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Article Reference Publishing data to support the fight against human vector-borne diseases
Vector-borne diseases are responsible for more than 17% of human cases of infectious diseases. In most situations, effective control of debilitating and deadly vector-bone diseases (VBDs), such as malaria, dengue, chikungunya, yellow fever, Zika and Chagas requires up-to-date, robust and comprehensive information on the presence, diversity, ecology, bionomics and geographic spread of the organisms that carry and transmit the infectious agents. Huge gaps exist in the information related to these vectors, creating an essential need for campaigns to mobilise and share data. The publication of data papers is an effective tool for overcoming this challenge. These peer-reviewed articles provide scholarly credit for researchers whose vital work of assembling and publishing well-described, properly-formatted datasets often fails to receive appropriate recognition. To address this, GigaScience’s sister journal GigaByte partnered with the Global Biodiversity Information Facility (GBIF) to publish a series of data papers, with support from the Special Programme for Research and Training in Tropical Diseases (TDR), hosted by the World Health Organisation (WHO). Here we outline the initial results of this targeted approach to sharing data and describe its importance for controlling VBDs and improving public health.
Located in Library / RBINS Staff Publications 2022
Article Reference The ants of the Galápagos Islands (Hymenoptera, Formicidae): a historical overview, checklist, and identification key
The Galápagos ant fauna has long been understudied, with the last taxonomic summary being published almost a century ago. Here, a comprehensive and updated overview of the known ant species of the Galápagos Islands is provided with updated species distributions. The list is based on an extensive review of literature, the identification of more than 382,000 specimens deposited in different entomological collections, and recent expeditions to the islands. The ant fauna is composed of five subfamilies (Dolichoderinae, Dorylinae, Formicinae, Myrmicinae, and Ponerinae), 22 genera, 50 species, and 25 subspecies, although three species (Crematogaster crinosa Mayr, 1862, Camponotus senex (Smith, 1858), and Solenopsis saevissima (Smith, 1855)) are considered dubious records. Finally, an illustrated identification key of the species found in the archipelago is presented.
Located in Library / RBINS Staff Publications 2023
Article Reference The HYPERMAQ dataset: bio-optical properties of moderately to extremely turbid waters
Because of the large diversity of case 2 waters ranging from extremely absorbing to extremely scattering waters and the complexity of light transfer due to external terrestrial inputs, retrieving main biogeochemical parameters such as chlorophyll-a or suspended particulate matter concentration in these waters is still challenging. By providing optical and biogeochemical parameters for 180 sampling stations with turbidity and chlorophyll-a concentration ranging from 1 to 700 FNU and from 0.9 to 180 mg m−3 respectively, the HYPERMAQ dataset will contribute to a better description of marine optics in optically complex water bodies and can help the scientific community to develop algorithms. The HYPERMAQ dataset provides biogeochemical parameters (i.e. turbidity, pigment and chlorophyll-a concentration, suspended particulate matter), apparent optical properties (i.e. water reflectance from above water measurements) and inherent optical properties (i.e. absorption and attenuation coefficients) from six different study areas. These study areas include large estuaries (i.e. the Rio de la Plata in Argentina, the Yangtze estuary in China, and the Gironde estuary in France), inland (i.e. the Spuikom in Belgium and Chascomùs lake in Argentina), and coastal waters (Belgium). The dataset is available from Lavigne et al. (2022) at https://doi.org/10.1594/PANGAEA.944313.
Located in Library / RBINS Staff Publications 2022
Article Reference Quality-control tests for OC4, OC5 and NIR-red satellite chlorophyll-a algorithms applied to coastal waters
Reliable satellite estimates of chlorophyll-a concentration (Chl-a) are needed in coastal waters for applications such as eutrophication monitoring. However, because of the optical complexity of coastal waters, retrieving accurate Chl-a is still challenging. Many algorithms exist and give quite different performance for different optical conditions but there is no clear definition of the limits of applicability of each algorithm and no clear basis for deciding which algorithm to apply to any given image pixel (reflectance spectrum). Poor quality satellite Chl-a data can easily reach end-users. To remedy this and provide a clear decision on when a specific Chl-a algorithm can be used, we propose simple quality control tests, based on MERIS water leaving reflectance (ρw) bands, to determine on a pixel-by-pixel basis if any of three popular and complementary algorithms can be used. The algorithms being tested are: 1. the OC4 blue-green band ratio algorithm which was designed for open ocean waters; 2. the OC5 algorithm which is based on look-up tables and corrects OC4 overestimation in moderately turbid waters and 3. a near infrared-red (NIR-red) band ratio algorithm designed for eutrophic waters. Using a dataset of 348 in situ Chl-a / MERIS matchups, the conditions for reliable performance of each of the selected algorithms are determined. The approach proposed here looks for the best compromise between the minimization of the relative difference between In situ measurements and satellite estimations and the number of pixels processed. Conditions for a reliable application of OC4 and OC5 depend on ρw412/ρw443 and ρw560, used as proxies of coloured dissolved organic matter and suspended particulate matter (SPM), as compared to ρw560/ρw490, used as a proxy for Chl-a. Conditions for reliable application of the NIR-red band ratio algorithm depend on Chl-a and SPM. These conditions are translated into pixel-based quality control (QC) tests with appropriately chosen thresholds. Results show that by removing data which do not pass QC, the performance of the three selected algorithms is significantly improved. After combining these algorithms, 70\% of the dataset could be processed with a median absolute percent difference of 30.5\%. The QC tests and algorithm merging methodology were then tested on four MERIS images of European waters. The OC5 algorithm was found to be suitable for most pixels, except in very turbid and eutrophic waters along the coasts where the NIR-red band ratio algorithm helps to fill the gap. Finally, a test was performed on an OLCI-S3A image. Although some validations of water reflectance are still needed for the OLCI sensors, results show similar behavior to the MERIS applications which suggests that when applied to OLCI data the present methodology will help to accurately estimate Chl-a in coastal waters for the next decade.
Located in Library / RBINS Staff Publications 2022
Book Reference Sand and Sustainability: 10 strategic recommendations to avert a crisis. GRID-Geneva, United Nations Environment Programme
Located in Library / RBINS Staff Publications 2022 OA
Techreport Reference Seabed CommUnity Initiative: communicating sustainability challenges of marine sand use in a changing world <Seabed4U>. Final Report.
Located in Library / RBINS Staff Publications 2022 OA
Techreport Reference Residual currents and transports near the C-Power and Norther wind farms
Located in Library / RBINS Staff Publications 2022 OA
Article Reference Tremadocian and Floian (Ordovician) linguliformean brachiopods from the Stavelot–Venn Massif (Avalonia; Belgium and Germany)
Located in Library / RBINS Staff Publications 2022
Article Reference One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus
Bacterial endosymbionts of the groups Wolbachia , Cardinium and Rickettsiaceae are well known for their diverse effects on their arthropod hosts, ranging from mutualistic relationships to reproductive phenotypes. Here, we analysed a unique system in which the dwarf spider Oedothorax gibbosus is co-infected with up to five different endosymbionts affiliated with Wolbachia , ‘Candidatus Tisiphia’ (formerly Torix group Rickettsia ), Cardinium and Rhabdochlamydia . Using short-read genome sequencing data, we show that the endosymbionts are heterogeneously distributed among O. gibbosus populations and are frequently found co-infecting spider individuals. To study this intricate host–endosymbiont system on a genome-resolved level, we used long-read sequencing to reconstruct closed genomes of the Wolbachia , ‘Ca. Tisiphia’ and Cardinium endosymbionts. We provide insights into the ecology and evolution of the endosymbionts and shed light on the interactions with their spider host. We detected high quantities of transposable elements in all endosymbiont genomes and provide evidence that ancestors of the Cardinium , ‘Ca. Tisiphia’ and Wolbachia endosymbionts have co-infected the same hosts in the past. Our findings contribute to broadening our knowledge about endosymbionts infecting one of the largest animal phyla on Earth and show the usefulness of transposable elements as an evolutionary ‘contact-tracing’ tool.
Located in Library / RBINS Staff Publications 2023
Article Reference Ocean acidification modifies behaviour of shelf seabed macrofauna: A laboratory study on two ecosystem engineers, Abra alba and Lanice conchilega
The feeding activity and burrow ventilation by benthic invertebrates importantly affect the biodiversity and functioning of seafloor sediments. Here we investigated how ocean acidification can modify these behavioural activities in two common and abundant macrofaunal ecosystem engineering species in temperate continental shelf communities: the white furrow shell Abra alba and the sand mason Lanice conchilega. Using time-lapse imagery and sediment porewater hydraulic signatures we show that both species adapt their behaviour in response to predicted future pH conditions (-0.3 units). During a three-week laboratory experiment, A. alba reduced the duration per feeding event when suspension and deposit feeding (by 86 and 53%, respectively), and almost completely ceased suspension feeding under reduced seawater pH in comparison to ambient seawater pH (pH ~ 8.2). This behavioural change reduces the intake of low pH water during feeding and respiration. L. conchilega increased its piston-pumping frequency by 30 and 52%, respectively, after one and two weeks of exposure to future pH conditions (-0.3 units) relative to ambient conditions. This change in irrigation activity suggests higher metabolic demands under low seawater pH, and also extended low water column pH conditions deeper into the seafloor. Because the distribution of other populations depends on the physicochemical setting by our focal species, we argue that the demonstrated behavioural plasticity will likely have cascading effects on seafloor diversity and functioning, highlighting the complexity of how ocean acidification, and climate change in general, will affect seafloor ecology.
Located in Library / RBINS Staff Publications 2023