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.

Analyses of the Dmrt family in a decapod crab, Eriocheir sinensis uncover new facets on the evolution of DM domain genes.

DM domain genes are a group of transcription factors that are integral to sexual development and its evolution in metazoans. Their functions and regulatory mechanisms are not well understood in Malacostraca (crabs and crayfish) while these sex regulators have been widely identified in the past decade. In this study, the Dmrt family was investigated in the decapod crab, Eriocheir sinensis. We find that most members of the EsDmrt family begin to enrich around the juvenile 1 stage. In reproductive organs, EsDsx1, EsDsx2, EsiDMY and EsiDmrt1a highly express in the male-specific androgenic gland (AG), while EsDmrt-like, EsDsx-like, EsDmrt11E, and EsiDmrt1b show relatively high expression in testis. Also, we find the highly aberrant expression of EsiDMY and EsiDmrt1a in the chimeric AG, strongly indicating their function in AG development. Moreover, RNA interference of EsDsx1, EsiDMY, and EsiDmrt1a results in a significant decrease in transcription of the Insulin-like androgenic hormone (IAG), respectively. Our findings suggest that Dmrt genes in E. sinensis primarily function in male sexual differentiation, especially in AG development. Besides, this study identifies two unique groups of Dmrt genes in Malacostraca: Dsx and iDmrt1. In Malacostraca Dsx, we uncover a cryptic mutation in the eight zinc motif-specific residues, which were firmly believed to be invariant across the Dmrt family. This mutation sets the Malacostraca Dsx apart from all the other Dmrt genes and implies a different way of transcriptional regulation. Genes from the iDmrt1 group show phylogenetical limitation to the malacostracan species and underwent positive selection, suggesting their highly specialized gene function to this class. Based on these findings, we propose that Dsx and iDmrt1 in Malacostraca have developed unique transcriptional regulation mechanisms to facilitate AG development. We hope that this study would contribute to our understandings of sexual development in Malacostraca and provide new insights into the evolutionary history of the Dmrt family.

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.

Description of a New Hamatipeda Species, with an 18S Molecular Phylogeny (Crustacea: Tanaidacea: Typhlotanaidae).

We describe a new typhlotanaid species, Hamatipeda kohtsukai sp. nov., collected from between 167 and 488 m depth in the Sagami Sea, Japan. This is the first record of Hamatipeda from the northern hemisphere. Hamatipeda kohtsukai resembles Hamatipeda trapezoida from the Subantarctic region in having pereonites 1-3 widest anteriorly (not rectangular), but differs from it in the length ratio of antennal articles 4/5; the number of setae on the dactyli of pereopods 1-3, ischia of pereopods 4-6, and carpi of pereopods 4-6; the shape of the unguis of pereopods 4-6; and the shape of the uropodal endopod. We determined partial sequences for the cytochrome c oxidase subunit I (COI; cox1) and 18S rRNA (18S) genes in H. kohtsukai. A phylogenetic reconstruction based on the 18S sequences recovered a highly supported Typhlotanaidae clade containing H. kohtsukai and Typhlotanais mixtus, with Paranarthrura sp. (Agathotanaidae) as the sister taxon. A key to species of Hamatipeda is presented.

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 diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae).

BACKGROUND: Vision is a crucial sense for the evolutionary success of many animal groups. Here we explore the diversity of visual pigments (opsins) in the transcriptomes of amphipods (Crustacea: Amphipoda) and conclude that it is restricted to middle (MWS) and long wavelength-sensitive (LWS) opsins in the overwhelming majority of examined species. RESULTS: We evidenced (i) parallel loss of MWS opsin expression in multiple species (including two independently evolved lineages from the deep and ancient Lake Baikal) and (ii) LWS opsin amplification (up to five transcripts) in both Baikal lineages. The number of LWS opsins negatively correlated with habitat depth in Baikal amphipods. Some LWS opsins in Baikal amphipods contained MWS-like substitutions, suggesting that they might have undergone spectral tuning. CONCLUSIONS: This repeating two-step evolutionary scenario suggests common triggers, possibly the lack of light during the periods when Baikal was permanently covered with thick ice and its subsequent melting. Overall, this observation demonstrates the possibility of revealing climate history by following the evolutionary changes in protein families.

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.

Description of a second deep-water species in the alpheid shrimp genus Bannereus Bruce, 1988 (Malacostraca: Caridea).

Bannereus chani sp. nov. (Caridea: Alpheidae) is described based on a single female specimen collected off south-eastern Taiwan, at a depth of 301-356 m, being the second only species in the genus Bannereus Bruce, 1988. The ovigerous female holotype of the new species differs from the female holotype of B. anomalus Bruce 1988, the type species of the genus, by a series of important morphological characters, for instance, on the major cheliped and third pereiopod, strongly indicating that they represent two distinct species. The non-type male specimen tentatively identified as B. anomalus by Bruce (1988) may well belong to the new species, since it differs from the holotype of B. anomalus essentially by the same criteria as the female holotype of B. chani sp. nov. In addition, B. anomalus is newly recorded from the New Caledonian side of the Coral Sea.

Taxonomic remarks on the alpheid shrimp genus Triacanthoneus Anker, 2010, with description of a second eastern Pacific species (Malacostraca: Decapoda).

The recently described alpheid genus Triacanthoneus Anker, 2010 is reassessed based on new material from the Pacific and Caribbean coasts of Panama, and the southern Gulf of Mexico. Salmoneus armatus Anker, 2010 is tentatively transferred to Triacanthoneus and the latter genus is redefined. A new eastern Pacific species of Triacanthoneus is described based on a single specimen collected by scuba diving off Coiba Island on the Pacific coast of Panama. Triacanthoneus blanca sp. nov. is closely related to its only eastern Pacific congener, T. pacificus Anker, 2010, which is reported for the first time from the Las Perlas Islands in the Gulf of Panama. Morphological variation in T. toro Anker, 2010 is discussed on the basis of new topotypical material from Bocas del Toro, Panama, and a single specimen tentatively reported as T. cf. toro from Sisal, Mexico. An identification key to the seven currently known species of Triacanthoneus, with updated distributional and ecological information, as well as high-resolution colour photographs of four species are also provided.

An annotated checklist of the Niphargidae (Crustacea: Amphipoda) of Greece.

Despite Greece being a global hotspot of subterranean biodiversity, its hypogean fauna is largely neglected from both an ecological and conservational point of view. An overview of the Niphargidae occurring in Greece is presented as an annotated list of all available published records. These records have resulted in an updated species list reflecting taxonomic corrections and species distribution range in the Greek peninsula. A total of 23 species, attributed to 3 genera, is up to date known from Greece with a high rate of endemicity found particularly in Crete. The endemic species of Greece amount to 21 (91% of total species richness), with the remaining species distributing also in the Republic of North Macedonia. Currently, none of them is listed in the national, European or global IUCN Red Lists of Threatened Species. Considering the increasing habitat degradation due to anthropic pressure, groundwater harvesting and climate change we could lose rare and endemic species without even acknowledging their existence.

The Eophreatoicus Nicholls, 1926 species flock from Kakadu and Arnhem Land, with a description of a new genus of Amphisopidae (Crustacea : Isopoda : Phreatoicidea).

We present descriptions of 28 new species of Amphisopidae from Arnhem Land and Kakadu National Park of Australia's Northern Territory. We identified five additional species that are not yet fully characterized and are not provided with formal species recognition. This is the first taxonomic treatment highlighting the high species richness within the Phreatoicidea that occur in Australia and likely elsewhere. We document each species fully with scanning electron and light micrographic images, diagnoses, detailed descriptions, keys to identification and justification of each species using parsimony analysis of their morphological and genetic characters. The distributional data show that all species, except for one, have microendemic distributions, with some sibling species occurring within a few kilometers of each other. Because of the age of this group of species, they appear to have spread throughout the region of the Arnhem sandstone plateau and then back-colonized the same habitats so that as many as three morphologically and genetically distinct species may co-occur syntopically. Our research has uncovered a new genus-level taxon of the family Amphisopidae, Kakadubeh gen. nov. This new genus is unlike Eophreatoicus, not only in its general appearance, but also in having an inferred reproductive strategy different from most of the other members of the family. While Eophreatoicus species have males that are much larger than the females and practice precopula, a form of pre-insemination mate guarding, males of the new species, Kakadubeh rangemyahwurd sp. nov., are much smaller than females. In addition, males of this species have a fourth walking leg that is not specialized for holding females, suggesting that they have a reproductive strategy that does not involve precopula of the form seen in Eophreatoicus and Eremisopus Wilson Keable, 2002a. Most of our research has been undertaken in Kakadu National Park, although recent collections have been made in Arnhem Land, yielding additional distinctive species. Given the size of unexplored territory around the Arnhem Plateau and the geographic frequency of discovering new species, we predict that the diversity of this group in the Northern Territory may be many more than the ~35 species described here. At this time, these microendemic isopods appear to be unthreatened by human activities, largely owing to the environmental protection afforded by Kakadu National Park and Arnhem Land, and their cryptic habits during the dry season. Because they are dependent on small springs of permanent groundwater, future changes in hydrology owing to water use and climate change, as well as invasive introduced species, may present risks to populations and species.

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.

Shedding Light on the Antimicrobial Peptide Arsenal of Terrestrial Isopods: Focus on Armadillidins, a New Crustacean AMP Family.

In crustaceans, antimicrobial peptides (AMPs) are clustered into four major groups according to their amino acid composition and structure: (1) single-domain peptides containing cysteine residues such as anti-lipopolysaccharide-factor (ALF), (2) multi-domain or chimeric AMPs such as crustins, (3) non-conventional AMPs, and (4) linear single-domain AMPs. The majority of AMPs has been described in commercially exploited crustaceans, particularly decapods living in aquatic environments (crab, shrimp, lobster, and crayfish). Here, we aimed at establishing the AMPs repertoire of terrestrial isopods (Oniscidea), an original suborder of crustaceans adapted to life outside of the aquatic environment. Using transcriptomic data from 21 species, we identified 110 ALF and 73 crustin sequences. We also characterized the full-length sequence of armadillidins from 17 species, similar to the AMP previously described in the terrestrial isopod Armadillidium vulgare. Furthermore, we tested the antimicrobial activity of three armadillidin peptides characterized from three distantly related species. This analysis revealed similar activity spectra against pathogens, despite extensive structural variation among the tested peptides. In addition to conventional crustacean AMPs, our work highlights armadillidins as a new and independent family of AMPs specific to the Oniscidea, thus opening new perspectives concerning the study of the immune system of terrestrial isopods.

Identification of putative neuropeptidergic signaling systems in the spiny lobster, Panulirus argus.

Members of the decapod infraorder Achelata, specifically species from the genus Panulirus, have storied histories as models for investigating the basic principles governing the generation, maintenance, and modulation of rhythmic motor behavior, including modulation by locally released and circulating peptides. Despite their contributions to our understanding of peptidergic neuromodulation, little is known about the identity of the native neuropeptides and neuronal peptide receptors present in these crustaceans. Here, a Panulirus argus nervous system-specific transcriptome was used to help fill this void, providing insight into the neuropeptidome and neuronal peptide receptome of this species. A neuropeptidome consisting of 266 distinct peptides was predicted using the P. argus assembly, 128 having structures placing them into a generally recognized arthropod peptide family: agatoxin-like peptide, allatostatin A (AST-A), allatostatin B, allatostatin C, bursicon, CCHamide, crustacean cardioactive peptide, crustacean hyperglycemic hormone/molt-inhibiting hormone, diuretic hormone 31 (DH31), ecdysis-triggering hormone (ETH), FMRFamide-like peptide (FLP), glycoprotein hormone (GPH), GSEFLamide, inotocin, leucokinin, myosuppressin, natalisin, neuroparsin, neuropeptide F, orcokinin, orcomyotropin, periviscerokinin, pigment-dispersing hormone, pyrokinin, red pigment-concentrating hormone, RYamide, short neuropeptide F (sNPF), SIFamide, sulfakinin, tachykinin-related peptide (TRP), and trissin. Twenty-five putative neuronal receptors, encompassing 15 peptide groups, were also identified from the P. argus transcriptome: AST-A, bursicon, CCHamide, DH31, diuretic hormone 44, ETH, FLP, GPH, inotocin, insulin-like peptide, myosuppressin, natalisin, periviscerokinin, sNPF, and TRP. Collectively, the reported data provide a powerful resource for expanding studies of neuropeptidergic control of physiology and behavior in members of the genus Panulirus specifically, and decapods generally.

A new species of Nebalia (Crustacea, Leptostraca) from a hydrothermal field in Kagoshima Bay, Japan.

A new species of Leptostraca, Nebalia tagiri sp. nov. is described and illustrated. This species was sampled from 200 m depth at a hydrothermal field in Wakamiko Caldera of Kagoshima Bay, Japan. Nebalia tagiri sp. nov. is different from known Nebalia species as follows: rostral length 2.4 times as long as width; article 4 of antennule with 3-5 robust distal spines; antennular scale approximately twice as long as wide; article 3 of antenna with eight spines and nine spine-like setae along proximal half, two thin setae and six spine-like setae on external lateral face, six spines and four simple setae on distal margin; article 1 of second maxilla longer than article 2; article 2 of mandibular palp with two thin setae; exopod of pleopod 1 with 21 spines along lateral margin; furcal rami longer than combined length of pleonite 7 and telson; rounded denticles of pleonite 6 and 7; anal-plates 'shoulder' not distinct. Furthermore, this specimen is the first genus Nebalia found in the hydrothermal vent. The distribution and ecology of this new species is also discussed and a key to all species of Nebalia is provided.

Two Hexapleomera species from Japan, with a new species description and discussion of phylogenetic relationships within Hexapleomera (Crustacea: Tanaidacea).

We describe Hexapleomera sasuke sp. nov. and provide a supplemental redescription of Hexapleomera urashima Tanabe et al., both of which are based on specimens collected in Japan. Hexapleomera sasuke closely resembles H. urashima, sharing a uropod with four articles, maxillipedal endites with two tiny dorso-subdistal and two distal spiniform setae, a labium with the palp fused to the outer lobe, and the pereopod-1 propodus with an inner subdistal plumose seta. The new species differs from H. urashima in having the basal article of pleopod 3 with three outer plumose setae, the chelipedal carpus with three or four dorsodistal simple setae, the region between the bases of the chelipedal dactylus and fixed finger with three or four simple setae, and deeply pigmented pleopodal rami. We determined partial sequences of the cytochrome c oxidase subunit I (COI) gene (655 nt) from H. sasuke, which proved to be 15.0-15.3% divergent from H. urashima in Kimura 2-parameter (K2P) distance; also in partial sequences of 18S rRNA gene (1888 nt after alignment), 0.8% divergent (K2P distance) was detected between two species. Based on morphology and molecular data, we discuss phylogenetic relationships within Hexapleomera, and propose two morphologically distinct groups, the robusta group and the wombat group.

Structure of the stomach cuticle in adult and larvae of the spider crab Maja brachydactyla (Brachyura, Decapoda).

The stomach of decapods is a complex organ with specialized structures that are delimited by a cuticle. The morphology and ontogeny of the stomach are largely described, but few studies have focused on the morphology of its cuticle. This study examined the morphology of the stomach cuticle of cardiac sacs, gastric mill ossicles, cardio-pyloric valve and pyloric filters, and during various stages (zoea I and II, megalopa, first juvenile, and adult) of the common spider crab Maja brachydactyla using dissection, histology and transmission electron microscopy. The results show that cuticle morphology varies among structures (e.g., cardiac sacs, urocardiac ossicle, cardio-pyloric valve, pyloric filters), within a single structure (e.g., different sides of the urocardiac ossicle) and among different life stages. The cuticle during the larval stages is very thin and the different layers (epicuticle, exocuticle, and endocuticle) are infrequently distinguishable by histology. Major changes during larval development regarding cuticle morphology are observed after the molt to megalopa, including the increment in thickness in the gastric mill ossicles and cardio-pyloric valve, and the disappearance of the long thickened setae of the cardio-pyloric valve. The cuticle of all the stomach structures in the adults is thicker than in larval and juvenile stages. The cuticle varies in thickness, differential staining affinity and morphology of the cuticle layers. The structure-function relationship of the cuticle morphology is discussed.

The complete mitochondrial genome of a euphausiid species: Pseudeuphausia sinica (Euphausiacea: Euphausiidae).

We describe the mitogenome sequence of Pseudeuphausia sinica collected in the adjacent waters of the Yangtze River Estuary. The assembled mitogenome is 16,192 bp in length and consists 13 protein-coding genes, 22 transfer-RNA genes, 2 ribosomal-RNA genes, and 1 non-coding region. The most common start codon for 13 PCGs is ATG and the most common termination codon is TAA. The overall G + C content was only 28.26% in the heavy strand. The result of phylogenetic analysis showed that the relationship of P. sinica was close to the species in the same order.