• Abyssal fauna of polymetallic nodule exploration areas, eastern Clarion-Clipperton Zone, central Pacific Ocean: Annelida: Capitellidae, Opheliidae, Scalibregmatidae, and Travisiidae

      Wiklund, H; Neal, L; Glover, AG; Drennan, Regan; Rabone, M; Dahlgren, TG (Pensoft Publishers, 2019-10-28)
      We present DNA taxonomy of abyssal polychaete worms from the eastern Clarion-Clipperton Zone (CCZ), central Pacific Ocean, using material collected as part of the Abyssal Baseline (ABYSSLINE) environmental survey cruises ‘AB01’ and ‘AB02’ to the UK Seabed Resources Ltd (UKSRL) polymetallic nodule exploration contract area ‘UK-1’, the Ocean Mineral Singapore exploration contract area ‘OMS-1’ and an Area of Particular Environmental Interest, ‘APEI-6’. This is the fourth paper in a series to provide regional taxonomic data with previous papers reporting on Cnidaria, Echinodermata and Mollusca. Taxonomic data are presented for 23 species from 85 records within four polychaete families: Capitellidae, Opheliidae, Scalibregmatidae and Travisiidae, identified by a combination of morphological and genetic data, including molecular phylogenetic analyses. Two taxa (genetically separated from one another) morphologically matched the same known cosmopolitan species, Ophelina abranchiata that has a type locality in a different ocean basin and depth from where no genetic data was available. These two species were assigned the open nomenclature ‘cf.’ as a precautionary approach in taxon assignments to avoid over-estimating species ranges. Twelve (12) taxa are here described as new species, Ammotrypanella keenani sp. nov., Ammotrypanella kersteni sp. nov., Ophelina curli sp. nov., Ophelina ganae sp. nov., Ophelina juhazi sp. nov., Ophelina martinezarbizui sp. nov., Ophelina meyerae sp. nov., Ophelina nunnallyi sp. nov., Oligobregma brasierae sp. nov., Oligobregma tani sp. nov., Oligobregma whaleyi sp. nov. and Travisia zieglerae sp. nov. For the remaining nine taxa, we have determined them to be potentially new species, for which we make the raw data, imagery and vouchers available for future taxonomic study. The CCZ is a region undergoing intense exploration for potential deep-sea mineral extraction from polymetallic nodules. We present these data to facilitate future taxonomic and environmental impact study by making both data and voucher materials available through curated and accessible biological collections.
    • Abyssal fauna of the UK-1 polymetallic nodule exploration area, Clarion-Clipperton Zone, central Pacific Ocean: Cnidaria

      Dahlgren, T; Wiklund, H; Rabone, M; Amon, D; Ikebe, C; Watling, L; Smith, C; Glover, AG (2016-06-30)
    • Abyssal fauna of the UK-1 polymetallic nodule exploration area, Clarion-Clipperton Zone, central Pacific Ocean: Mollusca

      Wiklund, H; Taylor, JD; Dahlgren, TG; Todt, C; Ikebe, C; Rabone, M; Glover, AG (2017-10-10)
    • Abyssal fauna of the UK-1 polymetallic nodule exploration claim, Clarion-Clipperton Zone, central Pacific Ocean: Echinodermata

      Glover, AG; Wiklund, H; Rabone, M; Amon, D; Smith, C; O'Hara, T; Mah, C; Dahlgren, Thomas (2016-01-25)
      We present data from a DNA taxonomy register of the abyssal benthic Echinodermata collected as part of the Abyssal Baseline (ABYSSLINE) environmental survey cruise ‘AB01’ to the UK Seabed Resources Ltd (UKSRL) polymetallic-nodule exploration claim ‘UK-1’ in the eastern Clarion-Clipperton Zone (CCZ), central Pacific Ocean abyssal plain. Morphological and genetic data are presented for 17 species (4 Asteroidea, 4 Crinoidea, 2 Holothuroidea and 7 Ophiuroidea) identified by a combination of morphological and genetic data. No taxa matched previously published genetic sequences, but 8 taxa could be assigned to previously-described species based on morphology, although here we have used a precautionary approach in taxon assignments to avoid over-estimating species ranges. The Clarion-Clipperton Zone is a region undergoing intense exploration for potential deep-sea mineral extraction. We present these data to facilitate future taxonomic and environmental impact study by making both data and voucher materials available through curated and accessible biological collections.
    • Access to Marine Genetic Resources (MGR): Raising Awareness of Best-Practice Through a New Agreement for Biodiversity Beyond National Jurisdiction (BBNJ)

      Rabone, M; Harden-Davies, H; Collins, JE; Zajderman, S; Appeltans, W; Droege, G; Brandt, A; Pardo-Lopez, L; Dahlgren, TG; Glover, AG; et al. (Frontiers Media SA, 2019-09-03)
      Better scientific knowledge of the poorly-known deep sea and areas beyond national jurisdiction (ABNJ) is key to its conservation, an urgent need in light of increasing environmental pressures. Access to marine genetic resources (MGR) for the biodiversity research community is essential to allow these environments to be better characterised. Negotiations have commenced under the auspices of the United Nations Convention on the Law of the Sea (UNCLOS) to develop a new treaty to further the conservation and sustainable use of marine biological diversity in ABNJ. It is timely to consider the relevant issues with the development of the treaty underway. Currently uncertainties surround the legal definition of MGR and scope of related benefit-sharing, against a background of regional and global governance gaps in ABNJ. These complications are mirrored in science, with recent major advances in the field of genomics, but variability in handling of the resulting increasing volumes of data. Here, we attempt to define the concept of MGR from a scientific perspective, review current practices for the generation of and access to MGR from ABNJ in the context of relevant regulations, and illustrate the utility of best-practice with a case study. We contribute recommendations with a view to strengthen best-practice in accessibility of MGR, including: funder recognition of the central importance of taxonomy/biodiversity research; support of museums/collections for long-term sample curation; open access to data; usage and further development of globally recognised data standards and platforms; publishing of datasets via open-access, quality controlled and standardised data systems and open access journals; commitment to best-practice workflows; a global registry of cruises; and lastly development of a clearing house to further centralised access to the above. We argue that commitment to best-practice would allow greater sharing of MGR for research and extensive secondary use including conservation and environmental monitoring, and provide an exemplar for access and benefit-sharing (ABS) to inform the biodiversity beyond national jurisdiction (BBNJ) process.
    • Accumulation and Dissolution of Magnetite Crystals in a Magnetically Responsive Ciliate

      Monteil, CL; Menguy, N; Prévéral, S; Warren, A; Pignol, D; Lefèvre, CT; Kelly, RM (American Society of Microbiology, 2018-02-09)
      Magnetotactic bacteria (MTB) represent a group of microorganisms that are widespread in aquatic habitats and thrive at the oxic-anoxic interfaces. They are able to scavenge high concentrations of iron thanks to the biomineralization of magnetic crystals in their unique organelle, the so-called magnetosome chain. Although their biodiversity has been intensively studied in recent years, their ecology and impact on iron cycling remain largely unexplored. Predation by protozoa was suggested as one of the ecological processes that could be involved in the release of iron back into the ecosystem. Magnetic protozoa have previously been observed in aquatic environments, but their diversity and the fate of particulate iron during grazing are poorly documented. In this study, we report the morphological and molecular characterization of a magnetically responsive MTB-grazing protozoan able to ingest high quantities of MTB. This protozoan is tentatively identified as Uronema marinum, a ciliate known to be a bacteria predator. Using light and electron microscopy, we investigate in detail the vacuoles in which lysis of phagocytized prokaryotes occurs. We carried out high-resolution observations of aligned magnetosome chains and ongoing dissolution of crystals. Particulate iron in the ciliate represented about 0.01% of its total volume. We show the ubiquity of this interaction in other types of environments and describe different grazing strategies. These data contribute to the mounting evidence that interaction between MTB-protozoan might play a significant role in iron turnover in microaerophilic habitats. IMPORTANCE Identifying participants of each biogeochemical cycle is a prerequisite to our understanding of ecosystems functioning. Magnetotactic bacteria (MTB) participate to iron cycling by concentrating large amounts of biomineralized iron minerals into their cells, which impacts their chemical environment at or below the oxic-anoxic transition zone in aquatic habitats. It was shown that some protozoa inhabiting this niche could become magnetic with the ingestion of magnetic crystals biomineralized by grazed MTB. In this study, we show that magnetic MTB-grazers are commonly observed in marine and freshwater sediments and can sometimes accumulate very large amounts of particulate iron. Using magnetic particles from MTB as tracers after their ingestion by the protozoa, different phagocytosis strategies are described. This study paves the way for potential scientific or medical applications using MTB-grazers as magnetosome-hyperaccumulators.
    • Ahead of the curve: three approaches to mass digitisation of vials with a focus on label data capture

      Dupont, Steen; Humphries, Josh; Butcher, Alice Jenny; Baker, E; Balcells, L; Price, BW (Pensoft Publishers, 2020-04-27)
      There has been little research on novel approaches to digitising liquid-preserved natural history specimens stored in jars or vials. This paper discusses and analyses three different prototypes for high-throughput digitisation using cheap, readily available components. This paper has been written for other digitisation teams or curators who want to trial or improve upon these new digitisation approaches in liquid preserved collections.
    • The Airless Project

      Allington-Jones, L; Trafford, A (Natural Sciences Collections Association, 2017-04-20)
      A project to combat pyrite oxidation at the NHM (London, UK) is currently in its second year. The project aims to undertake conservation treatments and store highest risk specimens in low oxygen microenvironments. An emergent benefit of the conservation-driven project has been the digitisation of specimens on the collection management system KE Emu, through the use of barcodes and web-based applications.
    • All Our Eggs In One Basket: Challenges of High Resolution X-Ray Micro-Computed Tomography of Great Auk Pinguinus impennis Eggshell

      Russell, D; Bernucci, A; Scott-Murray, A; Jackson, D; Ahmed, F; Garbout, A; Birkhead, T (2018-06-13)
    • The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata)

      Gao, F; Zhang, Q; Gong, J; Miao, M; Sun, P; Xu, D; Huang, J; Yi, Z; Song, W; Warren, A (2016-07)
    • Amazon plant diversity revealed by a taxonomically verified species list

      Cardoso, D; Särkinen, T; Alexander, S; Amorim, AM; Bittrich, V; Celis, M; Daly, DC; Fiaschi, P; Funk, VA; Giacomin, LL; et al. (2017-10-03)
    • Analyses of mitochondrial amino acid sequence datasets support the proposal that specimens of Hypodontus macropi from three species of macropodid hosts represent distinct species

      Jabbar, A; Beveridge, I; Mohandas, N; Chilton, NB; Littlewood, T; Jex, AR; Gasser, RB (Springer Science and Business Media LLC, 2013-11-21)
      Background: Hypodontus macropi is a common intestinal nematode of a range of kangaroos and wallabies (macropodid marsupials). Based on previous multilocus enzyme electrophoresis (MEE) and nuclear ribosomal DNA sequence data sets, H. macropi has been proposed to be complex of species. To test this proposal using independent molecular data, we sequenced the whole mitochondrial (mt) genomes of individuals of H. macropi from three different species of hosts (Macropus robustus robustus, Thylogale billardierii and Macropus [Wallabia] bicolor) as well as that of Macropicola ocydromi (a related nematode), and undertook a comparative analysis of the amino acid sequence datasets derived from these genomes. Results: The mt genomes sequenced by next-generation (454) technology from H. macropi from the three host species varied from 13,634 bp to 13,699 bp in size. Pairwise comparisons of the amino acid sequences predicted from these three mt genomes revealed differences of 5.8% to 18%. Phylogenetic analysis of the amino acid sequence data sets using Bayesian Inference (BI) showed that H. macropi from the three different host species formed distinct, well-supported clades. In addition, sliding window analysis of the mt genomes defined variable regions for future population genetic studies of H. macropi in different macropodid hosts and geographical regions around Australia. Conclusions: The present analyses of inferred mt protein sequence datasets clearly supported the hypothesis that H. macropi from M. robustus robustus, M. bicolor and T. billardierii represent distinct species.
    • Analysis of ultraconserved elements supports African origins of narrow-mouthed frogs

      Streicher, Jeffrey W; Loader, Simon; Varela-Jaramillo, Andrea; Montoya, Paola; de Sá, Rafael O (Elsevier BV, 2020-02)
      Narrow-mouthed frogs (Anura: Microhylidae) are globally distributed and molecular data suggest the rapid evolution of multiple subfamilies shortly after their origin. Despite recent progress, several subfamilial relationships remain unexplored using phylogenomic data. We analysed 1,796 nuclear ultraconserved elements, a total matrix of 400,664 nucleotides, from representatives of most microhylid subfamilies. Summary method species-tree and maximum likelihood analyses unambiguously supported Hoplophryninae as the earliest diverging microhylid and confirm Chaperininae as a junior synonym of Microhylinae. Given the emerging consensus that subfamilies from mainland Africa diverged early, microhylids have likely occupied the continent for more than 66 million years.
    • Analytical and Clinical Assessment of a Portable, Isothermal Recombinase Polymerase Amplification (RPA) Assay for the Molecular Diagnosis of Urogenital Schistosomiasis

      Archer, John; Barksby, Rebecca; Pennance, T; Rostron, Penelope; Bakar, Faki; Knopp, Stefanie; Allan, F; Kabole, Fatma; Ali, Said M; Ame, Shaali M; et al. (MDPI AG, 2020-09-11)
      Accurate diagnosis of urogenital schistosomiasis is crucial for disease surveillance and control. Routine diagnostic methods, however, lack sensitivity when assessing patients with low levels of infection still able to maintain pathogen transmission. Therefore, there is a need for highly sensitive diagnostic tools that can be used at the point-of-care in endemic areas. Recombinase polymerase amplification (RPA) is a rapid and sensitive diagnostic tool that has been used to diagnose several pathogens at the point-of-care. Here, the analytical performance of a previously developed RPA assay (RT-ShDra1-RPA) targeting the Schistosoma haematobium Dra1 genomic region was assessed using commercially synthesised S. haematobium Dra1 copies and laboratory-prepared samples spiked with S. haematobium eggs. Clinical performance was also assessed by comparing diagnostic outcomes with that of a reference diagnostic standard, urine-egg microscopy. The RT-ShDra1-RPA was able to detect 1 × 101 copies of commercially synthesised Dra1 DNA as well as one S. haematobium egg within laboratory-spiked ddH2O samples. When compared with urine-egg microscopy, the overall sensitivity and specificity of the RT-ShDra1-RPA assay was 93.7% (±88.7–96.9) and 100% (±69.1–100), respectively. Positive and negative predictive values were 100% (±97.5–100) and 50% (±27.2–72.8), respectively. The RT-ShDra1-RPA therefore shows promise as a rapid and highly sensitive diagnostic tool able to diagnose urogenital schistosomiasis at the point-of-care.
    • Ancestral origins and invasion pathways in a globally invasive bird correlate with climate and influences from bird trade

      Jackson, H; Strubbe, D; Tollington, S; Prys-Jones, Robert; Matthysen, E; Groombridge, JJ (2015-08)
    • Ancient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome Parasites

      Platt, Roy N; McDew-White, Marina; Le Clec’h, Winka; Chevalier, Frédéric D; Allan, Fiona; Emery, AM; Garba, Amadou; Hamidou, Amina A; Ame, Shaali M; Webster, Joanne P; et al. (Oxford University Press (OUP), 2019-06-27)
      Abstract - Introgression among parasite species has the potential to transfer traits of biomedical importance across species boundaries. The parasitic blood fluke Schistosoma haematobium causes urogenital schistosomiasis in humans across sub-Saharan Africa. Hybridization with other schistosome species is assumed to occur commonly, because genetic crosses between S. haematobium and livestock schistosomes, including S. bovis, can be staged in the laboratory, and sequencing of mtDNA and rDNA amplified from microscopic miracidia larvae frequently reveals markers from different species. However, the frequency, direction, age, and genomic consequences of hybridization are unknown. We hatched miracidia from eggs and sequenced the exomes from 96 individual S. haematobium miracidia from infected patients from Niger and the Zanzibar archipelago. These data revealed no evidence for contemporary hybridization between S. bovis and S. haematobium in our samples. However, all Nigerien S. haematobium genomes sampled show hybrid ancestry, with 3.3–8.2% of their nuclear genomes derived from S. bovis, providing evidence of an ancient introgression event that occurred at least 108–613 generations ago. Some S. bovis-derived alleles have spread to high frequency or reached fixation and show strong signatures of directional selection; the strongest signal spans a single gene in the invadolysin gene family (Chr. 4). Our results suggest that S. bovis/S. haematobium hybridization occurs rarely but demonstrate profound consequences of ancient introgression from a livestock parasite into the genome of S. haematobium, the most prevalent schistosome species infecting humans.
    • Ancient incomplete lineage sorting of Hyles and Rhodafra (Lepidoptera: Sphingidae)

      Hundsdoerfer, Anna K; Kitching, I (Springer Science and Business Media LLC, 2020-07-12)
      Abstract The hawkmoth genus Rhodafra comprises two African species with unclear relationships, as their wing patterns are markedly different, with one species closely resembling species of a related genus, Hyles. The present paper aims to investigate the monophyly and phylogenetic position of Rhodafra in relation to Hyles and other genera of the subtribe Choerocampina (Sphingidae: Macroglossinae: Macroglossini) using mitochondrial and nuclear sequence data from more species and individuals than have hitherto been studied. As no fresh tissue of Rhodafra was available, ancient-DNA methodology was applied. All data corroborate the genus as monophyletic and that a similar wing pattern is not a good indicator of close phylogenetic relationship in this group of moths. Phylogenetic trees based on mitochondrial data agree in placing Rhodafra within Hyles. In contrast, analysis of nuclear EF1alpha sequences produces a topology in which Rhodafra is placed as the sister clade to Hyles. Although multispecies coalescent analyses suggest a polytomy between Rhodafra, Hyles lineata and the remaining Hyles, total evidence analyses corroborate Rhodafra as sister to Hyles. This relationship is interpreted as the favoured topology. For a more robust result, the question should be re-examined using genomic approaches.