Search publications of the members of the Royal Belgian institute of natural Sciences
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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.
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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.
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Size-effect, asymmetry, and small-scale spatial variation in otolith shape of juvenile sole in the Southern North Sea
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Rapid Local Adaptations in an Invasive Frog (Xenopus laevis): the Importance of Functional Trait Measurements to Predict Future Invasions
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The oldest cereals in the coversand area along the North Sea coast of NW Europe, between ca. 4800 and 3500 cal BC, at the wetland site of ‘Bazel-Sluis’ (Belgium).
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The use of Scientific Techniques in the Study, Reconstruction of and Human Interaction with Woodlands
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CoastColour Round Robin data sets: a database to evaluate the performance of algorithms for the retrieval of water quality parameters in coastal waters
- The use of in situ measurements is essential in the validation and evaluation of the algorithms that provide coastal water quality data products from ocean colour satellite remote sensing. Over the past decade, various types of ocean colour algorithms have been developed to deal with the optical complexity of coastal waters. Yet there is a lack of a comprehensive intercomparison due to the availability of quality checked in situ databases. The CoastColour Round Robin (CCRR) project, funded by the European Space Agency (ESA), was designed to bring together three reference data sets using these to test algorithms and to assess their accuracy for retrieving water quality parameters. This paper provides a detailed description of these reference data sets, which include the Medium Resolution Imaging Spectrometer (MERIS) level 2 match-ups, in situ reflectance measurements, and synthetic data generated by a radiative transfer model (HydroLight). These data sets, representing mainly coastal waters, are available from doi:10.1594/PANGAEA.841950. The data sets mainly consist of 6484 marine reflectance (either multispectral or hyperspectral) associated with various geometrical (sensor viewing and solar angles) and sky conditions and water constituents: total suspended matter (TSM) and chlorophyll a (CHL) concentrations, and the absorption of coloured dissolved organic matter (CDOM). Inherent optical properties are also provided in the simulated data sets (5000 simulations) and from 3054 match-up locations. The distributions of reflectance at selected MERIS bands and band ratios, CHL and TSM as a function of reflectance, from the three data sets are compared. Match-up and in situ sites where deviations occur are identified. The distributions of the three reflectance data sets are also compared to the simulated and in situ reflectances used previously by the International Ocean Colour Coordinating Group (IOCCG, 2006) for algorithm testing, showing a clear extension of the CCRR data which covers more turbid waters.
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Classification of multibeam sonar image using the Weyl transform
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Surface movement above old coal longwalls after mine closure
- Although most subsidence occurs in the months and years after mining by the longwall method, surface movement is still occurring many decades after the mining. The aim of the study is to quantify the long term behavior. Satellite data (radar-interferometry) were analyzed to study an area of about 2km2 during the 18years following the closure of the underground infrastructure and the flooding of the underground workings and rock mass. It was observed that, on average, a residual downward movement took place till 7–12years after the closure, followed by a clear uplift. However, the first signs of an uplift occurred in certain sub-areas 3–4years after the closure. Zones within the area studied were identified with either larger or smaller movements. However, the spatial variation of the surface subsidence or uplift could not be directly explained by the characteristics of mining.
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Subsidence related to groundwater pumping for breweries in Merchtem area (Belgium), highlighted by Persistent Scaterrer Interferometry
- ERS, ENVISAT and TerraSAR-X Synthetic Aperture Radar scenes covering the time span 1992–2014 were processed using a Persistent Scatterer technique to study the ground movements in Merchtem (25km NW of Brussels, Belgium). The processed datasets, covering three consecutive time intervals, reveal that the investigated area is affected by a global subsidence trend related to the extraction of groundwater in the deeper Cambro-Silurian aquifer. Through time the subsidence pattern is reduced and replaced by an uplift related to the rising water table attested by piezometers located in this aquifer. The subsidence is finally reduced to a zone where currently three breweries are very active and pump groundwater in the Ledo-Paniselian aquifer and in the Cambro-Silurian for process water for the production.
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Understanding and predicting the impact of the interaction between oceanographic and biological factors on larval recruitment and population connectivity in flatfish
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L’eutrophisation : manifestations, causes, conséquences et prédictibilité. Synthèse de l’Expertise scientifique collective CNRS – IFREMER – INRA – Irstea (France), 148 pages.
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Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas
- Species and populations are disappearing at an alarming rate as a direct result of human activities. Loss of genetic diversity associated with population decline directly impacts species’ long-term survival. Therefore, preserving genetic diversity is of considerable conservation importance. However, to assist in conservation efforts, it is important to understand how genetic diversity is spatially distributed and how it changes due to anthropogenic pressures. In this study, we use historical museum and modern faecal samples of two critically endangered eastern gorilla taxa, Grauer’s (Gorilla beringei graueri) and mountain gorillas (Gorilla beringei beringei), to directly infer temporal changes in genetic diversity within the last century. Using over 100 complete mitochondrial genomes, we observe a significant decline in haplotype and nucleotide diversity in Grauer’s gorillas. By including historical samples from now extinct populations we show that this decline can be attributed to the loss of peripheral populations rather than a decrease in genetic diversity within the core range of the species. By directly quantifying genetic changes in the recent past, our study shows that human activities have severely impacted eastern gorilla genetic diversity within only four to five generations. This rapid loss calls for dedicated conservation actions, which should include preservation of the remaining peripheral populations.
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Reply to “Comment on “Ecological niche of Neanderthals from Spy Cave revealed by nitrogen isotopes of individual amino acids in collagen.” [J. Hum. Evol. 93 (2016) 82–90]” [J. Hum. Evol. 117 (2018) 53–55]
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Additional data on eastern Pantepui Orthalicoidea land snails (Mollusca, Gastropoda)
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Screening of suitability of pelitic rocks in Belgium for radio-active waste disposal
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Screening of suitability of pelitic rocks in Belgium for radio-active waste disposal
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Airborne monitoring of compliance to NOx emission regulations from ocean-going vessels in the Belgian North Sea
- Along the worldwide tightening of standards for sulphur emission from ocean going vessels (OGVs) come actions that are also being taken to reduce nitrogen emission. Particularly, as a milestone in this regard, on January 1st, 2021 the NOx Emission Control Area (NECA) for the North Sea and Baltic Sea came into effect. In response to the newly established NECA, the sniffer sensor system on the Belgian coastguard aircraft was modified and extended with a NOx sensor. Moreover, a methodology was developed to evaluate OGV compliance to the NOx emission limits through in situ measurements of the plume exhaust. The quality and uncertainty of the measurements demonstrate that it is likely to achieve an effective compliance monitoring of the NOx emission standards on the sea. Those emission standards are further divided into four tiers depending on the keel laying date. As has been proved by the results, NOx emissions for Tier II OGVs, contrary to what might be expected, are on average higher than those for Tier I OGVs. What is even more problematic, Tier II OGVs have also more often been found to be non-compliant than Tier I OGVs.
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VanNoten_Bruniquel
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Electric and passive seismic geophysical survey in a protected cave environment: the Bruniquel cave (France)
