Search publications of the members of the Royal Belgian institute of natural Sciences
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Microbiomes of aquatic animals
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Developing eDNA metabarcoding as a tool for zero-impact and internationally coordinated biodiversity monitoring
- Human impacts must be managed to minimize the global-scale degradation of natural ecosystems, but doing so requires biodiversity data to track possible changes. Traditional methods for obtaining such data are often destructive and require species being manually identified in a time-consuming and costly manner. High-throughput sequencing technologies now provide an additional method by metabarcoding environmental DNA (eDNA), which is non-destructive and relatively inexpensive. Studies on eDNA metabarcoding show promising results which quickly led to the technique becoming a hot-topic, but also indicate several obstacles for its large-scale application. The RBINS is involved in ongoing research initiatives in the Belgian part of the North Sea applying eDNA techniques to a wide range of organisms to obtain biodiversity data and improve metabarcoding research. We will describe the Belgian ZERO-IMPACT and the international Science for Good Environmental Status projects and present some preliminary results. Whilst eDNA metabarcoding isn’t expected to replace traditional monitoring methods, we can expect it to soon become essential for nations to monitor their marine impacts, including the Marine Strategy Framework Directive.
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Cryptic Diversity, Phylogeography and Genetic Connectivity of Abyssorchomene distinctus (Pacific Ocean and SE Indian Ridge)
- Polymetallic nodule mining is a growing commercial interest over the past three decades. It is critical to accurately estimate biodiversity before any minerals are exploited in the Clarion-Clipperton Zone (CCZ) in the Northeast Pacific Ocean. Scavenging amphipods are a large group in the abyssal biota and play an important role in the nutrient cycling system. This study uses both mitochondrial (COI) and nuclear (28S rRNA) DNA markers to investigate genetic diversity and connectivity in Abyssorchomene distinctus (Lysianassoidea – Uristidae) (Birstein & Vinogradov, 1960). The genetic sequences of 113 sampled individuals of Abyssorchomene distinctus, which originated from the CCZ, the Discol Experimental Area (DEA), the Atacama Trench and the Southeast Indian Ridge, revealed the absence of cryptic diversity for A. distinctus on a global scale. The findings contrasted with those for other closely related scavenging amphipods, which revealed the presence of cryptic species. Population genetics analyses calculated a low haplotype diversity (Hd) within the A. distinctus population across the Pacific Ocean, while a high Hd was found in the Indian Ocean populations. This is the first study to date providing preliminary indications of a possible genetic connectivity of the scavenging amphipod species Abyssorchomene distinctus between the CCZ and DEA, being geographically separated by a vast distance of 5,000 km. Shared haplotypes were also found between the CCZ, DEA, Atacama Trench and the Southeast Indian Ridge in the COI mitochondrial DNA dataset , which was congruent with results from previous studies on other scavenging amphipods.
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The amazing evolutionary diversity of a taxon: Genome sizes of twenty Antarctic amphipod species
- Polar ecosystems feature among the last pristine areas of planet Earth, but also among the fastest changing due to global change. The long isolation history of the Southern Ocean has led to high levels of endemism, resulting in a hotspot of biodiversity for many taxa, including crustaceans (Malacostraca). Genomes represent the blueprint of this long evolution. Geographic isolation in combination with harsh and challenging sampling conditions, has left considerable biological knowledge gaps in the Southern Ocean. Closing these knowledge gaps is challenging for Antarctic amphipods because their genome sizes are highly variable and they are hard to sample. Genome size of amphipods are widely varying, ranging from 0.68 to 64.62 pg with an average of 12.85 pg (± 4.46 pg). Unfortunately, information on the genome size of amphipods remains limited, especially from polar regions. Just 65 records of amphipod genome sizes are listed in the Animal Genome Size Database, of which 17 marine species. To close the knowledge gap, I used flow cytometry to estimate the genome size of 32 Antarctic amphipod species. I successfully estimated genome sizes for 20 species, ranging from 0.45 pg to 57.28 pg (> 120-fold difference). Preliminary analyses do not show any significant correlation between depth and genome size or body size and genome size. The results provide a valuable addition to the inventory of the genome size of amphipods, especially from extreme environments.
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Automated curve fitting and unsupervised clustering of manganese oxide Raman responses
- Natural manganese oxides characterization represents a challenge due to the broad variety of their structures and geochemical compositions along with a frequent poor crystallinity. This characterization requires the ability to conduct both a phase separation and a phase association operation. In this paper, the Raman spectra acquired on a selection of natural manganese oxide minerals are first processed with an automated curve-fitting model called MnOx. The adjustment of convolution envelope is realized, thanks to the Levenberg–Marquardt algorithm applied on a set of randomly generated seed pseudo-Voigt curves. The application conditions of the automated curve-fitting and, in particular, the number of seed curves are investigated with regards to the risk of overfitting. The MnOx model outputs are in a second step treated by data mining techniques and in particular by unsupervised clustering methods. This data processing shows promising results in terms of phase separation when the number of clusters is equivalent to the number of phases. By contrast, the decrease of number of clusters leads to a phase association which reflects spectral affinities between phases. This result shows the existence of 6 to 7 vibrational bands in Mn oxides Raman spectra, with contrasting behaviours between clustering. Thereby, vibrational bands located in the low wave number domain (<510 cm−1) are more mobile and therefore more sensitive to structural modifications, while bands with higher wave number are less affected by structural changes. Besides these results, Raman responses collected during this study provide new refinement regarding the spectral content of some Mn oxides in particular todorokite, nsutite, and chalcophanite.
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PSI analysis of multi-sensor archive data for urban geohazard risk management: a case-study from Brussels
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Subsidence Related To Groundwater Pumping For Breweries in Belgium
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Assessing Vertical Elevation Changes of Coastal Areas in Southern Chile to Improve The Understanding of Their Paleotsunami Sedimentary Records
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ShimoniIGARSS2017
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MAS DE VIGNOLLES XIV (NIMES, GARD, SOUTHERN FRANCE): DIFFERENT PERSPECTIVES ON LAND USE AND MANAGEMENT FROM THE PROTOHISTORY TO THE MIDDLE AGES
- The enlargement of a commercial centre in the vicinity of Nîmes (Southern France) offered evidence on land occupation and exploitation, from the Iron Age to the Middle Ages. The location of the living and working areas, paths and agrarian ‘structures’ uncovered was conditioned by the problematic topography and environment (humid depression; cyclic flooding) as identified by geomorphology and malacology. The diversity of the plant cover and of land management is also recognized by malacology, which emphasizes the importance of animal husbandry and pasture during the whole sequence, in agreement with data from pollen, beetles and domestic fauna. Concentrations of cattle remains rekindle the idea of a hypothetical link between significant consumption of cattle meat and humid areas. The impact of human activities on the plant cover is recognized in the low frequencies of arboreal pollen recorded since the Iron Age; however, fuelwood was apparently readily available as suggested by charcoal data. Further information on economic activities is provided by archaeobotany. The importance of Cannabis sativa and Linum usitatissimum may explain why this “ecologically problematic” area was exploited. Access to water is essential for the processing of plant fibres. Cereal cultivation, better recognized by palynology than by archaeobotany, appears to suffer fluctuations through time. The remains of Vitis constitute the first material proof of local vine cultivation during the Middle Ages.
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THEY ALL SMELL THE SAME (THOUGH...) BUT THEIR CONTENT MAY BE DIFFERENT: LOOKING AT LATE MEDIEVAL HUMAN EXCREMENTS AND GARBAGE PITS IN THE COUNTY OF HAINAUT, SOUTHERN LOW COUNTRIES
- Human excrements and garbage pits of two archaeological sites in the County of Hainaut (Southern Low Countries, Belgium) have been studied by the interdisciplinary team “Archaeo sciences” of the RBINS. Stone walled latrines dating from the 14th century have been uncovered at the site of Chièvres, while several garbage pits dating from the 12th to the 16th century were excavated at the site of “rue des Bouchers-Saint Jacques” in the city of Tournai. We are presenting the 14th century composition of the waste contexts for the two sites and a diachronic composition’s evolution for the garbage pits of “rue des Bouchers-Saint Jacques”. Archaeobotanical (seeds and fruit, wood and wood charcoal, pollen, spores and NPPs) and archaeozoological studies show that, in the majority, they contain digested food residues, food scraps and also some scarce remains of other non-food residues. The most common taxa found are vegetables, condiments, wild and/or cultivated fruits, cereals, fish and mammal remains. But if we look more closely, some cesspits contain outstanding elements such as honey (the first mention in Wallonia for the medieval period), waste of cereal processing that may have been used for the sanitation of such structures. This paper aims at: 1 / highlighting late Medieval period human food intake of the Southern Low Countries 2 / comparing data between two 14th century waste contexts and finally, 3 / showing differences in pit fillings, indicating different structure maintenance and/or different social status.
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Un manuel de terrain pour standardiser les prélèvements des restes biologiques : une nécessité ou un luxe ? trois années d’expérience belge
- Sur un chantier de fouille, l’archéologue est très fréquemment confronté à des vestiges organiques, ou biorestes. Qu’ils soient visibles ou invisibles, rares ou abondants, ils sont souvent source de questionnements : que prélever ? Où, comment et en quelle quantité ? Quelles sont les conditions de stockage idéales ¬? Quelle est la marche à suivre pour tamiser les sédiments ? Confrontés à des prélèvements très disparates, souvent à vue, ou sans réelle question de recherche ainsi qu’à des méthodologies d’extraction très différentes, l’équipe d’archéosciences de l’Institut royal des Sciences naturelles de Belgique a décidé de rédiger un ouvrage visant à répondre aux questions des archéologues et à standardiser les processus d’échantillonnage afin de pouvoir disposer d’un matériel d’étude pertinent et cohérent. Nous mentionnerons les problématiques qui ont concouru à la genèse de ce manuel par quelques exemples de terrain, parcourrons rapidement ce qu'il propose et ce qu'il n'aborde pas et ferons un bilan de son impact auprès des archéologues quelques années après sa première parution fin 2016.
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Evaluations palynologique, xylologique et antracologique des puits gallo-romains de Warnach (Fauvillers)
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Analyses palynologiques de Chièvres - Eglise Saint-Martin Latrines du 14e siècle (Moyen Âge, Hainaut)
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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.
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Where are we now with European forest multi-taxon biodiversity and where can we head to?
- The European biodiversity and forest strategies rely on forest sustainable management (SFM) to conserve forest biodiversity. However, current sustainability assessments hardly account for direct biodiversity indicators. We focused on forest multi-taxon biodiversity to: i) gather and map the existing information; ii) identify knowledge and research gaps; iii) discuss its research potential. We established a research network to fit data on species, standing trees, lying deadwood and sampling unit description from 34 local datasets across 3591 sampling units. A total of 8724 species were represented, with the share of common and rare species varying across taxonomic classes: some included many species with several rare ones (e.g., Insecta); others (e.g., Bryopsida) were repre sented by few common species. Tree-related structural attributes were sampled in a subset of sampling units (2889; 2356; 2309 and 1388 respectively for diameter, height, deadwood and microhabitats). Overall, multi taxon studies are biased towards mature forests and may underrepresent the species related to other developmental phases. European forest compositional categories were all represented, but beech forests were over represented as compared to thermophilous and boreal forests. Most sampling units (94%) were referred to a habitat type of conservation concern. Existing information may support European conservation and SFM strategies in: (i) methodological harmonization and coordinated monitoring; (ii) definition and testing of SFM indicators and thresholds; (iii) data-driven assessment of the effects of environmental and management drivers on multi-taxon forest biological and functional diversity, (iv) multi-scale forest monitoring integrating in-situ and remotely sensed information.
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Taphonomy of marine vertebrates of the Pisco Formation (Miocene, Peru): Insights into the origin of an outstanding Fossil-Lagerstätte
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Collagen stable isotopes provide insights into the end of the mammoth steppe in the central East European plains during the Epigravettian
- Higher δ15N values in bone collagen of mammoth (Mammuthus primigenius) compared with coeval large herbivores is a classic trait of the mammoth steppe. An exception applies to the Epigravettian site of Mezhyrich (ca. 18–17.4 ka cal BP) in the central East European plains, where mammoth bones have δ15N values equivalent to or in a lower range than those of horse specimens (Equus sp.). We expanded our preliminary dataset to a larger sampling size of mammoth, other large herbivores, and carnivores from contemporaneous and nearby sites of Buzhanka 2, Eliseevichi, and Yudinovo. The unusual low mammoth δ15N values were confirmed at Buzhanka 2 and for some specimens from Eliseevichi, while most individuals from Yudinovo displayed the expected high δ15N values, meaning similar to those of the large canids. The possibility of a contrast in migration pattern is not supported since the δ34S values, a marker of mobility, do not correlate with the δ15N values of mammoth bone collagen. No clear chronological tendency could be revealed, at least not at the scale of radiocarbon dating. The low range in δ15N values is likely to reflect a change in the specific niche of the mammoth in the southern part of its distribution.
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De wolharige mammoet in België
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Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda
- Mitochondrial DNA hyperdiversity is primarily caused by high mutation rates (µ) and has potential implications for mitogenome architecture and evolution. In the hyperdiverse mtDNA of Melarhaphe neritoides (Gastropoda: Littorinidae), high mutational pressure generates unusually large amounts of synonymous variation, which is expected to (1) promote changes in synonymous codon usage, (2) reflect selection at synonymous sites, (3) increase mtDNA recombination and gene rearrangement, and (4) be correlated with high mtDNA substitution rates. The mitogenome of M. neritoides was sequenced, compared to closely related littorinids and put in the phylogenetic context of Caenogastropoda, to assess the influence of mtDNA hyperdiversity and high µ on gene content and gene order. Most mitogenome features are in line with the trend in Mollusca, except for the atypical secondary structure of the methionine transfer RNA lacking the TΨC-loop. Therefore, mtDNA hyperdiversity and high µ in M. neritoides do not seem to affect its mitogenome architecture. Synonymous sites are under positive selection, which adds to the growing evidence of non-neutral evolution at synonymous sites. Under such non-neutrality, substitution rate involves neutral and non-neutral substitutions, and high µ is not necessarily associated with high substitution rate, thus explaining that, unlike high µ, a high substitution rate is associated with gene order rearrangement.
