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Microbiomes of aquatic animals
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RBINS Staff Publications 2023
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Automated curve fitting and unsupervised clustering of manganese oxide Raman responses
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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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RBINS Staff Publications 2017
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Publishing data to support the fight against human vector-borne diseases
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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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RBINS Staff Publications 2022
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Where are we now with European forest multi-taxon biodiversity and where can we head to?
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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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RBINS Staff Publications 2023
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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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RBINS Staff Publications 2021
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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
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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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RBINS Staff Publications 2018
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Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda
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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.
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RBINS Staff Publications 2018
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A scientific name for Pacific oysters
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RBINS Staff Publications 2018
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The Devonian–Carboniferous boundary in Belgium and surrounding areas
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The Devonian–Carboniferous boundary is associated with a major extinction event of the Phanerozoic. It was also a time marked by a rapid but short-lasting change in deposition called Hangenberg Event. In the Namur–Dinant Basin the uppermost Devonian (‘Strunian’) deposits recorded a third-order transgression that produced a progressive switch from coastal siliciclastic to proximal mixed deposits with an increase of the carbonate production on the ramp. Hence, the Comblain-au-Pont and lower Hastière formations are considered as the transgressive system tract, whereas the middle member of the Hastière Formation is interpreted as the highstand system tract, capped by an erosion surface corresponding to the third-order sequence boundary. Superimposed on these third-order sequences are well-marked orbitally forced precession cycles (wet–dry climate alternations) of c. 18.6 ka, appearing as irregular c. 30–80-cm-thick couplets of limestone and calcareous shale beds. The Hangenberg Black Shale Event is locally present as dark shales that likely spread over the shelf, marking the maximum flooding surface of the sequence. Before and after this event, carbonate facies rich in benthic macrofauna and microfauna continued to develop. The Hangenberg Sandstone Event, appearing as a sandstone bed in pelagic sections, is variously recorded at the base of the Hastière Formation, either as a sandy siltstone bed in proximal sections or as a horizon with limestone clasts and reworked fossils in more distal settings. The Hangenberg Sandstone Event beds occur sharply in the stratigraphic record and do not correspond to the long sea level fall of a third-order sequence boundary, but most probably to a short out-of-sequence event. The revision of the stratigraphic distribution of major fossil groups pleads for a continuous biostratigraphic succession with no obvious hiatus. The variable development of some micropalaeontological zones at the end of the Devonian is the result of complex ecobiostratigraphic interactions with the environment rather than the reflection of true hiatuses. It is marked by extinctions of Devonian taxa, concomitantly with the end of the reworking produced by the Hangenberg Sandstone Event, most probably immediately below the entry of the conodont Protognathodus kockeli. It is also coincident with the boundary between the foraminiferal zones DFZ7–MFZ1, rugose coral zones RC0–RC1 and between the palynozones LE–VI. After the short-lasting regressive phase of the Hangenberg Sandstone Event, normal depositional settings returned with the deposition of the Hastière Formation. Hence, the end of the Hangenberg Sandstone Event is proposed as the most natural proxy to pinpoint the Devonian– Carboniferous boundary.
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RBINS Staff Publications 2020
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A new basal ornithopod dinosaur from the Lower Cretaceous of China
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RBINS Staff Publications 2020
