which they inherited from Cambrian lobopodians. To date, the origin and ancestral structure of the lobopods and their transformation into the jointed appendages are all poorly understood. We therefore combined high-resolution computed tomography with high-speed camera recordings to characterize the functional anatomy of a trunk lobopod from the onychophoran Euperipatoides rowelli. Three-dimensional reconstruction of the complete set of muscles and muscle fibres as well as non-muscular structures revealed the spatial relationship and relative volumes of the muscular, excretory, circulatory and nervous systems within the leg. Locomotory movements of individual lobopods of E. rowelli proved far more diverse than previously thought and might be governed by a complex interplay of 15 muscles, including one promotor, one remotor, one levator, one retractor, two depressors, two rotators, one flexor and two constrictors as well as muscles for stabilization and haemolymph control. We discuss the implications of our findings for understanding the evolution of locomotion in panarthropods.

Trilobite compound eyes with crystalline cones and rhabdoms show mandibulate affinities

Most knowledge about the structure, function, and evolution of early compound eyes is based on investigations in trilobites. However, these studies dealt mainly with the cuticular lenses and little was known about internal anatomy. Only recently some data on crystalline cones and retinula cells were reported for a Cambrian trilobite species. Here, we describe internal eye structures of two other trilobite genera. The Ordovician Asaphus sp. reveals preserved crystalline cones situated underneath the cuticular lenses. The same is true for the Devonian species Archegonus (Waribole) warsteinensis, which in addition shows the fine structure of the rhabdom in the retinula cells. These results suggest that an apposition eye with a crystalline cone is ancestral for Trilobita. The overall similarity of trilobite eyes to those of myriapods, crustaceans, and hexapods corroborates views of a phylogenetic position of trilobites in the stem lineage of Mandibulata.

Little is known about the internal anatomy of early eyes. Here, Scholtz and colleagues show the internal eye structures from fossils of two genera of trilobites, which support an ancestral apposition eye with crystalline cones in Trilobita and a close affinity with Mandibulata.

Morphological study of the ovary in Hanseniella caldaria (Myriapoda; Symphyla): The position of oocyte-growth and evolution of ovarian structure in Arthropoda

In Arthropoda, the ovary is classified into Chelicerata-type and Mandibulata-type, based on the oocyte-growth position within the ovary. By contrast, oocytes of Diplopoda and Chilopoda grow within the hemocoelic space. However, as the position of oocyte-growth in Symphyla and Pauropoda has not been confirmed, whether the hemocoelic nature of oocyte-growth is common among myriapods remains ambiguous. This study described the ovarian structure of Hanseniella caldaria to reveal the oocyte-growth position in Symphyla. The oocyte is surrounded by the follicle epithelium, and the inner surface of the follicle epithelium, i.e., the space between follicle cells and oocytes, is lined with a basement membrane. The follicle epithelial layer continues to the ovarian epithelium via the follicle extension with a continuous layer of basement membrane. Data on the architecture of the follicle suggest that the follicle pouch opens to the hemocoel. Hence, the oocyte of H. caldaria grows within the hemocoelic space. Based on our findings in H. caldaria and previous studies in a millipede and in centipedes, the hemocoelic nature of oocyte-growth is considered as a common feature among myriapods and a synapomorphy of the Myriapoda for which morphological synapomorphies have been ambiguous.

Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics

Understanding the evolution of Tetraconata or Pancrustacea-the clade that includes crustaceans and insects-requires a well-resolved hypothesis regarding the relationships within and among its constituent taxa. Here, we assembled a taxon-rich phylogenomic dataset focusing on crustacean lineages based solely on genomes and new-generation Illumina-generated transcriptomes, including 89 representatives of Tetraconata. This constitutes, to our knowledge, the first phylogenomic study specifically addressing internal relationships of Malacostraca (with 26 species included) and Branchiopoda (36 species). Seven matrices comprising 81-684 orthogroups and 17 690-242 530 amino acid positions were assembled and analysed under five different analytical approaches. To maximize gene occupancy and to improve resolution, taxon-specific matrices were designed for Malacostraca and Branchiopoda. Key tetraconatan taxa (i.e. Oligostraca, Multicrustacea, Branchiopoda, Malacostraca, Thecostraca, Copepoda and Hexapoda) were monophyletic and well supported. Within Branchiopoda, Phyllopoda, Diplostraca, Cladoceromorpha and Cladocera were monophyletic. Within Malacostraca, the clades Eumalacostraca, Decapoda and Reptantia were well supported. Recovery of Caridoida or Peracarida was highly dependent on the analysis for the complete matrix, but it was consistently monophyletic in the malacostracan-specific matrices. From such examples, we demonstrate that taxon-specific matrices and particular evolutionary models and analytical methods, namely CAT-GTR and Dayhoff recoding, outperform other approaches in resolving certain recalcitrant nodes in phylogenomic analyses.

Postembryonic development of pycnogonids: A deeper look inside

Sea spiders form a small, enigmatic group of recent chelicerates, with an unusual bodyplan, oligosegmented larvae and a postembryonic development that is punctuated by many moults. To date, only a few papers examined the anatomical and ultrastructural modifications of the larvae and various instars. Here we traced both internal and external events of the whole postembryonic development in Nymphon brevirostre HODGE 1863 using histology, SEM, TEM and confocal microscopy. During postembryonic development, larvae of this species undergo massive reorganization: spinning apparatus and chelar glands disappear; larval legs redifferentiate; three new segments and the abdomen are formed with their corresponding internal organs and appendages; circulatory and reproductive systems develop anew and the digestive and the nervous systems change dramatically. The body cavity remains schizocoelic throughout development, and no traces of even transitory coeloms were found in any instar. In Nymphon brevirostre, just like in Artemia salina LINNAEUS 1758 the heart arises through differentiation of the already existing schizocoel, and thus the circulatory systems of arthropods and annelids are not homologous. We found that classical chelicerate tagmata, prosoma and opisthosoma, are inapplicable to adult pycnogonids, with the most striking difference being the fate and structure of the seventh appendage-bearing segment.

Scorpions pectines - Idiosyncratic chemo- and mechanosensory organs

Scorpions possess specialised chemosensory appendages, the pectines. These comb-shaped limbs are located ventrally behind the walking legs. Like the antennae of mandibulate arthropods, they also serve a mechanosensory function. However, more than 90% of the sometimes well above 100,000 sensory neurons projecting from a pectine to the central nervous system are chemosensory. There are two primary projection neuropils. The posterior one, immediately adjacent to the pectine nerve entrance, has an intriguing substructure reminiscent of the olfactory glomeruli observed in the primary chemosensory neuropils of many arthropods and indeed of most bilaterian animals. There are further similarities, particularly to the antennal lobes of mandibulate arthropods, including dense innervation by a relatively small number of putative serotonergic interneurons and the presence of GABA immunoreactivity, indicative of inhibitory interactions. Scorpion idiosyncrasies include the flattened shape and broad size range of the glomerulus-like neuropil compartments. Further, these compartments are often not clearly delimited and form layers in the neuropil that are arranged like onion peels. In summary, the pectine appendages of scorpions and their central nervous projections appear as promising study subjects, particularly regarding comparative examination of chemosensory representation and processing strategies. The possibility of combined, rather than discrete, representations of chemo- and mechanosensory inputs should merit further study.

The Evolution of Arthropod Body Plans: Integrating Phylogeny, Fossils, and Development-An Introduction to the Symposium

The last few years have seen a significant increase in the amount of data we have about the evolution of the arthropod body plan. This has come mainly from three separate sources: a new consensus and improved resolution of arthropod phylogeny, based largely on new phylogenomic analyses; a wealth of new early arthropod fossils from a number of Cambrian localities with excellent preservation, as well as a renewed analysis of some older fossils; and developmental data from a range of model and non-model pan-arthropod species that shed light on the developmental origins and homologies of key arthropod traits. However, there has been relatively little synthesis among these different data sources, and the three communities studying them have little overlap. The symposium "The Evolution of Arthropod Body Plans-Integrating Phylogeny, Fossils and Development" brought together leading researchers in these three disciplines and made a significant contribution to the emerging synthesis of arthropod evolution, which will help advance the field and will be useful for years to come.

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

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

Serotonergic neurons in the ventral nerve cord of Chilopoda - a mandibulate pattern of individually identifiable neurons

BACKGROUND

Given the numerous hypotheses concerning arthropod phylogeny, independent data are needed to supplement knowledge based on traditional external morphology and modern molecular sequence information. One promising approach involves comparisons of the structure and development of the nervous system. Along these lines, the morphology of serotonin-immunoreactive neurons in the ventral nerve cord has been investigated in numerous tetraconate taxa (Crustacea and Hexapoda). It has been shown that these neurons can be identified individually due to their comparably low number, characteristic soma position, and neurite morphology, thus making it possible to establish homologies at the single cell level. Within Chilopoda (centipedes), detailed analyses of major branching patterns of serotonin-immunoreactive neurons are missing, but are crucial for developing meaningful conclusions on the homology of single cells.

RESULTS

In the present study, we re-investigated the distribution and projection patterns of serotonin-immunoreactive neurons in the ventral nerve cord of three centipede species: Scutigera coleoptrata, Lithobius forficatus, and Scolopendra oraniensis. The centipede serotonergic system in the ventral nerve cord contains defined groups of individually identifiable neurons. An anterior and two posterior immunoreactive neurons per hemiganglion with contralateral projections, a pair of ipsilateral projecting lateral neurons (an autapomorphic character for Chilopoda), as well as a postero-lateral group of an unclear number of cells are present in the ground pattern of Chilopoda.

CONCLUSIONS

Comparisons to the patterns of serotonin-immunoreactive neurons of tetraconate taxa support the homology of anterior and posterior neurons. Our results thus support a sister group relationship of Myriapoda and Tetraconata and, further, a mandibulate ground pattern of individually identifiable serotonin-immunoreactive neurons in the ventral nerve cord. Medial neurons are not considered to be part of the tetraconate ground pattern, but could favor the 'Miracrustacea hypothesis', uniting Remipedia, Cephalocarida, and Hexapoda.

No sight, no smell? - Brain anatomy of two amphipod crustaceans with different lifestyles

The brain anatomy of Niphargus puteanus and Orchestia cavimana, two amphipod species with different lifestyles, has been studied using a variety of recent techniques. The general aspects of the brain anatomy of both species correspond to those of other malacostracans. However, both species lack hemiellipsoid bodies. Furthermore, related to their lifestyle certain differences have been observed. The aquatic subterranean species N. puteanus lacks eye structures, the optic nerve, and the two outer optic neuropils lamina and medulla. Only partial remains of the lobula have been detected. In contrast to this, the central complex in the protocerebrum and the olfactory glomeruli in the deutocerebrum are well differentiated. The terrestrial species Orchestia cavimana shows a reduced first antenna, the absence of olfactory neuropils in the deutocerebrum, and a reduction of the olfactory globular tract. The characteristics in defining the hemiellipsoid bodies are critically discussed. Contradictions about presence or absence of this neuropil are due to different conceptualizations. A comparison with other crustaceans that live in dark environments reveal similar patterns of optic system reduction, but to different degrees following a centripetal pattern. Retaining the olfactory system seems a general problem of terrestrialization in crustaceans with the notable exception of terrestrial hermit crabs.

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.

Origin and evolution of the panarthropod head - A palaeobiological and developmental perspective

The panarthropod head represents a complex body region that has evolved through the integration and functional specialization of the anterior appendage-bearing segments. Advances in the developmental biology of diverse extant organisms have led to a substantial clarity regarding the relationships of segmental homology between Onychophora (velvet worms), Tardigrada (water bears), and Euarthropoda (e.g. arachnids, myriapods, crustaceans, hexapods). The improved understanding of the segmental organization in panarthropods offers a novel perspective for interpreting the ubiquitous Cambrian fossil record of these successful animals. A combined palaeobiological and developmental approach to the study of the panarthropod head through deep time leads us to propose a consensus hypothesis for the intricate evolutionary history of this important tagma. The contribution of exceptionally preserved brains in Cambrian fossils - together with the recognition of segmentally informative morphological characters - illuminate the polarity for major anatomical features. The euarthropod stem-lineage provides a detailed view of the step-wise acquisition of critical characters, including the origin of a multiappendicular head formed by the fusion of several segments, and the transformation of the ancestral protocerebral limb pair into the labrum, following the postero-ventral migration of the mouth opening. Stem-group onychophorans demonstrate an independent ventral migration of the mouth and development of a multisegmented head, as well as the differentiation of the deutocerebral limbs as expressed in extant representatives. The anterior organization of crown-group Tardigrada retains several ancestral features, such as an anterior-facing mouth and one-segmented head. The proposed model aims to clarify contentious issues on the evolution of the panarthropod head, and lays the foundation from which to further address this complex subject in the future.

Gene expression reveals evidence for EGFR-dependent proximal-distal limb patterning in a myriapod

Evolution of segmented limbs is one of the key innovations of Arthropoda, allowing development of functionally specific specialized head and trunk appendages, a major factor behind their unmatched evolutionary success. Proximodistal limb patterning is controlled by two regulatory networks in the vinegar fly Drosophila melanogaster, and other insects. The first is represented by the function of the morphogens Wingless (Wg) and Decapentaplegic (Dpp); the second by the EGFR-signaling cascade. While the role of Wg and Dpp has been studied in a wide range of arthropods representing all main branches, that is, Pancrustacea (= Hexapoda + Crustacea), Myriapoda and Chelicerata, investigation of the potential role of EGFR-signaling is restricted to insects (Hexapoda). Gene expression analysis of Egfr, its potential ligands, and putative downstream factors in the pill millipede Glomeris marginata (Myriapoda: Diplopoda), reveals that-in at least mandibulate arthropods-EGFR-signaling is likely a conserved regulatory mechanism in proximodistal limb patterning.

A new crustacean from the Herefordshire (Silurian) Lagerstätte, UK, and its significance in malacostracan evolution

Cascolus ravitis gen. et sp. nov. is a three-dimensionally preserved fossil crustacean with soft parts from the Herefordshire (Silurian) Lagerstätte, UK. It is characterized by a head with a head shield and five limb pairs, and a thorax (pereon) with nine appendage-bearing segments followed by an apodous abdomen (pleon). All the appendages except the first are biramous and have a gnathobase. The post-mandibular appendages are similar one to another, and bear petal-shaped epipods that probably functioned as a part of the respiratory-circulatory system. Cladistic analysis resolves the new taxon as a stem-group leptostracan (Malacostraca). This well-preserved arthropod provides novel insights into the evolution of appendage morphology, tagmosis and the possible respiratory-circulatory physiology of a basal malacostracan.

Complete mitochondrial genomes of two flat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida)

A lack of mitochondrial genome data from myriapods is hampering progress across genetic, systematic, phylogenetic and evolutionary studies. Here, the complete mitochondrial genomes of two millipedes, Asiomorphacoarctata Saussure, 1860 (Diplopoda: Polydesmida: Paradoxosomatidae) and Xystodesmus sp. (Diplopoda: Polydesmida: Xystodesmidae) were assembled with high coverage using Illumina sequencing data. The mitochondrial genomes of the two newly sequenced species are circular molecules of 15,644 bp and 15,791 bp, within which the typical mitochondrial genome complement of 13 protein-coding genes, 22 tRNAs and two ribosomal RNA genes could be identified. The mitochondrial genome of Asiomorphacoarctata is the first complete sequence in the family Paradoxosomatidae (Diplopoda: Polydesmida) and the gene order of the two flat-backed millipedes is novel among known myriapod mitochondrial genomes. Unique translocations have occurred, including inversion of one half of the two genomes with respect to other millipede genomes. Inversion of the entire side of a genome (trnF-nad5-trnH-nad4-nad4L, trnP, nad1-trnL2-trnL1-rrnL-trnV-rrnS, trnQ, trnC and trnY) could constitute a common event in the order Polydesmida. Last, our phylogenetic analyses recovered the monophyletic Progoneata, subphylum Myriapoda and four internal classes.

Recognising moulting behaviour in trilobites by examining morphology, development and preservation: Comment on Błażejowski et al. 2015

A 365 million year-old trilobite moult-carcass assemblage was described by Błażejowski et al. (2015) as the oldest direct evidence of moulting in the arthropod fossil record. Unfortunately, their suppositions are insufficiently supported by the data provided. Instead, the morphology, configuration and preservational context of the highly fossiliferous locality (Kowala Quarry, Poland) suggest that the specimen consists of two overlapping, queued carcasses. The wider fossil record of moulting actually extends back 520 million years, providing an unparalleled opportunity to study behaviour, ecology and development in early animals. Taking cues from modern analogues, it is possible to quantify precise details about moulting behaviour to determine broad-scale evolutionary trends, ontogenetic sequences and morphological selection pressures. In this review, we argue that this rich source of data has been underused in evolutionary studies, though has great potential for investigating the life history and evolution of arthropods in deep time.

The fossil record of ecdysis, and trends in the moulting behaviour of trilobites

Ecdysis, the process of moulting an exoskeleton, is one of the key characters uniting arthropods, nematodes and a number of smaller phyla into Ecdysozoa. The arthropod fossil record, particularly trilobites, eurypterids and decapod crustaceans, yields information on moulting, although the current focus is predominantly descriptive and lacks a broader evolutionary perspective. We here review literature on the fossil record of ecdysis, synthesising research on the behaviour, evolutionary trends, and phylogenetic significance of moulting throughout the Phanerozoic. Approaches vary widely between taxonomic groups, but an overall theme uniting these works suggests that identifying moults in the palaeontological record must take into account the morphology, taphonomy and depositional environment of fossils. We also quantitatively analyse trends in trilobite ecdysis based on a newly generated database of published incidences of moulting behaviour. This preliminary work reveals significant taxonomic and temporal signal in the trilobite moulting fossil record, with free cheek moulting being prevalent across all Orders and throughout the Phanerozoic, and peaks of cephalic moulting in Phacopida during the Ordovician and rostral plate moulting in Redlichiida during the Cambrian. This study and a review of the literature suggest that it is feasible to extract large-scale evolutionary information from the fossil record of moulting.

The impact of taphonomic data on phylogenetic resolution: Helenodora inopinata (Carboniferous, Mazon Creek Lagerstätte) and the onychophoran stem lineage

BACKGROUND

The origin of the body plan of modern velvet worms (Onychophora) lies in the extinct lobopodians of the Palaeozoic. Helenodora inopinata, from the Mazon Creek Lagerstätte of Illinois (Francis Creek Shale, Carbondale Formation, Middle Pennsylvanian), has been proposed as an intermediate between the "weird wonders" of the Cambrian seas and modern terrestrial predatory onychophorans. The type material of H. inopinata, however, leaves much of the crucial anatomy unknown.

RESULTS

Here we present a redescription of this taxon based on more complete material, including new details of the head and posterior portion of the trunk, informed by the results of experimental decay of extant onychophorans. H. inopinata is indeed best resolved as a stem-onychophoran, but lacks several key features of modern velvet worms including, crucially, those that would suggest a terrestrial mode of life.

CONCLUSIONS

The presence of H. inopinata in the Carboniferous demonstrates the survival of a Cambrian marine morphotype, and a likely post-Carboniferous origin of crown-Onychophora. Our analysis also demonstrates that taphonomically informed tests of character interpretations have the potential to improve phylogenetic resolution.

An embryological perspective on the early arthropod fossil record

BACKGROUND

Our understanding of the early evolution of the arthropod body plan has recently improved significantly through advances in phylogeny and developmental biology and through new interpretations of the fossil record. However, there has been limited effort to synthesize data from these different sources. Bringing an embryological perspective into the fossil record is a useful way to integrate knowledge from different disciplines into a single coherent view of arthropod evolution.

RESULTS

I have used current knowledge on the development of extant arthropods, together with published descriptions of fossils, to reconstruct the germband stages of a series of key taxa leading from the arthropod lower stem group to crown group taxa. These reconstruction highlight the main evolutionary transitions that have occurred during early arthropod evolution, provide new insights into the types of mechanisms that could have been active and suggest new questions and research directions.

CONCLUSIONS

The reconstructions suggest several novel homology hypotheses - e.g. the lower stem group head shield and head capsules in the crown group are all hypothesized to derive from the embryonic head lobes. The homology of anterior segments in different groups is resolved consistently. The transition between "lower-stem" and "upper-stem" arthropods is highlighted as a major transition with a concentration of novelties and innovations, suggesting a gap in the fossil record. A close relationship between chelicerates and megacheirans is supported by the embryonic reconstructions, and I suggest that the depth of the mandibulate-chelicerate split should be reexamined.

Molecular developmental evidence for a subcoxal origin of pleurites in insects and identity of the subcoxa in the gnathal appendages

Pleurites are chitinous plates in the body wall of insects and myriapods. They are believed to be an adaptation to locomotion on land but their developmental and evolutionary origins are unclear. A widely endorsed explanation for their origin is through toughening pre-existing parts of the body wall; in contrast, the subcoxal theory suggests pleurites derive from a redeployment of the proximal-most section of the leg, the subcoxa. Here, by studying expression of appendage patterning genes in embryos and larvae of the beetle Tribolium castaneum, we provide the first molecular evidence for the existence of a cryptic subcoxal segment in developing legs. We follow this structure during development and show that the embryonic subcoxa later forms the pleurites of the larva as predicted by the subcoxal theory. Our data also demonstrate that subcoxal segments are present in all post-antennal appendages, including the first molecular evidence of a two-segmented mandible with a subcoxal segment in insects.

De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil

Background

The blue crab, Callinectes sapidus, is economically and ecologically important in western Atlantic and Gulf of Mexico coastal estuaries. In 2010 blue crabs in the northern Gulf of Mexico were exposed to crude oil and chemical dispersants from the Deepwater Horizon oil spill. To characterize the blue crab transcriptome and identify genes that could be regulated in response to oil exposure we sequenced transcriptomes from hepatopancreas and gill tissues of juvenile blue crabs after exposing them to a water-accommodated fraction of surrogate Macondo crude oil in the laboratory and compared them to transcriptomes from an unexposed control group.

Results

Illumina sequencing provided 42.5 million paired-end sequencing reads for the control group and 44.9 million paired-end reads for the treatment group. From these, 73,473 transcripts and 52,663 genes were assembled. Comparison of control and treatment transcriptomes revealed about 100 genes from each tissue type that were differentially expressed. However, a much larger number of transcripts, approximately 2000 from each tissue type, were differentially expressed. Several examples of alternatively spliced transcripts were verified by qPCR, some of which showed significantly different expression patterns. The combined transcriptome from all tissues and individuals was annotated to assign putative gene products to both major gene ontology categories as well as specific roles in responses to cold and heat, metabolism of xenobiotic compounds, defence, hypoxia, osmoregulation and ecdysis. Among the annotations for upregulated and alternatively-spliced genes were candidates for the metabolism of oil-derived compounds.

Conclusions

Previously, few genomic resources were available for blue crabs or related brachyuran crabs. The transcriptome sequences reported here represent a major new resource for research on the biology of blue crabs. These sequences can be used for studies of differential gene expression or as a source of genetic markers. Genes identified and annotated in this study include candidates for responses of the blue crab to xenobiotic compounds, which could serve as biomarkers for oil exposure. Changes in gene expression also suggest other physiological changes that may occur as the result of exposure to oil.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1739-2) contains supplementary material, which is available to authorized users.

Three Halloween genes from the Varroa mite, Varroa destructor (Anderson & Trueman) and their expression during reproduction

The ecdysteroid biosynthetic pathway involves sequential enzymatic hydroxylations by a group of enzymes collectively known as Halloween gene proteins. Complete sequences for three Halloween genes, spook (Vdspo), disembodied (Vddib) and shade (Vdshd), were identified in varroa mites and sequenced. Phylogenetic analyses of predicted amino acid sequences for Halloween orthologues showed that the acarine orthologues were distantly associated with insect and crustacean clades indicating that acarine genes had more ancestral characters. The lack of orthologues or pseudogenes for remaining genes suggests these pathway elements had not evolved in ancestral arthropods. Vdspo transcript levels were highest in gut tissues, while Vddib transcript levels were highest in ovary-lyrate organs. In contrast, Vdshd transcript levels were lower overall but present in both gut and ovary-lyrate organs. All three transcripts were present in eggs removed from gravid female mites. A brood cell invasion assay was developed for acquiring synchronously staged mites. Mites within 4 h of entering a brood cell had transcript levels of all three that were not significantly different from mites on adult bees. These analyses suggest that varroa mites may be capable of modifying 7-dehydro-cholesterol precursor and hydroxylations of other steroid precursors, but whether the mites directly produce ecdysteroid precursors and products remains undetermined.

The complete mitochondrial genome of the geophilomorph centipede Strigamia maritima

Strigamia maritima (Myriapoda; Chilopoda) is a species from the soil-living order of geophilomorph centipedes. The Geophilomorpha is the most speciose order of centipedes with over a 1000 species described. They are notable for their large number of appendage bearing segments and are being used as a laboratory model to study the embryological process of segmentation within the myriapods. Using a scaffold derived from the recently published genome of Strigamia maritima that contained multiple mitochondrial protein-coding genes, here we report the complete mitochondrial genome of Strigamia, the first from any geophilomorph centipede. The mitochondrial genome of S. maritima is a circular molecule of 14,938 base pairs, within which we could identify the typical mitochondrial genome complement of 13 protein-coding genes and 2 ribosomal RNA genes. Sequences resembling 16 of the 22 transfer RNA genes typical of metazoan mitochondrial genomes could be identified, many of which have clear deviations from the standard ‘cloverleaf’ secondary structures of tRNA. Phylogenetic trees derived from the concatenated alignment of protein-coding genes of S. maritima and >50 other metazoans were unable to resolve the Myriapoda as monophyletic, but did support a monophyletic group of chilopods: Strigamia was resolved as the sister group of the scolopendromorph Scolopocryptos sp. and these two (Geophilomorpha and Scolopendromorpha), along with the Lithobiomorpha, formed a monophyletic group the Pleurostigmomorpha. Gene order within the S. maritima mitochondrial genome is unique compared to any other arthropod or metazoan mitochondrial genome to which it has been compared. The highly unusual organisation of the mitochondrial genome of Strigamia maritima is in striking contrast with the conservatively evolving nuclear genome: sampling of more members of this order of centipedes will be required to see whether this unusual organization is typical of the Geophilomorpha or results from a more recent reorganisation in the lineage leading to Strigamia.

Fossil Crustaceans as Parasites and Hosts

Numerous crustacean lineages have independently moved into parasitism as a mode of life. In modern marine ecosystems, parasitic crustaceans use representatives from many metazoan phyla as hosts. Crustaceans also serve as hosts to a rich diversity of parasites, including other crustaceans. Here, we show that the fossil record of such parasitic interactions is sparse, with only 11 examples, one dating back to the Cambrian. This may be due to the limited preservation potential and small size of parasites, as well as to problems with ascribing traces to parasitism with certainty, and to a lack of targeted research. Although the confirmed stratigraphic ranges are limited for nearly every example, evidence of parasitism related to crustaceans has become increasingly more complete for isopod-induced swellings in decapods so that quantitative analyses can be carried out. Little attention has yet been paid to the origin of parasitism in deep time, but insight can be generated by integrating data on fossils with molecular studies on modern parasites. In addition, there are other traces left by parasites that could fossilize, but have not yet been recognized in the fossil record.

Making sense of 'lower' and 'upper' stem-group Euarthropoda, with comments on the strict use of the name Arthropoda von Siebold, 1848

The ever-increasing number of studies that address the origin and evolution of Euarthropoda - whose extant representatives include chelicerates, myriapods, crustaceans and hexapods - are gradually reaching a consensus with regard to the overall phylogenetic relationships of some of the earliest representatives of this phylum. The stem-lineage of Euarthropoda includes numerous forms that reflect the major morphological transition from a lobopodian-type to a completely arthrodized body organization. Several methods of classification that aim to reflect such a complex evolutionary history have been proposed as a consequence of this taxonomic diversity. Unfortunately, this has also led to a saturation of nomenclatural schemes, often in conflict with each other, some of which are incompatible with cladistic-based methodologies. Here, I review the convoluted terminology associated with the classification of stem-group Euarthropoda, and propose a synapomorphy-based distinction that allows 'lower stem-Euarthropoda' (e.g. lobopodians, radiodontans) to be separated from 'upper stem-Euarthropoda' (e.g. fuxianhuiids, Cambrian bivalved forms) in terms of the structural organization of the head region and other aspects of overall body architecture. The step-wise acquisition of morphological features associated with the origins of the crown-group indicate that the node defining upper stem-Euarthropoda is phylogenetically stable, and supported by numerous synapomorphic characters; these include the presence of a deutocerebral first appendage pair, multisegmented head region with one or more pairs of post-ocular differentiated limbs, complete body arthrodization, posterior-facing mouth associated with the hypostome/labrum complex, and post-oral biramous arthropodized appendages. The name 'Deuteropoda' nov. is proposed for the scion (monophyletic group including the crown-group and an extension of the stem-group) that comprises upper stem-Euarthropoda and Euarthropoda. A brief account of common terminological inaccuracies in recent palaeontological studies evinces the utility of Deuteropoda nov. as a reference point for discussing aspects of early euarthropod phylogeny.

The structure and function of thioester-containing proteins in arthropods

Thioester-containing proteins (TEPs) form an ancient and diverse family of secreted proteins that play central roles in the innate immune response. Two families of TEPs, complement factors and α₂-macroglobulins, have been known and studied in vertebrates for many years, but only in the last decade have crystal structures become available. In the same period, the presence of two additional classes of TEPs has been revealed in arthropods. In this review, we discuss the common structural features TEPs and how this knowledge can be applied to the many arthropod TEPs of unknown function. TEPs perform a wide variety of functions that are driven by different quaternary structures and protein-protein interactions between a common set of folded domains. A common theme is regulated conformational change triggered by proteolysis. Structure-function analysis of the diverse arthropod TEPs may identify not just new mechanisms in innate immunity but also interfaces between immunity, development and cell death.

The ovary structure and oogenesis in the basal crustaceans and hexapods. Possible phylogenetic significance

Recent large-scale phylogenetic analyses of exclusively molecular or combined molecular and morphological characters support a close relationship between Crustacea and Hexapoda. The growing consensus on this phylogenetic link is reflected in uniting both taxa under the name Pancrustacea or Tetraconata. Several recent molecular phylogenies have also indicated that the monophyletic hexapods should be nested within paraphyletic crustaceans. However, it is still contentious exactly which crustacean taxon is the sister group to Hexapoda. Among the favored candidates are Branchiopoda, Malacostraca, Remipedia and Xenocarida (Remipedia + Cephalocarida). In this context, we review morphological and ultrastructural features of the ovary architecture and oogenesis in these crustacean groups in search of traits potentially suitable for phylogenetic considerations. We have identified a suite of morphological characters which may prove useful in further comparative studies.

Arthropod fossil data increase congruence of morphological and molecular phylogenies

The relationships of major arthropod clades have long been contentious, but refinements in molecular phylogenetics underpin an emerging consensus. Nevertheless, molecular phylogenies have recovered topologies that morphological phylogenies have not, including the placement of hexapods within a paraphyletic Crustacea, and an alliance between myriapods and chelicerates. Here we show enhanced congruence between molecular and morphological phylogenies based on 753 morphological characters for 309 fossil and Recent panarthropods. We resolve hexapods within Crustacea, with remipedes as their closest extant relatives, and show that the traditionally close relationship between myriapods and hexapods is an artefact of convergent character acquisition during terrestrialisation. The inclusion of fossil morphology mitigates long-branch artefacts as exemplified by pycnogonids: when fossils are included, they resolve with euchelicerates rather than as a sister taxon to all other euarthropods.

Molecular phylogeny of Myriapoda provides insights into evolutionary patterns of the mode in post-embryonic development

Myriapoda, a subphylum of Arthropoda, comprises four classes, Chilopoda, Diplopoda, Pauropoda, and Symphyla. While recent molecular evidence has shown that Myriapoda is monophyletic, the internal phylogeny, which is pivotal for understanding the evolutionary history of myriapods, remains unresolved. Here we report the results of phylogenetic analyses and estimations of divergence time and ancestral state of myriapods. Phylogenetic analyses were performed based on three nuclear protein-coding genes determined from 19 myriapods representing the four classes (17 orders) and 11 outgroup species. The results revealed that Symphyla whose phylogenetic position has long been debated is the sister lineage to all other myriapods, and that the interordinal relationships within classes were consistent with traditional classifications. Ancestral state estimation based on the tree topology suggests that myriapods evolved from an ancestral state that was characterized by a hemianamorphic mode of post-embryonic development and had a relatively low number of body segments and legs.

Ultrastructure, functional morphology and evolution of recto-canal epidermal glands in Myriapoda

In Chilopoda, solitary epidermal glands are composed of a couple of cells only. These glands are highly abundant on the entire body surface and are distributed throughout the single-layered epidermis. Some authors provided more or less comprehensive observations on the structure of epidermal glands of specific chilopod taxa. However, no information is hitherto available on the ultrastructural diversity of these glands. Furthermore, potential homologies of these chilopod epidermal glands and of their characteristic cellular components remain unknown. Based on our results, we are now able to distinguish two types of epidermal glands in Chilopoda that can be clearly distinguished by their structure and the course of their conducting canal: recto-canal epidermal glands (rceg) and flexo-canal epidermal glands (fceg). In the present paper, we focus on the rceg. We examined the ultrastructural organization of these glands in the head region and on the anterior trunk segments of various representatives of the five extant chilopod orders by light- and electron-microscopy. According to our terminology, rceg consist of up to five different cell types including: a) distal canal cells, b) proximal canal cells, c) intermediary cells, and d) two different types of secretory cells. Intermediary and canal cells form a common conducting canal. The rceg may taxon-specifically differ in relative size and subcellular architecture, but all have the following features in common: 1) a wide distribution on various body regions among all five chilopod subtaxa, 2) the straight, broad and locally dilated conducting canal surrounded by closely packed microvilli or microvilliform infoldings around the apex of the canal cell(s), and 3) the tendency to aggregate to form compound glandular organs of massive size and complexity. Tricellular glandular units established by three different cell types are observed in Scutigeromorpha and Geophilomorpha, whereas four cell types constitute rceg in Lithobiomorpha and Craterostigmomorpha. Five different cell types per glandular unit are found only in Scolopendromorpha. The partial cuticularization of the lower part of the conducting canal formed by the intermediary cell, as found in Chilopoda, differs from the pattern described for equivalent euarthropod epidermal glands, as for instance in Hexapoda. Their wide distribution in Chilopoda and Progoneata makes it likely that tricellular rceg were at least present in the last common ancestor of the Myriapoda. Concerning Chilopoda, the evolution of highly diverse rceg is well explained on the basis of the Pleurostigmophora concept. Glands of the recto-canal type are also found in other arthropods. The paper discusses cases where homology of rceg and also fceg may be assumed beyond Myriapoda and briefly evaluates the potentials and the still-to-be-solved issues prior to use them as an additional character system to reconstruct the phylogeny of the Euarthropoda.

Comparative analysis of mitochondrial genomes in Diplura (hexapoda, arthropoda): taxon sampling is crucial for phylogenetic inferences

Two-pronged bristletails (Diplura) are traditionally classified into three major superfamilies: Campodeoidea, Projapygoidea, and Japygoidea. The interrelationships of these three superfamilies and the monophyly of Diplura have been much debated. Few previous studies included Projapygoidea in their phylogenetic considerations, and its position within Diplura still is a puzzle from both morphological and molecular points of view. Until now, no mitochondrial genome has been sequenced for any projapygoid species. To fill in this gap, we determined and annotated the complete mitochondrial genome of Octostigma sinensis (Octostigmatidae, Projapygoidea), and of three more dipluran species, one each from the Campodeidae, Parajapygidae, and Japygidae. All four newly sequenced dipluran mtDNAs encode the same set of genes in the same gene order as shared by most crustaceans and hexapods. Secondary structure truncations have occurred in trnR, trnC, trnS1, and trnS2, and the reduction of transfer RNA D-arms was found to be taxonomically correlated, with Campodeoidea having experienced the most reduction. Partitioned phylogenetic analyses, based on both amino acids and nucleotides of the protein-coding genes plus the ribosomal RNA genes, retrieve significant support for a monophyletic Diplura within Pancrustacea, with Projapygoidea more closely related to Campodeoidea than to Japygoidea. Another key finding is that monophyly of Diplura cannot be recovered unless Projapygoidea is included in the phylogenetic analyses; this explains the dipluran polyphyly found by past mitogenomic studies. Including Projapygoidea increased the sampling density within Diplura and probably helped by breaking up a long-branch-attraction artifact. This finding provides an example of how proper sampling is significant for phylogenetic inference.

When integration fails: Prokaryote phylogeny and the tree of life

Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today's literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history (often called 'universal phylogeny'). Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a 'meta-heuristic' in the normative commitments guiding scientific practice.

An analysis of segmentation dynamics throughout embryogenesis in the centipede Strigamia maritima

BACKGROUND

Most segmented animals add segments sequentially as the animal grows. In vertebrates, segment patterning depends on oscillations of gene expression coordinated as travelling waves in the posterior, unsegmented mesoderm. Recently, waves of segmentation gene expression have been clearly documented in insects. However, it remains unclear whether cyclic gene activity is widespread across arthropods, and possibly ancestral among segmented animals. Previous studies have suggested that a segmentation oscillator may exist in Strigamia, an arthropod only distantly related to insects, but further evidence is needed to document this.

RESULTS

Using the genes even skipped and Delta as representative of genes involved in segment patterning in insects and in vertebrates, respectively, we have carried out a detailed analysis of the spatio-temporal dynamics of gene expression throughout the process of segment patterning in Strigamia. We show that a segmentation clock is involved in segment formation: most segments are generated by cycles of dynamic gene activity that generate a pattern of double segment periodicity, which is only later resolved to the definitive single segment pattern. However, not all segments are generated by this process. The most posterior segments are added individually from a localized sub-terminal area of the embryo, without prior pair-rule patterning.

CONCLUSIONS

Our data suggest that dynamic patterning of gene expression may be widespread among the arthropods, but that a single network of segmentation genes can generate either oscillatory behavior at pair-rule periodicity or direct single segment patterning, at different stages of embryogenesis.