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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
Conference Reference Abc Taxa: series of peer-reviewed manuals dedicated to capacity building in taxonomy & collection management
Today, the so-called taxonomic impediment, i.e., the lack of taxonomic (inclusive of genetic) information, taxonomic and curatorial expertise, and infrastructure in many parts of the world, means that accessing and generating taxonomic information remains extremely difficult. To alter this trend, the Convention on Biological Diversity installed the Global Taxonomy Initiative (GTI) and endorsed it with an operational program of work. Its objectives are to remedy the knowledge gaps in our taxonomic system, increase the number of well-trained taxonomists and curators, optimize the infrastructure needed to do sound taxonomic research, significantly improve access to taxonomic collections, data, and metadata, and, thereby, to improve decision- making in conservation of biodiversity. To speed up taxonomic capacity building the Belgian GTI Focal Point has established the series Abc Taxa (www.abctaxa.be), a toll-free information highway between experts and novices. It is believed that this artery will speed up the construction of taxonomic capacity, as it does not evoke the expensive, long-term teacher-apprentice relationships previously utilized to install operational, high-quality taxonomists and collection managers. Since 2005, 19 volumes have been released with subjects as diverse as taxonomy of sea cucumbers of the Comoros, good practices in collection management of mollusc collections, taxonomy of the amphibians of Cuba and of Guyana, taxonomy of algae of Sri Lanka, bee taxonomy in sub-Saharan Africa, mushroom taxonomy of Central Africa, introduction to the taxonomy of mites, taxonomy of invasive succulents of South Africa, taxonomy of the sawflies of southern Africa, taxonomy of the diatoms of the Congo, taxonomy of fish parasites of African Freshwater fishes and taxonomy of the brittle and basket stars of South Africa. This contribution briefly details the scope and aims of Abc Taxa, demonstrates the value of the series for development, and acts as a call for future manuscripts.
Located in Library / RBINS Staff Publications 2021
Inproceedings Reference Rapid Local Adaptations in an Invasive Frog (Xenopus laevis): the Importance of Functional Trait Measurements to Predict Future Invasions
Located in Library / RBINS Staff Publications 2020
Inproceedings Reference Classification of multibeam sonar image using the Weyl transform
Located in Library / RBINS Staff Publications 2019
Inproceedings Reference Geodiversity of a stone deposit in the old city centre of Antwerp. Source of information on roman and medieval trade and use. 8th International Geologica Belgica Meeting 2024, 11-13 September 2024, Liège.
Located in Library / RBINS Staff Publications 2024
Inproceedings Reference Bedrock morphology modelling using geologically-dependent empirical equations between resonance frequency and bedrock depth
Calculating thickness variations of soft sediments above bedrock is important for site effect characterisation, earthquake ground motion amplification and for hydrogeological and geothermal purposes. In case seismic array instrumentation is not available and hence shear-wave velocity profiles cannot be obtained, other correlation techniques need to be applied to accurately deduce bedrock depth. Nakamura’s H/V Spectral Ratio (HVSR) analysis of ambient noise is a powerful seismological method to reveal a site’s resonance frequency. The conversion from a resonance map to a bedrock depth map in areas with a different sedimentary cover in terms of layer thickness and lithologies is, however, not straightforward. Converting resonance frequencies to depth by applying a mean shear-wave velocity (Vs) will under- and overestimate bedrock depth at higher and lower topographies, respectively. Applying an empirical log-log (powerlaw) relationship between resonance frequency (obtained from HVSR analyses) and bedrock depth (obtained from boreholes) provides a much better depth estimation that considers the non-linear increase of Vs with depth. Accurate empirical equations can however only be constructed from HVSR measurements performed in areas with similar lithological sediments. In this study we present a high-resolution microzonation study performed in Brussels (Belgium) where both the sedimentary cover and the fractured top of the bedrock (i.e. the Brabant Massif) are of interest for their geothermal potential. Using 88 ambient noise measurements above boreholes we constructed four different powerlaw equations that are applicable to convert resonance frequency to depth in areas with a clayey, sandy-clayey, alluvial-clayey and alluvial sedimentary cover. Subsequently, 405 ambient noise measurements were conducted and converted to virtual boreholes using these four empirical equations. Measurements were used to map out bedrock depth in a 15km2 and a 25 km2 area applying a 200 m and 500 m station density spacing, respectively. The results demonstrate the presence of NW-SE oriented, 20 m-high ridges at 100 m depth that stand out because of differential erosion between less-resistant slaty (Tubize Formation) and hard quartzitic (Blanmont Formation) rock formations of the Brabant Massif. Separating seismic data according to their subsurface geology results in more accurate empirical frequency-depth conversion equations than if only one equation would be used for an entire area.
Located in Library / RBINS Staff Publications 2018
Inproceedings Reference Integration of corrective parameters to merge multiple-sourced online macroseismic data
Located in Library / RBINS Staff Publications 2018
Inproceedings Reference Incorporating data uncertainty in 3D voxel modelling and the importance in decision making
Geological databases resulting from the merging of various data sources and time periods jeopardize harmonization of data products. Data standardization is already common practice and a first step in avoiding semantic overlap. European marine data management infrastructures provide such standards, e.g., Geo-Seas (http://www.geo-seas.eu/) for geological data and SeaDataNet (https://www.seadatanet.org/) for marine metadata in general. In addition, metadata quality control is important, though data uncertainty is seldom quantified and to be used in modelling. Preliminary uncertainty analyses were worked out to provide an extra dimension to the cross-border 3D voxel models of the geological subsurface of the Belgian and southern Netherlands part of the North Sea (http://odnature.naturalsciences.be/tiles/). Starting from simple quality flagging in geological databases and model uncertainty calculations (probability and entropy) in the 3D modelling, data uncertainty (e.g., related to qualities in positioning, sampling and vintage) is now quantified. Combining all uncertainties remains a challenge, as well as communicating their importance in decision making. A demonstration will be given on the status of the uncertainty analyses and how these are incorporated in a newly developed decision support tool allowing interactive querying of the 3D voxel model, now comprising geological, as well as entropy, probability and data uncertainty attributes (figure 1).
Located in Library / RBINS Staff Publications 2018
Inproceedings Reference “Memor”: Créer un inventaire des restes humaines archéologiques en Flandres, Belgique.
Located in Library / RBINS Staff Publications 2024
Inproceedings Reference A possible case of pes planus in the convent of Friars Minor in Brussels, Belgium (13-18th centuries CE).
Located in Library / RBINS Staff Publications 2024