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Inproceedings Reference Metagenomics of tsunami deposits
Onshore deposits of tsunamis provide information on the long-term frequency-magnitude patterns of events, which may not be covered by historical or instrumental records. Such information is crucial to assess coastal hazards and mitigation measures against the loss of life and assets. The identification of tsunami deposits in the coastal sedimentary record and the reconstruction of flooding processes requires reliable proxies, which are based on studies of recent tsunami deposits. Microfossils (e.g. foraminifera, ostracods, diatoms) are often applied to recognize tsunami deposits and differentiate them from storm deposits. 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 (Engel et al., 2016). However, dissolution of microfossils often prevents identification and reduces their value as a proxy (e.g. Yawsangratt et al., 2012). We address the problem of post-depositional dissolution of foraminiferal tests in tsunami deposits by applying high- throughput metagenomic sequencing techniques to identify foraminiferal associations based on DNA remains. Metagenomics (or environmental genomics) is related to sequencing DNA directly from the sediment record, where the genetic material may persist for tens of thousands of years. Among the broad range of organisms tackled in metagenomic studies so far, foraminifera (single-celled protists) were chosen as they show a water depth-related zonation in subtidal environments and were the first group to have been identified successfully in palaeo-tsunami deposits by their DNA (Szczuciński et al., 2016). The core study area are the Shetland Islands, exposed to the mega-tsunami triggered by the early Holocene Storegga submarine slide off the coast of Norway. Tsunami run-up of more than 25 m left a distinct landward-thinning sand layer with an erosive lower contact, locally large rip- up clasts, fining-upward sequences and marine diatoms in coastal lakes and peat lowlands. In addition to Storegga tsunami deposits, two younger tsunami deposits dated to c. 5 and 1.5 ka (Bondevik et al., 2005) were sampled during a field campaign in March 2018. Preliminary microscope analysis reveals rich foraminiferal associations in the shallow subtidal muddy sands of protected fjords, which represent the main source area for tsunami deposits. The onshore tsunami deposits, however, vertically confined by ubiquitous dystrophic peat, are void of any carbonate, which seems to have quickly dissolved after deposition in the low-pH environment. This setting paves the way for developing a new eDNA-based proxy to support the identification of tsunamis in the sedimentary record. Funding by a BELSPO BRAIN-be pioneer grant (BR/175/PI/GEN-EX) is gratefully acknowledged. References: 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. Quat. Sci. Rev. 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 Sci. Rev. 163, 260–296. Szczuciński, W., Pawłowska, J., Lejzerowicz, F., Nishimura, Y., Kokociński, M., Majewski, W., Nakamura, Y., Pawlowski, J., 2016. Ancient sedimentary DNA reveals past tsunami deposits. Mar. Geol. 381, 29–33. Yawsangratt, S., Szczuciński, W., Chaimanee, N., Chatprasert, S., Majewski, W., Lorenc, S., 2012. Evidence of probable paleotsunami deposits on Kho Khao Island, Phang Nga Province, Thailand. Nat. Hazards 63, 151–163.
Located in Library / RBINS Staff Publications 2018
Inproceedings Reference Reef-top platform coral boulders of Eastern Samar demonstrate the long-term coastal hazard of extreme waves
The Eastern Visayas region in the Philippines experiences some of the most violent tropical cyclones on Earth, exemplified by Typhoon Haiyan (7–9 November 2013) or Typhoon Hagupit (6–8 December 2014). Moreover, strong earthquakes along the Philippine Trench have triggered tsunamis in the past, both implying significant hazards of coastal flooding through extreme waves for the Pacific coast of the island of Samar. Due to the very short and fragmented historical record of the region, not much is known about frequency-magnitude relationships and maximum magnitudes on centennial and millennial scales, which can be derived from geological traces and which should be considered in coastal hazard management. We studied a large boulder field along the north coast of Eastern Samar distributed over an elevated reef platform to understand mechanisms of boulder transport and to derive implications for the maximum spatial extent, depth and velocity of coastal flooding. In this paper, we compare the field observations to physical experiments of boulder transport by extreme waves currently undertaken in a flume of the Methods: (i) Documentation of location, shape, morphological features, length, orientation of main axes of >250 boulders (1.5 m<a-axes<11.9 m) in the field; (ii) UAV-based 2D/3D- mapping; (iii) creation of SfM-based models of prominent boulders; (iv) interviewing elders of the local community for past events; (v) inverse modelling of coastal flooding and comparison with Deft3D-based numerical models of Haiyan and Hagupit; (vi) multi-temporal analyses of Pléiades and Worldview-3 scenes to reconstruct boulder movement during recent events; (vii) estimate the age of the carbonate platform and the timing of transport through 230U/Th dating. Preliminary results: (i) the platform’s age is mid-/late Holocene and formed through relative sea-level fall; boulder transport occurred over the late Holocene; (ii) Haiyan and Hagupit shifted boulders up to 115 t in steps of <32 m only at the seaward margin of the boulder field; (iii) transport during Haiyan and Hagupit clearly reflects the individual approaching angle of waves; (iv) size-distance relationships of the entire boulder field are unclear (r2=0.46 at best) and large clasts are located up to 1.3 km from the platform edge indicating that also major long-period waves (infragravity waves, tsunamis) have occurred in the past; (vi) flow velocities of up to 6–7 m/s were inferred for Hagupit, while largest clasts more inland (up to 11.9x8.1x4.2 m3; 433 t) require minimum values >10 m/s.
Located in Library / RBINS Staff Publications 2018
Inproceedings Reference Anthropogenic and environmental controls of barchan dune dynamics in Qatar
Barchan dunes are crescentic aeolian landforms of loose, mostly well-sorted sand with a convex side directed upwind and two horns pointing downwind. Their migration is mainly controlled by sand supply, dune size, wind patterns, vegetation cover and human impact. In Qatar, their distribution is limited to the southeastern part of the peninsula, where they play an important role for tourism and camping activities among locals. We investigate the variability of dune migration in Qatar over a time period of 50 years using high-resolution satellite and aerial imagery. We then explore its relation to the regional Shamal wind system (NNW–SSE), teleconnection patterns, and limitations in sand supply associated with the transgression of the Arabian Gulf, which explain the fact that Qatar is gradually being stripped from aeolian landforms with a remaining dune population in the southeast. Strong size-dependent differences in migration rates of individual dunes as well as significant decadal variability on a dune-field scale are detected, the latter closely correlating with summer Shamal activity. The summer Shamal itself is mainly driven by pressure differences between the stationary anticyclone over the eastern Mediterranean and the established summer heat low over Iran and adjacent areas. It seems to be related to the intensity of the North Atlantic Oscillation and the Indian Summer Monsoon, in particular during years of relatively strong (weak) summer Shamals. High uncertainties associated with the extrapolation of migration rates back into the Holocene, however, do not permit further refining of the timing of the loss of sand supply and the onset of the mid-Holocene relative sea-level (RSL) highstand. For the youngest phase considered in this study (2006–2015), human impact has significantly accelerated dune migration under a more or less stable Shamal regime through systematic sand mining and excessive vehicle traffic upwind of the core study area, which started in 2007.
Located in Library / RBINS Staff Publications 2018
Inproceedings Reference object code Micro-and Macrofossils as indicators of Early Holocene palaeoenvironmental changes in the northwestern Saudi Arabia
Located in Library / RBINS Staff Publications 2018
Inproceedings Reference chemical/x-genbank GEN-EX - Metagenomics of Extreme-Wave Events
Located in Library / RBINS Staff Publications 2018
Inproceedings Reference text/texmacs CARTS - the database of CARibbean Tsunami depositS
Located in Library / RBINS Staff Publications 2018
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