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Article Reference Toxoplasma gondii in stranded marine mammals from the North Sea and Eastern Atlantic Ocean: Findings and diagnostic difficulties
Located in Library / RBINS Staff Publications 2016
Article Reference Trace-element imaging at macroscopic scale in a Belgian sphalerite-galena ore using Laser-Induced Breakdown Spectroscopy (LIBS).
Located in Library / RBINS Staff Publications 2021
Inproceedings Reference Tracing ancient DNA of Foraminifera in tsunami deposits (GEN-EX)
1. Background Tsunami deposits provide information on the long-term frequency-magnitude patterns of events, which may not be covered by the historical and instrumental record. Such information is crucial for the assessment of coastal hazards and mitigation measures against the loss of life and assets. In order to identify tsunami deposits in the coastal sedimentary record and to infer tsunami characteristics, a wide range of proxies has been established based on studies of recent tsunami deposits. Microfossils (e.g. foraminifera, ostracods, diatoms) are often used to recognize tsunami deposits, and to differentiate them from those of other processes. In terms of foraminifera, tsunami deposits mostly contain allochthonous associations dominated by benthic intertidal to inner shelf taxa. Specimens may originate from outer shelf to bathyal depths; even planktonic forms may occur. Furthermore, changes in test numbers, taphonomy, size or adult/juvenile ratios compared to background sedimentation are common (Pilarczyk et al., 2014; Engel et al., 2016). However, dissolution of microfossils often prevent identification and diminish their value as a proxy (Yawsangratt et al., 2012). 2. Study goals and concept To address the problem of post-depositional alteration of microfossil associations in tsunami deposits, high-throughput metagenomic sequencing techniques are applied by the GEN-EX project to identify marine organisms in onshore sand layers based on their DNA remains. Metagenomics (or environmental genomics) is related to sequencing DNA directly from the environmental samples, where the genetic material may have been preserved in sedimentary records covering tens of thousands of years. Metagenomics is an emerging technique in environmental research and is used to characterize the diversity of bacterial communities but also higher organisms such as animals, plants and fungi of recent and ancient origin in a variety of settings, including ice, lake sediments, soils, cave deposits, and various types of surface waters. Metagenomics can also be used to detect cryptic diversity, ultimately providing more accurate estimates of biodiversity (Pedersen et al., 2015). Among the broad range of organisms, foraminifera (single-celled protists) show a water depth-related zonation in subtidal environments, and are the first to have been identified successfully in palaeo- tsunami deposits by their DNA (SzczuciĔski et al., 2016). The main objectives of GEN-EX include: quantifying the relationship between water depth and the distribution of different foraminiferal taxa where known tsunami deposits are present, using a comparative classic micropalaeontological and metagenomic approach; assessing the potential (based on both approaches) for identifying key indicator species in tsunami deposits in different coastal settings; and establishing how metagenomic approaches can contribute to the differentiation between storm and tsunami deposits. 3. DNA extraction DNA will be analysed in two types of material – modern extant foraminifera and sediments (tsunami deposits and adjacent layers). DNA extracted from single foraminiferal specimens will be followed by whole genome amplification to obtain sufficient DNA concentrations. Either part of the nuclear 18S rRNA region or the mitochondrial genome (mtDNA) will be amplified, before high-throughput sequencing of the amplicons. Sequences will be edited and aligned, and their identity verified by BLAST (Altschul et al., 1990) searches in Genbank and the Forambarcoding project (http://forambarcoding.unige.ch). A project-specific database of 18S and mtDNA data of the identified recent foraminifera will be constructed. Sampling of tsunami deposits and DNA extraction follows the protocol of SzczuciĔski et al. (2016). Suitable primers will be developed from our reference database of recent foraminifera to amplify overlapping short fragments of 18S or mtDNA of the target species. Amplicon concentration will be quantified and prepared for high-throughput sequencing. Sequence data will be analysed with different bioinformatics pipelines (e.g. QIIME), including quality control, removal of barcodes and adaptors, identification and removal of chimeric and redundant sequences, and comparisons with our own and open access databases of 18S data for defining Operational Taxonomic Units with 95% and 97% similarity cut-offs. 4. Study area One of the study areas, where the eDNA approach is applied, are the Shetland Islands, exposed to the mega-tsunami triggered by the early Holocene Storegga submarine slide off the coast of Norway. Sediment run-up of more than 25 m left a distinct landward-thinning sand layer with an erosive lower contact, large rip-up clasts, fining-upward sequences and marine diatoms in near-shore lakes and coastal peat lowlands. In addition to sediments associated with the Storegga tsunami, two younger tsunami deposits dated to c. 5 and 1.5 ka (Bondevik et al., 2005) are investigated. Sampling for the planned foraminiferal analyses and eDNA extraction of the deposits and their source area, comprising along the beach and subtidal area to the central shelf area is scheduled for the second half of March 2018. 5. Acknowledgements Funding is kindly provided by a BELSPO BRAIN-be pioneer grant (BR/175/PI/GEN-EX). 6. References Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J., 1990. Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410. Bondevik, S., Mangerud, J., Dawson, S., Dawson, A. & Lohne, Ø., 2005. Evidence for three North Sea tsunamis at the Shetland Islands between 8000 and 1500 years ago. Quaternary Science Reviews, 24, 1757–1775. Engel, M., Oetjen, J., May, S.M. & Brückner, H., 2016. Tsunami deposits of the Caribbean – Towards an improved coastal hazard assessment. Earth-Science Reviews, 163, 260–296. Pedersen, M.W., Overballe-Petersen, S., Ermini, L., Sarkissian, C.D., Haile, J., Hellstrom, M., Spens, J., Thomsen, P.F., Bohmann, K., Cappellini, E., Bærholm Schnell, I., Wales, N.A., Carøe, C., Campos, P.F., Schmidt, A.M.Z., Gilbert, M.T.P., Hansen, A.J., Orlando, L. & Willerslev, E., 2015. Ancient and modern environmental DNA. Philosophical Transactions of the Royal Society B, 370, 20130383. Pilarczyk, J.E., Dura, T., Horton, B.P., Engelhart, S.E., Kemp, A.C. & Sawai, Y., 2014. Microfossils in coastal environments as indicators of paleo-earthquakes, tsunamis and storms. Palaeogeography, Palaeoclimatology, Palaeoecology, 413, 144–157. SzczuciĔski, W., Pawłowska, J., Lejzerowicz, F., Nishimura, Y., KokociĔski, M., Majewski, W., Nakamura, Y. & Pawlowski, J., 2016. Ancient sedimentary DNA reveals past tsunami deposits. Marine Geology, 381, 29–33. Yawsangratt, S., SzczuciĔski, W., Chaimanee, N., Chatprasert, S., Majewski, W. & Lorenc, S., 2012. Evidence of probable paleotsunami deposits on Kho Khao Island, Phang Nga Province, Thailand. Natural Hazards, 63, 151–163.
Located in Library / RBINS Staff Publications 2018
Article Reference Tracking ancient ship routes through the analysis of caulking material from shipwrecks? The case study of two 14th century cogs from Doel (northern Belgium).
Located in Library / RBINS Staff Publications
Article Reference Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series
Summary Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN “speed gene,” only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.
Located in Library / RBINS Staff Publications 2019
Article Reference Tracking Invasive Alien Species (TrIAS): Building a data-driven framework to inform policy
Imagine a future where dynamically, from year to year, we can track the progression of alien species (AS), identify emerging problem species, assess their current and future risk and timely inform policy in a seamless data-driven workflow. One that is built on open science and open data infrastructures. By using international biodiversity standards and facilities, we would ensure interoperability, repeatability and sustainability. This would make the process adaptable to future requirements in an evolving AS policy landscape both locally and internationally. In recent years, Belgium has developed decision support tools to inform invasive alien species (IAS) policy, including information systems, early warning initiatives and risk assessment protocols. However, the current workflows from biodiversity observations to IAS science and policy are slow, not easily repeatable, and their scope is often taxonomically, spatially and temporally limited. This is mainly caused by the diversity of actors involved and the closed, fragmented nature of the sources of these biodiversity data, which leads to considerable knowledge gaps for IAS research and policy. We will leverage expertise and knowledge from nine former and current BELSPO projects and initiatives: Alien Alert, Invaxen, Diars, INPLANBEL, Alien Impact, Ensis, CORDEX.be, Speedy and the Belgian Biodiversity Platform. The project will be built on two components: 1) The establishment of a data mobilization framework for AS data from diverse data sources and 2) the development of data-driven procedures for risk evaluation based on risk modelling, risk mapping and risk assessment. We will use facilities from the Global Biodiversity Information Facility (GBIF), standards from the Biodiversity Information Standards organization (TDWG) and expertise from Lifewatch to create and facilitate a systematic workflow. Alien species data will be gathered from a large set of regional, national and international initiatives, including citizen science with a wide taxonomic scope from marine, terrestrial and freshwater environments. Observation data will be funnelled in repeatable ways to GBIF. In parallel, a Belgian checklist of AS will be established, benefiting from various taxonomic and project-based checklists foreseen for GBIF publication. The combination of the observation data and the checklist will feed indicators for the identification of emerging species; their level of invasion in Belgium; changes in their invasion status and the identification of areas and species of concern that could be impacted upon by bioinvasions. Data-driven risk evaluation of identified emerging species will be supported by niche and climate modelling and consequent risk mapping using critical climatic variables for the current and projected future climate periods at high resolution. The resulting risk maps will complement risk assessments performed with the recently developed Harmonia+ protocol to assess risks posed by emergent species to biodiversity and human, plant, and animal health. The use of open data will ensure that interested stakeholders in Belgium and abroad can make use of the information we generate. The open science ensures everyone is free to adopt and adapt the workflow for different scenarios and regions. The checklist will be used at national level, but will also serve as the Belgian reference for international databases (IUCN - GRIIS, EASIN) and impact assessments (IPBES, SEBI). The workflow will be showcased through GEO BON, the Invasivesnet network and the COST Actions Alien Challenge and ParrotNet. The observations and outcomes of risk evaluations will be used to provide science-based support for the implementation of IAS policies at the regional, federal and EU levels. The publication of Belgian data and checklists on IAS is particularly timely in light of the currently ongoing EU IAS Regulation and its implementation in Belgium. By proving that automated workflows can provide rapid and repeatable production of information, we will open up this technology for other conservation assessments.
Located in Library / RBINS Staff Publications 2017
Article Reference Tracking the origin of worked elephant ivory of a medieval chess piece from Belgium through analysis of ancient DNA
Located in Library / RBINS Staff Publications 2022 OA
Article Reference Traits allowing some ant species to nest syntopically with the fire ant Solenopsis saevissima in its native range.
Supercolonies of the red fire ant Solenopsis saevissima (Smith) develop in disturbed environments and likely alter the ant community in the native range of the species. For example, in French Guiana only 8 ant species were repeatedly noted as nesting in close vicinity to its mounds. Here, we verified if a shared set of biological, ecological, and behavioral traits might explain how these 8 species are able to nest in the presence of S. saevissima. We did not find this to be the case. We did find, however, that all of them are able to live in disturbed habitats. It is likely that over the course of evolution each of these species acquired the capacity to live syntopically with S. saevissima through its own set of traits, where colony size (4 species develop large colonies), cuticular compounds which do not trigger aggressiveness (6 species) and submissive behaviors (4 species) complement each other.
Located in Library / RBINS Staff Publications
Article Reference Traits allowing some ant species to nest syntopically with the fire ant Solenopsis saevissima in its native range
Located in Library / RBINS Staff Publications
Article Reference Transcription, signaling receptor activity, oxidative phosphorylation and fatty acid metabolism mediate the presence of closely-related cryptic species in distinct intertidal and cold-seep habitats
Located in Library / RBINS Staff Publications 2016