Two new species of parasitic copepods from the genera Nothobomolochus and Unicolax (Cyclopoida: Bomolochidae) from Australian waters

A 2016 collaborative survey of commercial fish parasites in Moreton Bay, Queensland, Australia led to the discovery of two new species of parasitic copepods belonging to the family Bomolochidae. Females of Nothobomolochus johndaveorum n. sp. were found attached to the gill filaments of Gerres subfasciatus and Gerres oyena. The new species most closely resembles N. leiognathicola and N. quadriceros. All 3 species possess 3 modified setae on the first antennulary segment that are approximately the same length and have a robust seta on the second antennulary segment adjacent to the 3 modified setae giving a superficial appearance of 4 modified setae on the antennule. The new species can be distinguished from these two species in its possession of longer inner setae on the first two endopodal segments of leg 4: the seta on endopodal segment 1 extends past the midline of the distal segment in the new species vs to the proximal margin of the distal segment in the other two species, and the seta on segment 2 extends well beyond the distal margin of the endopod in the new species vs just to the margin in the other two species. Females and males of Unicolax longicrus n. sp. were found in the nasal sinuses of Sillago maculata and Sillago ciliata. The new species differs from 6 of its 7 congeners in having a leg 4 exopod formula of II, I, 4 rather than II, I, 3 or II, I, 5. The new species resembles U. anonymous in this feature, but differs in its possession of a leg 5 that is relatively longer and less wide, and, whereas U. anonymous possesses inner and outer distal spines on leg 5 that are approximately the same length, those of the new species are relatively longer and asymmetrical. Unicolax longicrus n. sp. is unique among its congeners in its possession of a leg 4 with highly elongated endopodal segments 2 and 3, from which its name is derived. In addition to describing the two new species, host and locality reports for all species of Nothobomolochus and Unicolax are reviewed

First record of Caligus dussumieri Rangnekar, 1957 (Copepoda, Siphonostomatoida, Caligidae) from Malaysia, with notes on caligids found from Malaysia and on host-specificity of caligids on lutjanid fishes

In total, 13 species of Caligus have been reported from Malaysia. Amongst them, four species are reported from lutjanid fishes.Caligus dussumieri Rangnekar, 1957 is reported from Malabar snapper, Lutjanus malabaricus, purchased from a local wet market in Terengganu, Peninsular Malaysia. This is the first record of this species in Malaysia and it is only the second species assigned to the bonito-group of the genus Caligus to be reported from Malaysia. A key to species of the bonito-group is presented herein. The list of caligids infecting lutjanid fishes and the geographical distributions plus the known hosts of members of the bonito-group of Caligus are discussed

Testing data types implementations from algebraic specifications

Algebraic specifications of data types provide a natural basis for testing data types implementations. In this framework, the conformance relation is based on the satisfaction of axioms. This makes it possible to formally state the fundamental concepts of testing: exhaustive test set, testability hypotheses, oracle. Various criteria for selecting finite test sets have been proposed. They depend on the form of the axioms, and on the possibilities of observation of the implementation under test. This last point is related to the well-known oracle problem. As the main interest of algebraic specifications is data type abstraction, testing a concrete implementation raises the issue of the gap between the abstract description and the concrete representation. The observational semantics of algebraic specifications bring solutions on the basis of the so-called observable contexts. After a description of testing methods based on algebraic specifications, the chapter gives a brief presentation of some tools and case studies, and presents some applications to other formal methods involving datatypes

Unconstrained three-dimensional reaching in Rhesus monkeys

To better understand normative behavior for quantitative evaluation of motor recovery after injury, we studied arm movements by non-injured Rhesus monkeys during a food-retrieval task. While seated, monkeys reached, grasped, and retrieved food items. We recorded three-dimensional kinematics and muscle activity, and used inverse dynamics to calculate joint moments due to gravity, segmental interactions, and to the muscles and tissues of the arm. Endpoint paths showed curvature in three dimensions, suggesting that maintaining straight paths was not an important constraint. Joint moments were dominated by gravity. Generalized muscle and interaction moments were less than half of the gravitational moments. The relationships between shoulder and elbow resultant moments were linear during both reach and retrieval. Although both reach and retrieval required elbow flexor moments, an elbow extensor (triceps brachii) was active during both phases. Antagonistic muscles of both the elbow and hand were co-activated during reach and retrieval. Joint behavior could be described by lumped-parameter models analogous to torsional springs at the joints. Minor alterations to joint quasi-stiffness properties, aided by interaction moments, result in reciprocal movements that evolve under the influence of gravity. The strategies identified in monkeys to reach, grasp, and retrieve items will allow the quantification of prehension during recovery after a spinal cord injury and the effectiveness of therapeutic interventions

Computing with bacterial constituents, cells and populations: from bioputing to bactoputing

The relevance of biological materials and processes to computing—aliasbioputing—has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These could be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments both as individuals and as populations of bacteria plus bacteriophage. New principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. This computing might even extend to developing a high level language appropriate to using populations of bacteria and bacteriophage. Here, we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria for calculating

Site specificity and attachment mode of Symcallio and Calliobothrium species (Cestoda: “Tetraphyllidea”) in smoothhound sharks of the genus Mustelus (Carcharhiniformes: Triakidae)

Previous studies suggest that cestodes (i.e., tapeworms) of the sister genera Symcallio and Calliobothrium attach in different specific regions of the spiral intestine of their triakid shark hosts, with species of Symcallio attaching in the anterior region of the spiral intestine and species of Calliobothrium attaching with a broader distribution centered around the middle of the spiral intestine. In the present study, we tested the generality of this pattern of site specificity in two additional species pairs: Symcallio peteri and Calliobothrium euzeti in Mustelus palumbes and S. leuckarti and C. wightmanorum in M. asterias. Finding that these cestodes also exhibit the aforementioned pattern, we investigated a series of functional explanations that might account for this phylogenetically conserved pattern of site specificity. The mucosal surface of the spiral intestine of both shark species was characterized, as were the attachment mechanisms of all four cestode species. Although anatomical differences in mucosal surface were seen along the length of the spiral intestine in both shark species, these differences do not appear to correspond to the attachment mode of these cestodes. We find that while species of Symcallio, like most cestodes, attach using their scolex, species of Calliobothrium attach with their scolex and, to a much greater extent, also with their strobila. Furthermore, attachment of Calliobothrium species appears to be enhanced by laciniations (flap-like extensions on the posterior margins of the proglottids) that interdigitate with elements of the mucosal surface of the spiral intestine. The role of proglottid laciniations in attachment in species of Calliobothrium helps reconcile a number of morphological features that differ between these two closely related cestode genera

A synthesis tree of the Copepoda: Integrating phylogenetic and taxonomic data reveals multiple origins of parasitism

The Copepoda is a clade of pancrustaceans containing 14,485 species that are extremely varied in their morphology and lifestyle. Not only do copepods dominate marine plankton and sediment communities and make up a sizeable component of the freshwater plankton, but over 6,000 species are symbiotically associated with every major phylum of marine metazoans, mostly as parasites. Unfortunately, our understanding of copepod evolutionary relationships is relatively limited in part because of their extremely divergent morphology, sparse taxon sampling in molecular phylogenetic analyses, a reliance on only a handful of molecular markers, and little taxonomic overlap between phylogenetic studies. Here, a synthesis tree method is used to integrate published phylogenies into a more comprehensive tree of copepods by leveraging phylogenetic and taxonomic data. A literature review in this study finds fewer than 500 species of copepods have been sampled in molecular phylogenetic studies. Using the Open Tree of Life platform, those taxa that have been sampled in previous phylogenetic studies are grafted together and combined with the underlying copepod taxonomic hierarchy from the Open Tree of Life Taxonomy to make a synthesis phylogeny of all copepod species. Taxon sampling with respect to molecular phylogenetic analyses is reviewed for all orders of copepods and shows only 3% of copepod species have been sampled in phylogenetic studies. The resulting synthesis phylogeny reveals copepods have transitioned to a parasitic lifestyle on at least 14 occasions. We examine the underlying phylogenetic, taxonomic, and natural history data supporting these transitions to parasitism; review the species diversity of each parasitic clade; and identify key areas for further phylogenetic investigation

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

Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes

BACKGROUND: The barnacles are a group of \u3e2,000 species that have fascinated biologists, including Darwin, for centuries. Their lifestyles are extremely diverse, from free-swimming larvae to sessile adults, and even root-like endoparasites. Barnacles also cause hundreds of millions of dollars of losses annually due to biofouling. However, genomic resources for crustaceans, and barnacles in particular, are lacking. RESULTS: Using 62× Pacific Biosciences coverage, 189× Illumina whole-genome sequencing coverage, 203× HiC coverage, and 69× CHi-C coverage, we produced a chromosome-level genome assembly of the gooseneck barnacle Pollicipes pollicipes. The P. pollicipes genome is 770 Mb long and its assembly is one of the most contiguous and complete crustacean genomes available, with a scaffold N50 of 47 Mb and 90.5% of the BUSCO Arthropoda gene set. Using the genome annotation produced here along with transcriptomes of 13 other barnacle species, we completed phylogenomic analyses on a nearly 2 million amino acid alignment. Contrary to previous studies, our phylogenies suggest that the Pollicipedomorpha is monophyletic and sister to the Balanomorpha, which alters our understanding of barnacle larval evolution and suggests homoplasy in a number of naupliar characters. We also compared transcriptomes of P. pollicipes nauplius larvae and adults and found that nearly one-half of the genes in the genome are differentially expressed, highlighting the vastly different transcriptomes of larvae and adult gooseneck barnacles. Annotation of the genes with KEGG and GO terms reveals that these stages exhibit many differences including cuticle binding, chitin binding, microtubule motor activity, and membrane adhesion. CONCLUSION: This study provides high-quality genomic resources for a key group of crustaceans. This is especially valuable given the roles P. pollicipes plays in European fisheries, as a sentinel species for coastal ecosystems, and as a model for studying barnacle adhesion as well as its key position in the barnacle tree of life. A combination of genomic, phylogenetic, and transcriptomic analyses here provides valuable insights into the evolution and development of barnacles