A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata

CAT-Posterior Mean Site Frequencies Improves Phylogenetic Modeling Under Maximum Likelihood and Resolves Tardigrada as the Sister of Arthropoda Plus Onychophora

Tardigrada, the water bears, are microscopic animals with walking appendages that are members of Ecdysozoa, the clade of molting animals that also includes Nematoda (round worms), Nematomorpha (horsehair worms), Priapulida (penis worms), Kinorhyncha (mud dragons), Loricifera (loricated animals), Arthropoda (insects, spiders, centipedes, crustaceans, and their allies), and Onychophora (velvet worms). The phylogenetic relationships within Ecdysozoa are still unclear, with analyses of molecular and morphological data yielding incongruent results. Accounting for across-site compositional heterogeneity using mixture models that partition sites in frequency categories, CATegories (CAT)-based models, has been shown to improve fit in Bayesian analyses. However, CAT-based models such as CAT-Poisson or CAT-GTR (where CAT is combined with a General Time Reversible matrix to account for replacement rate heterogeneity) have proven difficult to implement in maximum likelihood. Here, we use CAT-posterior mean site frequencies (CAT-PMSF), a new method to export dataset-specific mixture models (CAT-Poisson and CAT-GTR) parameterized using Bayesian methods to maximum likelihood software. We developed new maximum likelihood-based model adequacy tests using parametric bootstrap and show that CAT-PMSF describes across-site compositional heterogeneity better than other across-site compositionally heterogeneous models currently implemented in maximum likelihood software. CAT-PMSF suggests that tardigrades are members of Panarthropoda, a lineage also including Arthropoda and Onychophora. Within Panarthropoda, our results favor Tardigrada as sister to Onychophora plus Arthropoda (the Lobopodia hypothesis). Our results illustrate the power of CAT-PMSF to model across-site compositionally heterogeneous datasets in the maximum likelihood framework and clarify the relationships between the Tardigrada and the Ecdysozoa.

Arthropod Phylotranscriptomics With a Special Focus on the Basal Phylogeny of the Myriapoda

Arthropoda represents the most diverse animal phylum, but clarifying the phylogenetic relationships among arthropod taxa remains challenging given the numerous arthropod lineages that diverged over a short period of time. In order to resolve the most controversial aspects of deep arthropod phylogeny, focusing on the Myriapoda, we conducted phylogenetic analyses based on ten super-matrices comprised of 751 to 1,233 orthologous genes across 64 representative arthropod species, including 28 transcriptomes that were newly generated in this study. Our findings provide unambiguous support for the monophyly of the higher arthropod taxa, Chelicerata, Mandibulata, Myriapoda, Pancrustacea, and Hexapoda, while the Crustacea are paraphyletic, with the class Remipedia supported as the lineage most closely related to hexapods. Within the Hexapoda, our results largely affirm previously proposed phylogenetic relationships among deep hexapod lineages, except that the Paraneoptera (Hemiptera, Thysanoptera, and Psocodea) was recovered as a monophyletic lineage in some analyses. The results corroborated the recently proposed phylogenetic framework of the four myriapod classes, wherein Symphyla and Pauropoda, as well as Chilopoda and Diplopoda, are each proposed to be sister taxa. The findings provide important insights into understanding the phylogeny and evolution of arthropods.

An updated world checklist of velvet worms (Onychophora) with notes on nomenclature and status of names

More than a decade has passed since the publication of the only world checklist available for Onychophora. During this period, numerous nomenclatural acts and taxonomic changes have been suggested within the group and a wealth of novel data has been published on many taxa. Herein, the up-to-date taxonomic scenario within Onychophora is presented, with appraisal of name status. This checklist covers both extant (Peripatidae and Peripatopsidae) and fossil taxa, and each species is accompanied by information on synonyms, type designation, holotype location, type locality, and language of original description. Additional remarks include nomenclatural inconsistencies, synonymizations, name misspellings, conflicting collecting event data, availability of taxonomically informative molecular data, etc. According to the data, 237 species are currently assigned to Onychophora: 140 of Peripatopsidae, 92 of Peripatidae, and five fossil species with unclear relationship to extant taxa. Since the previous checklist, 37 species have been added to Onychophora, representing an increase of 18.5% in the diversity described for the group. Yet, taxonomic descriptions seem slow-paced, with an average of 3.6 onychophoran species being described annually. From the taxonomic standpoint, 216 species are valid, although many of them require morphological revision and molecular characterization; 21 species exhibit major taxonomic ambiguities and have been regarded as nomina dubia. Recurrent taxonomic issues identified in the literature include inaccurate collecting event data, doubtful taxonomic assignment of molecular sequences, and non-observance of nomenclatural rules. These and other taxonomic aspects are addressed herein in the light of the directives established by the International Code of Zoological Nomenclature.

Musculature of an Early Cambrian cycloneuralian animal

Cycloneuralians are ecdysozoans with a fossil record extending to the Early Cambrian Fortunian Age and represented mostly by cuticular integuments. However, internal anatomies of Fortunian cycloneuralians are virtually unknown, hampering our understanding of their functional morphology and phylogenetic relationships. Here we report the exceptional preservation of cycloneuralian introvert musculature in Fortunian rocks of South China. The musculature consists of an introvert body-wall muscular grid of four circular and 36 radially arranged longitudinal muscle bundles, as well as an introvert circular muscle associated with 19 roughly radially arranged, short retractors. Collectively, these features support at least a scalidophoran affinity, and the absence of muscles associated with a mouth cone and scalids further indicates a priapulan affinity. As in modern scalidophorans, the fossil musculature, and particularly the introvert circular muscle retractors, may have controlled introvert inversion and facilitated locomotion and feeding. This work supports the evolution of scalidophoran-like or priapulan-like introvert musculature in cycloneuralians at the beginning of the Cambrian Period.

Repellent efficacy of 20 essential oils on Aedes aegypti mosquitoes and Ixodes scapularis ticks in contact-repellency assays

Cases of mosquito- and tick-borne diseases are rising worldwide. Repellent products can protect individual users from being infected by such diseases. In a previous study, we identified five essential oils that display long-distance mosquito repellency using a Y-tube olfactometer assay. In the current study, the contact repellent efficacy of 20 active ingredients from the Environmental Protection Agency's (EPA) Minimum Risk Pesticides list were tested using Aedes aegypti and Ixodes scapularis. We utilized an arm-in-cage assay to measure complete protection time from mosquito bites for these active ingredients. To measure tick repellency, we used an EPA-recommended procedure to measure the complete protection time from tick crossings. We found that of the 20 ingredients tested, 10% v/v lotion emulsions with clove oil or cinnamon oil provided the longest protection from both mosquito bites and tick crossings. We conclude that in a 10% v/v emulsion, specific active ingredients from the EPA Minimum Risk Pesticides list can provide complete protection from mosquito bites and tick crossings for longer than one hour.

Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny

An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although datasets of several hundred thousand amino acids are nowadays routinely used to test phylogenetic hypotheses, key deep nodes in the metazoan tree remain unresolved: the root of animals, the root of Bilateria, and the monophyly of Deuterostomia. Instead of using the standard approach of amino acid datasets, we performed analyses of newly assembled genome gene content and morphological datasets to investigate these recalcitrant nodes in the phylogeny of animals. We explored extensively the choices for assembling the genome gene content dataset and model choices of morphological analyses. Our results are robust to these choices and provide additional insights into the early evolution of animals, they are consistent with sponges as the sister group of all the other animals, the worm-like bilaterian lineage Xenacoelomorpha as the sister group of the other Bilateria, and tentatively support monophyletic Deuterostomia.

Re-evaluating and dating myriapod diversification with phylotranscriptomics under a regime of dense taxon sampling

Recent transcriptomic studies of myriapod phylogeny have been based on relatively small datasets with <40 myriapod terminals and variably supported or contradicted the traditional morphological groupings of Progoneata and Dignatha. Here we amassed a large dataset of 104 myriapod terminals, including multiple species for each of the four myriapod classes. Across the tree, most nodes are stable and well supported. Most analyses across a range of gene occupancy levels provide moderate to strong support for a deep split of Myriapoda into Symphyla + Pauropoda (=Edafopoda) and an uncontradicted grouping of Chilopoda + Diplopoda (=Pectinopoda nov.), as in other recent transcriptome-based analyses; no analysis recovers Progoneata or Dignatha as clades. As in all recent multi-locus and phylogenomic studies, chilopod interrelationships resolve with Craterostigmus excluded from Amalpighiata rather than uniting with other centipedes with maternal brood care in Phylactometria. Diplopod ordinal interrelationships are largely congruent with morphology-based classifications. Chilognathan clades that are not invariably advocated by morphologists include Glomerida + Glomeridesmida, such that the volvation-related characters of pill millipedes may be convergent, and Stemmiulida + Polydesmida more closely allied to Juliformia than to Callipodida + Chordeumatida. The latter relationship implies homoplasy in spinnerets and contradicts Nematophora. A time-tree with nodes calibrated by 25 myriapod and six outgroup fossil terminals recovers Cambrian-Ordovician divergences for the deepest splits in Myriapoda, Edafopoda and Pectinopoda, predating the terrestrial fossil record of myriapods as in other published chronograms, whereas age estimates within Chilopoda and Diplopoda overlap with or do not appreciably predate the calibration fossils. The grouping of Chilopoda and Diplopoda is recovered in all our analyses and is formalized as Pectinopoda nov., named for the shared presence of mandibular comb lamellae. New taxonomic proposals for Chilopoda based on uncontradicted clades are Tykhepoda nov. for the three blind families of Scolopendromorpha that share a "sieve-type" gizzard, and Taktikospina nov. for Scolopendromorpha to the exclusion of Mimopidae.

The unbearable uncertainty of panarthropod relationships

Panarthropoda, the clade comprising the phyla Onychophora, Tardigrada and Euarthropoda, encompasses the largest majority of animal biodiversity. The relationships among the phyla are contested and resolution is key to understanding the evolutionary assembly of panarthropod bodyplans. Molecular phylogenetic analyses generally support monophyly of Onychophora and Euarthropoda to the exclusion of Tardigrada (Lobopodia hypothesis), which is also supported by some analyses of morphological data. However, analyses of morphological data have also been interpreted to support monophyly of Tardigrada and Euarthropoda to the exclusion of Onychophora (Tactopoda hypothesis). Support has also been found for a clade of Onychophora and Tardigrada that excludes Euarthropoda (Protarthropoda hypothesis). Here we show, using a diversity of phylogenetic inference methods, that morphological datasets cannot discriminate statistically between the Lobopodia, Tactopoda and Protarthropoda hypotheses. Since the relationships among the living clades of panarthropod phyla cannot be discriminated based on morphological data, we call into question the accuracy of morphology-based phylogenies of Panarthropoda that include fossil species and the evolutionary hypotheses based upon them.

The phylogeny of Syntrichia: An ecologically diverse clade of mosses with an origin in South America

PREMISE

To address the biodiversity crisis, we need to understand the evolution of all organisms and how they fill geographic and ecological space. Syntrichia is one of the most diverse and dominant genera of mosses, ranging from alpine habitats to desert biocrusts, yet its evolutionary history remains unclear.

METHODS

We present a comprehensive phylogenetic analysis of Syntrichia, based on both molecular and morphological data, with most of the named species and closest outgroups represented. In addition, we provide ancestral-state reconstructions of water-related traits and a global biogeographic analysis.

RESULTS

We found 10 major well-resolved subclades of Syntrichia that possess geographical or morphological coherence, in some cases representing previously accepted genera. We infer that the extant species diversity of Syntrichia likely originated in South America in the early Eocene (56.5-43.8 million years ago [Mya]), subsequently expanded its distribution to the neotropics, and finally dispersed to the northern hemisphere. There, the clade experienced a recent diversification (15-12 Mya) into a broad set of ecological niches (e.g., the S. caninervis and S. ruralis complexes). The transition from terricolous to either saxicolous or epiphytic habitats occurred more than once and was associated with changes in water-related traits.

CONCLUSIONS

Our study provides a framework for understanding the evolutionary history of Syntrichia through the combination of morphological and molecular characters, revealing that migration events that shaped the current distribution of the clade have implications for morphological character evolution in relation to niche diversity.

Resolving tricky nodes in the tree of life through amino acid recoding

Genomic data allowed a detailed resolution of the Tree of Life, but "tricky nodes" such as the root of the animals remain unresolved. Genome-scale datasets are heterogeneous as genes and species are exposed to different pressures, and this can negatively impacts phylogenetic accuracy. We use simulated genomic-scale datasets and show that recoding amino acid data improves accuracy when the model does not account for the compositional heterogeneity of the amino acid alignment. We apply our findings to three datasets addressing the root of the animal tree, where the debate centers on whether sponges (Porifera) or comb jellies (Ctenophora) represent the sister of all other animals. We show that results from empirical data follow predictions from simulations and suggest that, at the least in phylogenies inferred from amino acid sequences, a placement of the ctenophores as sister to all the other animals is best explained as a tree reconstruction artifact.

Cutting the long branches: Consilience as a path to unearth the evolutionary history of Gnetales

The Gnetales are one of the most fascinating groups within seed plants. Although the advent of molecular phylogenetics has generated some confidence in their phylogenetic placement of Gnetales within seed plants, their macroevolutionary history still presents many unknowns. Here, we review the reasons for such unknowns, and we focus the discussion on the presence of “long branches” both in their molecular and morphological history. The increased rate of molecular evolution and genome instability as well as the numerous unique traits (both reproductive and vegetative) in the Gnetales have been obstacles to a better understanding of their evolution. Moreover, the fossil record of the Gnetales, though relatively rich, has not yet been properly reviewed and investigated using a phylogenetic framework. Despite these apparent blocks to progress we identify new avenues to enable us to move forward. We suggest that a consilience approach, involving different disciplines such as developmental genetics, paleobotany, molecular phylogenetics, and traditional anatomy and morphology might help to “break” these long branches, leading to a deeper understanding of this mysterious group of plants.

The problematic Cambrian arthropod Tuzoia and the origin of mandibulates revisited

The origin of mandibulates, the hyperdiverse arthropod group that includes pancrustaceans and myriapods, dates back to the Cambrian. Bivalved arthropod groups such as hymenocarines have been argued to be early mandibulates, but many species are still poorly known, and their affinities remain uncertain. One of the most common and globally distributed Cambrian bivalved arthropods is Tuzoia. Originally described in 1912 from the Burgess Shale based on isolated carapaces, its full anatomy has remained largely unknown. Here, we describe new specimens of Tuzoia from the Canadian Burgess Shale (Wuliuan, Cambrian) showcasing exceptionally preserved soft tissues, allowing for the first comprehensive reconstruction of its anatomy, ecology and evolutionary affinities. The head bears antennae and differentiated cephalic appendages. The body is divided into a cephalothorax, a homonomous trunk bearing ca 10 pairs of legs with heptopodomerous endopods and enlarged basipods, and a tail fan with two pairs of caudal rami. These traits suggest that Tuzoia swam along the seafloor and used its spinose legs for predation or scavenging. Tuzoia is retrieved by a Bayesian phylogenetic analysis as an early mandibulate hymenocarine lineage, exemplifying the rapid diversification of this group in open marine environments during the Cambrian Explosion.

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.

A Practical Guide to Design and Assess a Phylogenomic Study

Over the last decade, molecular systematics has undergone a change of paradigm as high-throughput sequencing now makes it possible to reconstruct evolutionary relationships using genome-scale datasets. The advent of "big data" molecular phylogenetics provided a battery of new tools for biologists but simultaneously brought new methodological challenges. The increase in analytical complexity comes at the price of highly specific training in computational biology and molecular phylogenetics, resulting very often in a polarized accumulation of knowledge (technical on one side and biological on the other). Interpreting the robustness of genome-scale phylogenetic studies is not straightforward, particularly as new methodological developments have consistently shown that the general belief of "more genes, more robustness" often does not apply, and because there is a range of systematic errors that plague phylogenomic investigations. This is particularly problematic because phylogenomic studies are highly heterogeneous in their methodology, and best practices are often not clearly defined. The main aim of this article is to present what I consider as the ten most important points to take into consideration when planning a well-thought-out phylogenomic study and while evaluating the quality of published papers. The goal is to provide a practical step-by-step guide that can be easily followed by nonexperts and phylogenomic novices in order to assess the technical robustness of phylogenomic studies or improve the experimental design of a project.

The origin and early evolution of arthropods

The rise of arthropods is a decisive event in the history of life. Likely the first animals to have established themselves on land and in the air, arthropods have pervaded nearly all ecosystems and have become pillars of the planet's ecological networks. Forerunners of this saga, exceptionally well-preserved Palaeozoic fossils recently discovered or re-discovered using new approaches and techniques have elucidated the precocious appearance of extant lineages at the onset of the Cambrian explosion, and pointed to the critical role of the plankton and hard integuments in early arthropod diversification. The notion put forward at the beginning of the century that the acquisition of extant arthropod characters was stepwise and represented by the majority of Cambrian fossil taxa is being rewritten. Although some key traits leading to Euarthropoda are indeed well documented along a diversified phylogenetic stem, this stem led to several speciose and ecologically diverse radiations leaving descendants late into the Palaeozoic, and a large part, if not all of the Cambrian euarthropods can now be placed on either of the two extant lineages: Mandibulata and Chelicerata. These new observations and discoveries have altered our view on the nature and timing of the Cambrian explosion and clarified diagnostic characters at the origin of extant arthropods, but also raised new questions, especially with respect to cephalic plasticity. There is now strong evidence that early arthropods shared a homologous frontalmost appendage, coined here the cheira, which likely evolved into antennules and chelicerae, but other aspects, such as brain and labrum evolution, are still subject to active debate. The early evolution of panarthropods was generally driven by increased mastication and predation efficiency and sophistication, but a wealth of recent studies have also highlighted the prevalent role of suspension-feeding, for which early panarthropods developed their own adaptive feedback through both specialized appendages and the diversification of small, morphologically differentiated larvae. In a context of general integumental differentiation and hardening across Cambrian metazoans, arthrodization of body and limbs notably prompted two diverging strategies of basipod differentiation, which arguably became founding criteria in the divergence of total-groups Mandibulata and Chelicerata. The kinship of trilobites and their relatives remains a source of disagreement, but a recent topological solution, termed the 'deep split', could embed Artiopoda as sister taxa to chelicerates and constitute definitive support for Arachnomorpha. Although Cambrian fossils have been critical to all these findings, data of exceptional quality have also been accumulating from other Palaeozoic Konservat-Lagerstätten, and a better integration of this information promises a much more complete and elaborate picture of early arthropod evolution in the near future. From the broader perspective of a total-evidence approach to the understanding of life's history, and despite persisting systematic debates and new interpretative challenges, various advances based on palaeontological evidence open the prospect of finally using the full potential of the most diverse animal phylum to investigate macroevolutionary patterns and processes.

Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes

Phylogenetic relationships within many lineages of the phylum Nematoda remain unresolved, despite numerous morphology-based and molecular analyses. We performed several phylogenomic analyses using 286 published genomes and transcriptomes and 19 new transcriptomes by focusing on Trichinellida, Spirurina, Rhabditina, and Tylenchina separately, and by analyzing a selection of species from the whole phylum Nematoda. The phylogeny of Trichinellida supported the division of Trichinella into encapsulated and non-encapsulated species and placed them as sister to Trichuris. The Spirurina subtree supported the clades formed by species from Ascaridomorpha and Spiruromorpha respectively, but did not support Dracunculoidea. The analysis of Tylenchina supported a clade that included all sampled species from Tylenchomorpha and placed it as sister to clades that included sampled species from Cephalobomorpha and Panagrolaimomorpha, supporting the hypothesis that postulates the single origin of the stomatostylet. The Rhabditina subtree placed a clade composed of all sampled species from Diplogastridae as sister to a lineage consisting of paraphyletic Rhabditidae, a single representative of Heterorhabditidae and a clade composed of sampled species belonging to Strongylida. It also strongly supported all suborders within Strongylida. In the phylum-wide analysis, a clade composed of all sampled species belonging to Enoplia were consistently placed as sister to Dorylaimia + Chromadoria. The topology of the Nematoda backbone was consistent with previous studies, including polyphyletic placement of sampled representatives of Monhysterida and Araeolaimida.

The velvet worm brain unveils homologies and evolutionary novelties across panarthropods

BACKGROUND

The evolution of the brain and its major neuropils in Panarthropoda (comprising Arthropoda, Tardigrada and Onychophora) remains enigmatic. As one of the closest relatives of arthropods, onychophorans are regarded as indispensable for a broad understanding of the evolution of panarthropod organ systems, including the brain, whose anatomical and functional organisation is often used to gain insights into evolutionary relations. However, while numerous recent studies have clarified the organisation of many arthropod nervous systems, a detailed investigation of the onychophoran brain with current state-of-the-art approaches is lacking, and further inconsistencies in nomenclature and interpretation hamper its understanding. To clarify the origins and homology of cerebral structures across panarthropods, we analysed the brain architecture in the onychophoran Euperipatoides rowelli by combining X-ray micro-computed tomography, histology, immunohistochemistry, confocal microscopy, and three-dimensional reconstruction.

RESULTS

Here, we use this detailed information to generate a consistent glossary for neuroanatomical studies of Onychophora. In addition, we report novel cerebral structures, provide novel details on previously known brain areas, and characterise further structures and neuropils in order to improve the reproducibility of neuroanatomical observations. Our findings support homology of mushroom bodies and central bodies in onychophorans and arthropods. Their antennal nerve cords and olfactory lobes most likely evolved independently. In contrast to previous reports, we found no evidence for second-order visual neuropils, or a frontal ganglion in the velvet worm brain.

CONCLUSION

We imaged the velvet worm nervous system at an unprecedented level of detail and compiled a comprehensive glossary of known and previously uncharacterised neuroanatomical structures to provide an in-depth characterisation of the onychophoran brain architecture. We expect that our data will improve the reproducibility and comparability of future neuroanatomical studies.

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.

Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca)

It is still a challenge to reconstruct the deep phylogenetic relationships within spinicaudatans, and there are several different competing hypotheses regarding the interrelationships among Eocyzicidae, Cyzicidae s. s., Leptestheriidae, and Limnadiidae of the Suborder Spinicaudata. In order to explore the source of the inconsistencies, we focus on the sequence variation and the structure model of two rRNA genes based on extensive taxa sampling. The comparative sequence analysis revealed heterogeneity across species and the existence of conserved motifs in all spinicaudatan species. The level of intraspecific heterogeneity differed among species, which suggested that some species might have undergone a relaxed concerted evolution with respect to the 28S rRNA gene. The Bayesian analyses were performed on nuclear (28S rRNA, EF1α) and mitochondrial (16S rRNA, COI) genes. Further, we investigated compositional heterogeneity between lineages and assessed the potential for phylogenetic noise compared to signal in the combined data set. Reducing the non-phylogenetic signals and application of optimal rRNA model recovered a topology congruent with inference from the transcriptome data, whereby Limnadiidae was placed as a sister group to Leptestheriidae + Eocyzicidae with high support (topology I). Tests of alternative hypotheses provided implicit support for four competing topologies, and topology I was the best.

The evolution of insect biodiversity

Insects comprise over half of all described animal species. Together with the Protura (coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form the Hexapoda, a terrestrial arthropod lineage characterised by possessing six legs. Exponential growth of genome-scale data for the hexapods has substantially altered our understanding of the origin and evolution of insect biodiversity. Phylogenomics has provided a new framework for reconstructing insect evolutionary history, resolving their position among the arthropods and some long-standing internal controversies such as the placement of the termites, twisted-winged insects, lice and fleas. However, despite the greatly increased size of phylogenomic datasets, contentious relationships among key insect clades remain unresolved. Further advances in insect phylogeny cannot rely on increased depth and breadth of genome and taxon sequencing. Improved modelling of the substitution process is fundamental to countering tree-reconstruction artefacts, while gene content, modelling of duplications and deletions, and comparative morphology all provide complementary lines of evidence to test hypotheses emerging from the analysis of sequence data. Finally, the integration of molecular and morphological data is key to the incorporation of fossil species within insect phylogeny. The emerging integrated framework of insect evolution will help explain the origins of insect megadiversity in terms of the evolution of their body plan, species diversity and ecology. Future studies of insect phylogeny should build upon an experimental, hypothesis-driven approach where the robustness of hypotheses generated is tested against increasingly realistic evolutionary models as well as complementary sources of phylogenetic evidence.

Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci

Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.

Taxonomic Sampling and Rare Genomic Changes Overcome Long-Branch Attraction in the Phylogenetic Placement of Pseudoscorpions

Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with long-branch attraction artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale data sets. Pseudoscorpion placement is particularly variable across data sets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount long-branch attraction, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (new definition), as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.

Large-Scale Annotation and Evolution Analysis of MiRNA in Insects

Insects are among the most diverse and successful groups of animals and exhibit great morphological diversity and complexity. The innovation of wings and metamorphosis are some examples of the fascinating biological evolution of insects. Most microRNAs (miRNAs) contribute to canalization by conferring robustness to gene networks and thus increase the heritability of important phenotypes. Though previous studies have demonstrated how miRNAs regulate important phenotypes, little is still known about miRNA evolution in insects. Here, we used both small RNA-seq data and homology searching methods to annotate the miRNA repertoires of 152 arthropod species, including 135 insects and 17 noninsect arthropods. We identified 16,212 miRNA genes, and classified them into highly conserved (62), insect-conserved (90), and lineage-specific (354) miRNA families. The phylogenetic relationship of miRNA binary presence/absence dynamics implies that homoplastic loss of conserved miRNA families tends to occur in far-related morphologically simplified taxa, including scale insects (Coccoidea) and twisted-wing insects (Strepsiptera), leading to inconsistent phylogenetic tree reconstruction. The common ancestor of Insecta shares 62 conserved miRNA families, of which five were rapidly gained in the early winged-insects (Pterygota). We also detected extensive miRNA losses in Paraneoptera that are correlated with morphological reduction, and miRNA gains in early Endopterygota around the time holometabolous metamorphosis appeared. This was followed by abundant miRNA gains in Hymenoptera and Lepidoptera. In summary, we provide a comprehensive data set and a detailed evolutionary analysis of miRNAs in insects. These data will be important for future studies on miRNA functions associated with insect morphological innovation and trait biodiversity.

Systemic paralogy and function of retinal determination network homologs in arachnids

BACKGROUND

Arachnids are important components of cave ecosystems and display many examples of troglomorphisms, such as blindness, depigmentation, and elongate appendages. Little is known about how the eyes of arachnids are specified genetically, let alone the mechanisms for eye reduction and loss in troglomorphic arachnids. Additionally, duplication of Retinal Determination Gene Network (RDGN) homologs in spiders has convoluted functional inferences extrapolated from single-copy homologs in pancrustacean models.

RESULTS

We investigated a sister species pair of Israeli cave whip spiders, Charinus ioanniticus and C. israelensis (Arachnopulmonata, Amblypygi), of which one species has reduced eyes. We generated embryonic transcriptomes for both Amblypygi species, and discovered that several RDGN homologs exhibit duplications. We show that duplication of RDGN homologs is systemic across arachnopulmonates (arachnid orders that bear book lungs), rather than being a spider-specific phenomenon. A differential gene expression (DGE) analysis comparing the expression of RDGN genes in field-collected embryos of both species identified candidate RDGN genes involved in the formation and reduction of eyes in whip spiders. To ground bioinformatic inference of expression patterns with functional experiments, we interrogated the function of three candidate RDGN genes identified from DGE using RNAi in the spider Parasteatoda tepidariorum. We provide functional evidence that one of these paralogs, sine oculis/Six1 A (soA), is necessary for the development of all arachnid eye types.

CONCLUSIONS

Our work establishes a foundation to investigate the genetics of troglomorphic adaptations in cave arachnids, and links differential gene expression to an arthropod eye phenotype for the first time outside of Pancrustacea. Our results support the conservation of at least one RDGN component across Arthropoda and provide a framework for identifying the role of gene duplications in generating arachnid eye diversity.

Arthropod Origins: Integrating Paleontological and Molecular Evidence

Phylogenomics underpins a stable and mostly well-resolved hypothesis for the interrelationships of extant arthropods. Exceptionally preserved fossils are integrated into this framework by coding their morphological characters, as exemplified by total-evidence dating approaches that treat fossils as dated tips in analyses numerically dominated by molecular data. Cambrian fossils inform on the sequence of character acquisition in the arthropod stem group and in the stems of its main extant clades. The arthropod head problem incorporates unique appendage combinations and remains of the nervous system in fossils into a scheme mostly based on neuroanatomy and Hox expression domains for extant forms. Molecular estimates of arthropod origins in the Cryogenian or Ediacaran predate a coherent picture from the arthropod fossil record, which commences as trace fossils in the earliest Cambrian. Probabilistic morphological clock analysis of trilobites, which exemplify the earliest arthropod body fossils, supports a Cambrian origin, without the need to posit an unfossilized Ediacaran history.

Fossils from South China redefine the ancestral euarthropod body plan

BACKGROUND

Early Cambrian Lagerstätten from China have greatly enriched our perspective on the early evolution of animals, particularly arthropods. However, recent studies have shown that many of these early fossil arthropods were more derived than previously thought, casting uncertainty on the ancestral euarthropod body plan. In addition, evidence from fossilized neural tissues conflicts with external morphology, in particular regarding the homology of the frontalmost appendage.

RESULTS

Here we redescribe the multisegmented megacheirans Fortiforceps and Jianfengia and describe Sklerolibyon maomima gen. et sp. nov., which we place in Jianfengiidae, fam. nov. (in Megacheira, emended). We find that jianfengiids show high morphological diversity among megacheirans, both in trunk ornamentation and head anatomy, which encompasses from 2 to 4 post-frontal appendage pairs. These taxa are also characterized by elongate podomeres likely forming seven-segmented endopods, which were misinterpreted in their original descriptions. Plesiomorphic traits also clarify their connection with more ancestral taxa. The structure and position of the "great appendages" relative to likely sensory antero-medial protrusions, as well as the presence of optic peduncles and sclerites, point to an overall homology with the anterior head of radiodontans. This is confirmed by our Bayesian phylogeny, which places jianfengiids as the basalmost euarthropods, paraphyletic with other megacheirans, and in contiguity with isoxyids and radiodontans.

CONCLUSIONS

Sklerolibyon and other jianfengiids expand the disparity of megacheirans and suggest that the common euarthropod ancestor possessed a remarkable phenotypic variability associated with the externalized cephalon, as well as endopods that were already heptopodomerous, which differs from previous hypotheses and observations. These animals also demonstrate that the frontalmost pair of arthrodized appendage is homologous between radiodontans and megacheirans, refuting the claim that the radiodontan frontal appendages evolved into the euarthropod labrum, and questioning its protocerebral identity. This evidence based on external anatomy now constitutes a solid benchmark upon which we should address issues of homology, with the help of carefully examined palaeoneurological data.

Correction to 'A possible case of inverted lifestyle in a new bivalved arthropod from the Burgess Shale'

[This corrects the article DOI: 10.1098/rsos.191350.].

A possible case of inverted lifestyle in a new bivalved arthropod from the Burgess Shale

The origin of the arthropod carapace, an enlargement of cephalic tergites, can be traced back to the Cambrian period. However, its disparity and evolution are still not fully understood. Here, we describe a new 'bivalved' arthropod, Fibulacaris nereidis gen. et sp. nov., based on 102 specimens from the middle Cambrian (Wuliuan Stage) Burgess Shale, Marble Canyon area in British Columbia's Kootenay National Park, Canada. The laterally compressed carapace covers most of the body. It is fused dorsally and merges anteriorly into a conspicuous postero-ventrally recurved rostrum as long as the carapace and positioned between a pair of backwards-facing pedunculate eyes. The body is homonomous, with approximately 40 weakly sclerotized segments bearing biramous legs with elongate endopods, and ends in a pair of small flap-like caudal rami. Fibulacaris nereidis is interpreted as a suspension feeder possibly swimming inverted, in a potential case of convergence with some branchiopods. A Bayesian phylogenetic analysis places it within a group closely related to the extinct Hymenocarina. Fibulacaris nereidis is unique in its carapace morphology and overall widens the ecological disparity of Cambrian arthropods and suggests that the evolution of a 'bivalved' carapace and an upside-down lifestyle may have occurred early in stem-group crustaceans.

A millipede compound eye mediating low-resolution vision

Millipedes are a species-rich and ancient arthropod clade which typically bear a pair of lateral compound eyes with a small number of large facets. To understand the visual tasks that underlie the evolution of millipede eyes, their spatial resolving performance is of key importance. We here investigate the spatial resolution of the millipede Cylindroiulus punctatus using behavioural assays. Individual animals were placed in the centre of a cylindrical arena under bright downwelling light, with dark stimuli of varying angular dimensions placed on the arena wall. We used continuous isoluminant stimuli based on a difference of Gaussians signal to test for orientation to the dark target via object taxis. Headings of individual animals were tracked in relation to the stimuli to determine whether the animals oriented towards the stimulus. We implemented a multilevel logistic regression model to identify the arc width of the stimulus that animals could resolve. We then modelled the angular sensitivity needed to identify this. We also related the visual performance to the 3D anatomy of the eye. We found that C. punctatus can resolve a stimulus of 56° period (sufficient to detect a 20° dark target). Assuming a contrast threshold of 10%, this requires a receptor acceptance angle of 72° or narrower. Spatial resolving power this low would only suffice for the simplest visual tasks, such as shelter-seeking.

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.

Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida

Chelicerates are a diverse group of arthropods, represented by such forms as predatory spiders and scorpions, parasitic ticks, humic detritivores, and marine sea spiders (pycnogonids) and horseshoe crabs. Conflicting phylogenetic relationships have been proposed for chelicerates based on both morphological and molecular data, the latter usually not recovering arachnids as a clade and instead finding horseshoe crabs nested inside terrestrial Arachnida. Here, using genomic-scale datasets and analyses optimised for countering systematic error, we find strong support for monophyletic Acari (ticks and mites), which when considered as a single group represent the most biodiverse chelicerate lineage. In addition, our analysis recovers marine forms (sea spiders and horseshoe crabs) as the successive sister groups of a monophyletic lineage of terrestrial arachnids, suggesting a single colonisation of land within Chelicerata and the absence of wholly secondarily marine arachnid orders.

Characterization of the salmon louse Lepeophtheirus salmonis miRNome: Sex-biased differences related to the coding and non-coding RNA interplay

The salmon louse Lepeophtheirus salmonis is a marine ectoparasite that has a detrimental impact on salmon farms. Genomic knowledge of adult stages is critical to understand the reproductive success and lifecycle completion of this species. Here, we report a comprehensive characterization of the L. salmonis miRNome with emphasis on the sex-differences of the parasite. Small-RNA sequencing was conducted on males and females, and mRNA-sequencing was also conducted to identify miRNA-targets at these stages. Based on bioinformatics analyses, 3101 putative miRNAs were found in L. salmonis, including precursors and variants. The most abundant and over-expressed miRNAs belonged to the bantam, mir-100, mir-1, mir-263a and mir-276 families, while the most differentially expressed mRNAs corresponded to genes related to reproduction and other biological processes involved in cell-differentiation. Target analyses revealed that the most up-regulated miRNAs in males can act by inhibiting the expression of genes related to female differentiation such as vitellogenin genes. Target prediction and expression patterns suggested a pivotal role of miRNAs in the reproductive development of L. salmonis.

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.

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.

The sensory equipment of a sandokanid: An extreme case of tarsal reduction in harvestmen (Arachnida, Opiliones, Laniatores)

The study of sensory structures has the potential to provide insights into the natural history and evolution of animals. The sensory structures of arachnids are usually concentrated on the pedipalps (the tritocerebral appendages) or on the distal podomere (tarsus) of the anterior walking legs, the latter being the case for armored harvestmen (Opiliones, Laniatores). Therefore, modifications of the tarsus could have direct impacts on the sensory equipment of these animals. Using scanning electron microscopy, we investigated the sensory equipment in an extreme case of reduction in tarsal articles in the harvestman Sandokan truncatus (Sandokanidae), which bears a single tarsomere in all legs, and the potential consequences of this reduction. Additionally, we review the literature on the natural history of the family Sandokanidae. Tarsomeres of all legs are equipped with gustatory sensilla, mechanoreceptors, and a pore organ, but wall-pored olfactory sensilla are restricted to tarsi I and II. Tarsi II present a higher density of olfactory sensilla and also putative campaniform sensilla (strain detectors), which indicates a special sensory function of this pair of legs. Other podomeres are covered with shelled sensilla, a probable chemoreceptor previously unreported in Opiliones. Overall, S. truncatus has types of sensilla largely comparable to harvestmen with longer and subdivided tarsi. However, S. truncatus also exhibits extra-tarsal sensory fields of sensilla basiconica (putative thermo-/hygroreceptors) in previously undescribed sites, and the unique pore organs. Our results establish a basis for further research investigating the natural history, as well as the evolutionary correlations and mechanistic causes of the tarsal reduction in this enigmatic lineage.

Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss

microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.

Waptia fieldensis Walcott, a mandibulate arthropod from the middle Cambrian Burgess Shale

Waptia fieldensis Walcott, 1912 is one of the iconic animals from the middle Cambrian Burgess Shale biota that had lacked a formal description since its discovery at the beginning of the twentieth century. This study, based on over 1800 specimens, finds that W. fieldensis shares general characteristics with pancrustaceans, as previous authors had suggested based mostly on its overall aspect. The cephalothorax is covered by a flexible, bivalved carapace and houses a pair of long multisegmented antennules, palp-bearing mandibles, maxillules, and four pairs of appendages with five-segmented endopods-the anterior three pairs with long and robust enditic basipods, the fourth pair with proximal annulations and lamellae. The post-cephalothorax has six pairs of lamellate and fully annulated appendages which appear to be extensively modified basipods rather than exopods. The front part of the body bears a pair of stalked eyes with the first ommatidia preserved in a Burgess Shale arthropod, and a median 'labral' complex flanked by lobate projections with possible affinities to hemi-ellipsoid bodies. Waptia confirms the mandibulate affinity of hymenocarines, retrieved here as part of an expanded Pancrustacea, thereby providing a novel perspective on the evolutionary history of this hyperdiverse group. We construe that Waptia was an active swimming predator of soft prey items, using its anterior appendages for food capture and manipulation, and also potentially for clinging to epibenthic substrates.

Early fossil record of Euarthropoda and the Cambrian Explosion

Euarthropoda is one of the best-preserved fossil animal groups and has been the most diverse animal phylum for over 500 million years. Fossil Konservat-Lagerstätten, such as Burgess Shale-type deposits (BSTs), show the evolution of the euarthropod stem lineage during the Cambrian from 518 million years ago (Ma). The stem lineage includes nonbiomineralized groups, such as Radiodonta (e.g., Anomalocaris) that provide insight into the step-by-step construction of euarthropod morphology, including the exoskeleton, biramous limbs, segmentation, and cephalic structures. Trilobites are crown group euarthropods that appear in the fossil record at 521 Ma, before the stem lineage fossils, implying a ghost lineage that needs to be constrained. These constraints come from the trace fossil record, which show the first evidence for total group Euarthropoda (e.g., Cruziana, Rusophycus) at around 537 Ma. A deep Precambrian root to the euarthropod evolutionary lineage is disproven by a comparison of Ediacaran and Cambrian lagerstätten. BSTs from the latest Ediacaran Period (e.g., Miaohe biota, 550 Ma) are abundantly fossiliferous with algae but completely lack animals, which are also missing from other Ediacaran windows, such as phosphate deposits (e.g., Doushantuo, 560 Ma). This constrains the appearance of the euarthropod stem lineage to no older than 550 Ma. While each of the major types of fossil evidence (BSTs, trace fossils, and biomineralized preservation) have their limitations and are incomplete in different ways, when taken together they allow a coherent picture to emerge of the origin and subsequent radiation of total group Euarthropoda during the Cambrian.

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.

Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies

The interrelationships of the four classes of Myriapoda have been an unresolved question in arthropod phylogenetics and an example of conflict between morphology and molecules. Morphology and development provide compelling support for Diplopoda (millipedes) and Pauropoda being closest relatives, and moderate support for Symphyla being more closely related to the diplopod-pauropod group than any of them are to Chilopoda (centipedes). In contrast, several molecular datasets have contradicted the Diplopoda-Pauropoda grouping (named Dignatha), often recovering a Symphyla-Pauropoda group (named Edafopoda). Here we present the first transcriptomic data including a pauropod and both families of symphylans, allowing myriapod interrelationships to be inferred from phylogenomic data from representatives of all main lineages. Phylogenomic analyses consistently recovered Dignatha with strong support. Taxon removal experiments identified outgroup choice as a critical factor affecting myriapod interrelationships. Diversification of millipedes in the Ordovician and centipedes in the Silurian closely approximates fossil evidence whereas the deeper nodes of the myriapod tree date to various depths in the Cambrian-Early Ordovician, roughly coinciding with recent estimates of terrestrialisation in other arthropod lineages, including hexapods and arachnids.

Fossils and the Evolution of the Arthropod Brain

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

Mandibulate convergence in an armoured Cambrian stem chelicerate

BACKGROUND

Chelicerata represents a vast clade of mostly predatory arthropods united by a distinctive body plan throughout the Phanerozoic. Their origins, however, with respect to both their ancestral morphological features and their related ecologies, are still poorly understood. In particular, it remains unclear whether their major diagnostic characters were acquired early on, and their anatomical organization rapidly constrained, or if they emerged from a stem lineage encompassing an array of structural variations, based on a more labile "panchelicerate" body plan.

RESULTS

In this study, we reinvestigated the problematic middle Cambrian arthropod Habelia optata Walcott from the Burgess Shale, and found that it was a close relative of Sanctacaris uncata Briggs and Collins (in Habeliida, ord. nov.), both retrieved in our Bayesian phylogeny as stem chelicerates. Habelia possesses an exoskeleton covered in numerous spines and a bipartite telson as long as the rest of the body. Segments are arranged into three tagmata. The prosoma includes a reduced appendage possibly precursor to the chelicera, raptorial endopods connected to five pairs of outstandingly large and overlapping gnathobasic basipods, antennule-like exopods seemingly dissociated from the main limb axis, and, posteriorly, a pair of appendages morphologically similar to thoracic ones. While the head configuration of habeliidans anchors a seven-segmented prosoma as the chelicerate ground pattern, the peculiar size and arrangement of gnathobases and the presence of sensory/tactile appendages also point to an early convergence with the masticatory head of mandibulates.

CONCLUSIONS

Although habeliidans illustrate the early appearance of some diagnostic chelicerate features in the evolution of euarthropods, the unique convergence of their cephalons with mandibulate anatomies suggests that these traits retained an unusual variability in these taxa. The common involvement of strong gnathal appendages across non-megacheirans Cambrian taxa also illustrates that the specialization of the head as the dedicated food-processing tagma was critical to the emergence of both lineages of extant euarthropods-Chelicerata and Mandibulata-and implies that this diversification was facilitated by the expansion of durophagous niches.

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

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