Genome assemblies of two species of porcelain crab, Petrolisthes cinctipes and Petrolisthes manimaculis (Anomura: Porcellanidae)

Crabs are a large subtaxon of the Arthropoda, the most diverse and species-rich metazoan group. Several outstanding questions remain regarding crab diversification, including about the genomic capacitors of physiological and morphological adaptation, that cannot be answered with available genomic resources. Physiologically and ecologically diverse Anomuran porcelain crabs offer a valuable model for investigating these questions and hence genomic resources of these crabs would be particularly useful. Here, we present the first two genome assemblies of congeneric and sympatric Anomuran porcelain crabs, Petrolisthes cinctipes and Petrolisthes manimaculis from different microhabitats. Pacific Biosciences high-fidelity sequencing led to genome assemblies of 1.5 and 0.9 Gb, with N50s of 706.7 and 218.9 Kb, respectively. Their assembly length difference can largely be attributed to the different levels of interspersed repeats in their assemblies: The larger genome of P. cinctipes has more repeats (1.12 Gb) than the smaller genome of P. manimaculis (0.54 Gb). For obtaining high-quality annotations of 44,543 and 40,315 protein-coding genes in P. cinctipes and P. manimaculis, respectively, we used RNA-seq as part of a larger annotation pipeline. Contrarily to the large-scale differences in repeat content, divergence levels between the two species as estimated from orthologous protein-coding genes are moderate. These two high-quality genome assemblies allow future studies to examine the role of environmental regulation of gene expression in the two focal species to better understand physiological response to climate change, and provide the foundation for studies in fine-scale genome evolution and diversification of crabs.

Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling

The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80% of animal species and half of animal biomass. It has been the subject of several recent phylogenomic analyses, yet relationships within Pancrustacea show a notable lack of stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly of malacostracans. We show small changes in taxon sampling have large impacts on phylogenetic estimation. By analyzing identical orthologs between two slightly different taxon sets, we show that the differences in the resulting topologies are due primarily to the effects of taxon sampling on the phylogenetic reconstruction method. We compare trees resulting from our phylogenomic analyses with those from the literature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statistical topology tests reject the previously published trees in favor of the maximum likelihood trees produced here. Our results reject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. Notably, we find Copepoda nested within Allotriocarida with high support and recover a novel relationship between decapods, euphausiids, and syncarids that we refer to as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister to this latter clade, which we collectively name Stomatocarida, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocarida. A new Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results in the context of other pancrustacean phylogenetic hypotheses and highlight 15 key taxa to sample in future studies.

Sound detection and production mechanisms in aquatic decapod and stomatopod crustaceans

The sensory systems of crustaceans (aquatic decapods and stomatopods) have adapted to a diverse range of aquatic ecosystems. Sound production in aquatic crustaceans is more widespread than previously thought, and has been shown to play a major role in many of their life-history strategies; however, there are still many gaps in our understanding of their sound reception abilities. Crustaceans have three main sensory receptors for sound - the statocyst, superficial hair cells and chordotonal organs - which are all sensitive to the particle motion component of the sound field, rather than the pressure component. Our current understanding of these receptors is that they are sensitive to low-frequency sounds (<2000 Hz). There are a wide variety of sound-producing mechanisms employed by these animals, ranging from stridulation to implosive cavitation (see Glossary). These signals are used for a range of social behaviours, such as courtship, territorial defence and assessing 'resource guarding'. Furthermore, there are examples of sound signals that exceed their hearing range, highlighting a mismatch in our understanding of their hearing systems. This mismatch provides weight to the suggestion that another sound transmission channel - substrate-borne vibrations - might be at play, particularly because most crustaceans live on or near the seafloor. Finally, suggestions are made regarding potential future work that is needed to fill the substantial gaps in our understanding of how crustaceans hear and produce sound.

A new species of Sarsinebalia (Crustacea, Leptostraca) from Japan

A new species of Leptostraca, Sarsinebaliaagoensis sp. nov., from Ago Bay, Japan is described from specimens found at a depth of 120 m. The new species differs from other known Sarsinebalia species as follows: the compound eye has three distal lobes; the anterior margin of the first antennal segment has one distal process covered with setae; and the lateral margin of pleopod 1 exopod bears 5-6 simple, robust spines. A taxonomic key to all species of Sarsinebalia is also provided.

The lobula plate is exclusive to insects

Just one superorder of insects is known to possess a neuronal network that mediates extremely rapid reactions in flight in response to changes in optic flow. Research on the identity and functional organization of this network has over the course of almost half a century focused exclusively on the order Diptera, a member of the approximately 300-million-year-old clade Holometabola defined by its mode of development. However, it has been broadly claimed that the pivotal neuropil containing the network, the lobula plate, originated in the Cambrian before the divergence of Hexapoda and Crustacea from a mandibulate ancestor. This essay defines the traits that designate the lobula plate and argues against a homologue in Crustacea. It proposes that the origin of the lobula plate is relatively recent and may relate to the origin of flight.

Shore crabs reveal novel evolutionary attributes of the mushroom body

Neural organization of mushroom bodies is largely consistent across insects, whereas the ancestral ground pattern diverges broadly across crustacean lineages resulting in successive loss of columns and the acquisition of domed centers retaining ancestral Hebbian-like networks and aminergic connections. We demonstrate here a major departure from this evolutionary trend in Brachyura, the most recent malacostracan lineage. In the shore crab Hemigrapsus nudus, instead of occupying the rostral surface of the lateral protocerebrum, mushroom body calyces are buried deep within it with their columns extending outwards to an expansive system of gyri on the brain’s surface. The organization amongst mushroom body neurons reaches extreme elaboration throughout its constituent neuropils. The calyces, columns, and especially the gyri show DC0 immunoreactivity, an indicator of extensive circuits involved in learning and memory.

First in Situ Observations of Behavior in Deep-Sea Tanaidacean Crustaceans

We report on the behavior of a deep-sea tanaidacean, Gigantapseudes sp. (Apseudomorpha: Gigantapseudidae), recorded at the depths of 6446-6447 m by the manned submersible Shinkai 6500. From recordings of at least three individuals walking on the sea floor, we confirm that Gigantapseudes sp. is epibenthic, as previously inferred from leg shape. One individual was recorded entering a hole. All individuals in the videos kept pereopods 4 raised from the seafloor while walking, implying that those legs have a function other than for walking, such as mechano- or chemoreception, or posture control. Our in situ observations of behavior are the first for any deep-sea tanaidacean and illustrate the importance of recording high-resolution videos in the deep sea and archiving them for future use. Our identification of Gigantapseudes sp. from video footage provides the first record of this genus from Japanese waters and extends the northern limit of the known generic distribution.

Haimormus shimojiensis, a new genus and species of Pseudozeuxidae (Crustacea: Tanaidacea) from a submarine limestone cave in Northwestern Pacific

We establish a new pseudozeuxid genus Haimormus gen. nov. based on a new species Haimormus shimojiensis sp. nov. which was collected from a submarine limestone cave with the entrance at 35 m depth, in the Northwestern Pacific Ocean. H. shimojiensis differs from the other confamilial members, Pseudozeuxo belizensisSieg, 1982 and Charbeitanais spongicolaBamber & Bird, 1997, in having the pleonite 1 without the pleopod, the pereopods 2 and 3 propodus with a ventral spiniform seta, and the pereopods 4–6 propodus with one long and two short dorsodistal setae. A key to females of species of Pseudozeuxidae is presented. This is the first tanaidacean report from submarine caves around Japan.

Crustacean olfactory systems: A comparative review and a crustacean perspective on olfaction in insects

Malacostracan crustaceans display a large diversity of sizes, morphs and life styles. However, only a few representatives of decapod taxa have served as models for analyzing crustacean olfaction, such as crayfish and spiny lobsters. Crustaceans bear multiple parallel chemosensory pathways represented by different populations of unimodal chemosensory and bimodal chemo- and mechanosensory sensilla on the mouthparts, the walking limbs and primarily on their two pairs of antennae. Here, we focus on the olfactory pathway associated with the unimodal chemosensory sensilla on the first antennal pair, the aesthetascs. We explore the diverse arrangement of these sensilla across malacostracan taxa and point out evolutionary transformations which occurred in the central olfactory pathway. We discuss the evolution of chemoreceptor proteins, comparative aspects of active chemoreception and the temporal resolution of crustacean olfactory system. Viewing the evolution of crustacean brains in light of energetic constraints can help us understand their functional morphology and suggests that in various crustacean lineages, the brains were simplified convergently because of metabolic limitations. Comparing the wiring of afferents, interneurons and output neurons within the olfactory glomeruli suggests a deep homology of insect and crustacean olfactory systems. However, both taxa followed distinct lineages during the evolutionary elaboration of their olfactory systems. A comparison with insects suggests their olfactory systems ö especially that of the vinegar fly ö to be superb examples for "economy of design". Such a comparison also inspires new thoughts about olfactory coding and the functioning of malacostracan olfactory systems in general.

Tube construction by a tanaidacean crustacean using a novel mucus secretion system involving the anal opening

BACKGROUND

Animals in diverse aquatic groups construct tubes using mucus and filaments, and the acquisition of this capability has likely played an important role in the evolution and diversification of small benthic animals. Tanaidacea is a crustacean order that includes tube-constructing species, most of which belong to Tanaidoidea and Paratanaoidea, with a few in Kalliapseudidae (Apseudoidea). Two previously reported systems used in tube construction are the thoracic-gland system, with secretory glands in thoracic segments (pereonites), and the pereopodal-gland system, with glands in pereopods.

RESULTS

Parapseudidae (Apseudoidea) also includes a tube-constructing species, Parapseudes algicola (Shiino, 1952), which lacks large secretory glands in all pereonites and pereopods, but has a pair of acinar glands in the pleotelson, lateral to the gut. Each gland connects to the gut via a short duct, and thence to the exterior via the anal opening. Secretions released from these glands are used to construct tubes, and contain acidic and neutral mucopolysaccharides.

CONCLUSION

We report in P. algicola a third, novel secretory system, here termed the pleotelsonal-gland system, used for tube construction in Tanaidacea. It is similar to the secretory system in some "thalassinidean" decapods; both systems have secretory glands connecting to the gut and thence to the anal opening as the outlet; however, these gland systems likely evolved independently. Recent discoveries of novel secretory systems for tube construction in Tanaidacea suggest that information from smaller, less well-known groups will be necessary to understand how acquisitions of tube-constructing capability affected diversification in animals.

Circadian signaling in the Northern krill Meganyctiphanes norvegica: In silico prediction of the protein components of a putative clock system using a publicly accessible transcriptome

The Northern krill Meganyctiphanes norvegica is a significant component of the zooplankton community in many regions of the North Atlantic Ocean. In the areas it inhabits, M. norvegica is of great importance ecologically, as it is both a major consumer of phytoplankton/small zooplankton and is a primary food source for higher-level consumers. One behavior of significance for both feeding and predator avoidance in Meganyctiphanes is diel vertical migration (DVM), i.e., a rising from depth at dusk and a return to depth at dawn. In this and other euphausiids, an endogenous circadian pacemaker is thought, at least in part, to control DVM. Currently, there is no information concerning the identity of the genes/proteins that comprise the M. norvegica circadian system. In fact, there is little information concerning the molecular underpinnings of circadian rhythmicity in crustaceans generally. Here, a publicly accessible transcriptome was used to identify the molecular components of a putative Meganyctiphanes circadian system. A complete set of core clock proteins was deduced from the M. norvegica transcriptome (clock, cryptochrome 2, cycle, period and timeless), as was a large suite of proteins that likely function as modulators of the core clock (e.g., doubletime), or serves as inputs to it (cryptochrome 1) or outputs from it (pigment dispersing hormone). This is the first description of a "complete" (core clock through putative output pathway signals) euphausiid clock system, and as such, provides a foundation for initiating molecular investigations of circadian signaling in M. norvegica and other krill species, including how clock systems may regulate DVM and other behaviors.

Comparative genomic analysis of innate immunity reveals novel and conserved components in crustacean food crop species

BACKGROUND

Growing global demands for crustacean food crop species have driven large investments in aquaculture research worldwide. However, large-scale production is susceptible to pathogen-mediated destruction particularly in developing economies. Thus, a thorough understanding of the immune system components of food crop species is imperative for research to combat pathogens.

RESULTS

Through a comparative genomics approach utilising extant data from 55 species, we describe the innate immune system of the class Malacostraca, which includes all food crop species. We identify 7407 malacostracan genes from 39 gene families implicated in different aspects of host defence and demonstrate dynamic evolution of innate immunity components within this group. Malacostracans have achieved flexibility in recognising infectious agents through divergent evolution and expansion of pathogen recognition receptors genes. Antiviral RNAi, Toll and JAK-STAT signal transduction pathways have remained conserved within Malacostraca, although the Imd pathway appears to lack several key components. Immune effectors such as the antimicrobial peptides (AMPs) have unique evolutionary profiles, with many malacostracan AMPs not found in other arthropods. Lastly, we describe four putative novel immune gene families, potentially representing important evolutionary novelties of the malacostracan immune system.

CONCLUSION

Our analyses across the broader Malacostraca have allowed us to not only draw analogies with other arthropods but also to identify evolutionary novelties in immune modulation components and form strong hypotheses as to when key pathways have evolved or diverged. This will serve as a key resource for future immunology research in crustacean food crops.

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.

Phylogeography of Semiterrestrial Isopod, Tylos granuliferus, on East Asian Coasts

We conducted phylogenetic analyses using mitochondrial COI gene sequences of Tylos granuliferus, a semiterrestrial coastal isopod in East Asia, to clarify possible phylogeographic patterns and to assess relationships between present and past marine environments and genetic population structures. Our results strongly suggest the presence of four clades of T. granuliferus, one of which consists of three subclades. The distribution pattern of clades and subclades seems to have been affected by ocean current activities. Our results also suggest that historical changes in oceanic environments and the subsequence bifurcation of current streamlines affected the first and second divergences of T. granuliferus during the late Miocene and near the beginning of the Pliocene, respectively.

Evolution of eumalacostracan development-new insights into loss and reacquisition of larval stages revealed by heterochrony analysis

BACKGROUND

Within Malacostraca (Crustacea), direct development and development through diverse forms of larvae are found. Recent investigations suggest that larva-related developmental features have undergone heterochronic evolution in Malacostraca. In the light of current phylogenetic hypotheses, the free-swimming nauplius larva was lost in the lineage leading to Malacostraca and evolved convergently in the malacostracan groups Dendrobranchiata and Euphausiacea. Here we reconstruct the evolutionary history of eumalacostracan (Malacostraca without Phyllocarida) development with regard to early appendage morphogenesis, muscle and central nervous system development, and determine the heterochronic transformations involved in changes of ontogenetic mode.

RESULTS

Timing of 33 developmental events from the different tissues was analyzed for six eumalacostracan species (material for Euphausiacea was not available) and one outgroup, using a modified version of Parsimov-based genetic inference (PGi). Our results confirm previous suggestions that the event sequence of nauplius larva development is partly retained in embryogenesis of those species which do not develop such a larva. The ontogenetic mode involving a nauplius larva was likely replaced by direct development in the malacostracan stem lineage. Secondary evolution of the nauplius larva of Dendrobranchiata from this ancestral condition, involved only a very small number of heterochronies, despite the drastic change of life history. In the lineage leading to Peracarida, timing patterns of nauplius-related development were lost. Throughout eumalacostracan evolution, events related to epidermal and neural tissue development were clearly less affected by heterochrony than events related to muscle development.

CONCLUSIONS

Weak integration between mesodermal and ectodermal development may have allowed timing in muscle formation to be altered independently of ectodermal development. We conclude that heterochrony in muscle development played a crucial role in evolutionary loss and secondary evolution of a nauplius larva in Malacostraca.

Iberian Peninsula and Balearic Island Bathynellacea (Crustacea, Syncarida) database

This is the first published database of Bathynellacea. It includes all data of bathynellids (Crustacea, Bathynellacea) collected in the last 64 years (1949 to 2013) on the Iberian Peninsula and Balearic Island. The samples come from groundwater (caves, springs, wells and hyporrheic habitat associated rivers) from both sampling campaigns and occasional sampling conducted throughout the Iberian Peninsula and Balearic Islands. The dataset lists occurrence data of bathynellids distribution, sampling sites (with localities, county and geographic coordinates), taxonomic information (from family to species level) and sampling sources (collector and sampling dates) for all records. The descriptions of new species and species identifications have been carried out by an expert taxonomist (AIC) with 25 years experience in the bathynellids studies (see references). Many of the sampling sites are type localities of endemic species from Iberian Peninsula. The dataset includes 409 samples record corresponding to two families, 12 genera and 58 species, 42 of them formally described plus 16 taxa unpublished and 47 samples in study. All species known from the study area are included, which nearly sum up a quarter of species of Bathynellacea known in the world (250 species).