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Article Reference Octet Stream Combined High-Throughput Imaging and Sequencing: Addressing the collections on demand requirement in SYNTHESYS+ project
Imagine you are a scientist, working on collections. You have your pet taxon and you need information which is distributed in a number of books and publications but also in the specimens deposited in Museums or Herbaria. Instead of paying visits to these establishments, around the world, you wish there was a means to transform all the information you need into a digitized form of the physical objects, you can reach from the screen of your laptop, tablet or cell phone. You dream you were able to watch, inspect and even dissect the type material you need online but also to compare it with others they way sequences are blasted against large databases, these days. You plan to make global research on this taxon and try to derive patterns from both the molecular and organismal level of the biological organization and to link the patterns resulting to the drivers of change for this taxon. This is the vision of the Virtual Museum of Natural History and one of the ways to achieve this vision is to address the “collections on demand” requirement. One of the possible means to address this requirement is the digitization through the use of the micro-ct technology. The micro-CT virtual laboratory (vLab), developed by LifeWatchGreece research infrastructure (RI), makes it possible the online exploration and dissemination of micro-CT datasets, which are only rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. This presentation shows the development of such a “collections on demand” function, implemented by the SYNTHESYS+ project (DiSSCo RI), which combines such high-throughput technologies, that is micro-ct and genomics, to address the scientific community’s requirements. We show that this approach to combine patterns deriving from the application of novel techniques, which represent different kinds of observations is possible and we propose certain case studies as examples. The innovation aspects of this function include: Expansion and development of cost models for Collections on Demand; Development of standards and guidelines for exchange of collection-derived imaging data; Construction of new data pipelines and standard workflows, enabling access to complex digital content such as 3D scans; Development of novel molecular lab protocols, workflows and informatics pipelines, to enable large scale; DNA sequencing of NH collections.
Located in Library / RBINS Staff Publications 2019
Inproceedings Reference A diverse Miocene toothed whale (Odontoceti) fauna from Calvert Cliffs, Atlantic Coastal Plain, U.S.A.
Located in Library / RBINS Staff Publications 2019
Inproceedings Reference Early dispersal for quadrupedal cetaceans: an amphibious whale from the middle Eocene of the southeastern Pacific
Located in Library / RBINS Staff Publications 2019
Inproceedings Reference New fossils of paroxyclaenids (Placentalia, Mammalia) from the early Eocene of France shed light on the origin and evolution of these endemic European mammals
Paroxyclaenidae is an enigmatic archaic group of middle size placental mammals. They are known only from Europe, and are recorded from the early Eocene (Ypresian) to the middle Eocene (Bartonian). Paroxyclaenids are divided into two distinct subfamilies: Paroxyclaeninae and Merialinae. They have been variously placed by different authors in Carnivora, Creodonta, ‘Condylarthra’, and Insectivora, but are considered since 1970’s as members of Pantolesta. The dentition of paroxyclaenids is complete (4 premolars, 3 molars); it is highly specialized, with relatively enlarged posterior premolars, spaced out cheek teeth, but primitive, for instance, in the absence of hypocone on upper molars. The molars decrease in size from M1/m1 to M3/m3; the M3 and m3 are sometimes well reduced. A particularity of the dentition of some paroxyclaenids is the tendency to enlargement and molarisation of the third and fourth upper and lower premolars, generally exceeding the succeeding molars in size. We recently studied unpublished fossils from the first half of the Ypresian: these fossils originate from the French localities of Le Lien (Hérault), Pourcy, Mutigny, Avenay (Marne), and Condé-en-Brie (Aisne). They allow to describe new specimens of Merialus martinae (the oldest paroxyclaenid) and three new species – the oldest paroxyclaenine and two merialines. Their study is the opportunity to review the evolution of this family – the last extensive and comprehensive review of the paroxyclaenids has been published in 1988. The two paroxyclaenid subfamilies – Paroxyclaeninae and Merialinae – are rarely recorded together: this case only occurs in the Paris Basin during the early Eocene (Mutigny, Avenay, Condé-en-Brie). Half of the merialines are present in the Southern European Province, while the paroxyclaenines are only recorded in Northern European Province. The two subfamilies reach their maximum size (+/- 3-4 kg) (e.g., Spaniella, Kopidodon) around the early/middle Eocene boundary (47.8 Myr). However, some smaller paroxyclaenids (body mass around 1 kg) have co-existed together with the larger ones. The small middle Eocene paroxyclaenids, which are as small as the taxa found in the early Eocene, have been the last representatives of the group (Bartonian). The maximum of diversity of the Paroxyclaenids occurred during the Lutetian (middle Eocene). Finally, because the new fossils provide information on the morphology of the earliest paroxyclaenids, their study is the opportunity to question the origin of this group and its relationships among Placentalia. Grant Information: This abstract is a contribution to the project BR/121/A3/PALEURAFRICA funded by the Belgian Science Policy Office.
Located in Library / RBINS Staff Publications 2017
Inproceedings Reference Platychelone emarginata gigantic Cretaceous marine turtle from Belgium
Platychelone emarginata Dollo, 1909 is a large turtle from the Late Cretaceous (Maastrichtian) chalk sediments of Limburg, Belgium. Hitherto, only the name was given to this turtle without describing details or providing figures. A single well articulated carapace (IRScNB. Reg. 1681), lacking nuchal, peripherals, and pygal plates, is preserved. The distance from the first costal to the distal end of the eighth costal is 180 cm, indicating that the original carapace was about 210 cm long. Its gigantic size, flattened shell, reduction of distal half of costals, and loss of scute sulcus, indicate that Platychelone is a member of true marine turtles (superfamily Chelonioidea). Neurals are rectangular shape and inclination of the first thoracic vertebra is almost vertical, suggesting this turtle belongs to either Protostegidae or Dermochelyidae. Seventh and eighth costals are medially meeting due to the loss of neurals; this condition is shared with the genus Mesodermochelys from the Late Cretaceous (Santonian to Maastrichtian) of Japan. Thus, it seems most probable that Platychelone is a closest relative of Mesodermochelys among basal dermochelyids. Platychelone has presumed autoapomorphic characters such as very thickened distal ends of thoracic ribs and irregular sculptures on carapace, not seen in any other chelonioids. This genus is only known by the holotype, whereas Allopleuron hoffmanni, a very common cheloniid marine turtle from in the Maastrichtian deposits of Belgium and Netherland, is known from some hundred specimens. So far, there is no ancestral or related taxon of Platychelone from the Campanian deposits of Belgium. The occurrence of Platychelone is very rare but evokes a high taxonomic diversity of gigantic chelonioids in the Cretaceous Tethys.
Located in Library / RBINS Staff Publications 2017
Inproceedings Reference The small-mammal assemblage from Caverne Marie-Jeanne (Hastière-Lavaux, Belgium): environmental and climatic approach of the marine isotope stage 3 in North-Western Europe
Small mammal faunas from the Pleistocene of Belgium are not well-known. Some have been studied from the second half of the Late Pleistocene and the Early Holocene. However, only a few sites from the first half of the Late Pleistocene (Marine Isotope Stage 3, MIS 3, ca. 60-30 ka) have yielded small mammal assemblages. Among them is the Marie-Jeanne Cave that is situated in the southeast of Belgium, in the Ardennes region. It is formed in the Early Carboniferous limestone deposits above the Meuse River, near the town of Hastière-Lavaux. The excavated deposits evidenced ten different layers but only the layers 6 to 2 yieldeda large collection of faunal remains. Recent dating of the stratigraphic sequence of the Marie-Jeanne Cave shows that these layers have a chronological range pertaining to MIS 3 (about 50-40 ka BP). During the first field campaign in 1943, about 40 m3 of sedimentswereextracted recovering a large collection of disarticulated bone fragments and several plant, mollusc and archaeological remains housed at the RBINS. A first study of this material underlined the presence of 29 taxa of insectivores, bats and rodents. The recent revision of the material revealed 9897 identified specimens, corresponding to a minimum of 4980 individuals. This permitted us to add to the previous list two vole species, the steppe lemming Lagurus lagurus and the European pine vole Microtus (Terricola) subterraneus. We also undertook new paleoenvironmental and paleoclimatic reconstructions based on alternative methods from those previously used for the MIS 3 sequence of the Marie-Jeanne Cave. Our results indicate that MIS 3 is characterized by dynamic alternations of forest expansion with semiarid area expansion in accordance with the warming and cooling, respectively, of the sea-surface temperatures. It was in this context of rapid fluctuations that the terrestrial sequence of the Marie-Jeanne Cave in north-western Europe was formed. The fossiliferous layers underwent cold and dry environmental and climatic conditions. This is indicated by lower temperatures and slightly higher precipitation than today, together with an environment dominated by open woodland formations and open dry meadows. Our results are consistent with the available chronological, large-mammal, herpetofaunal, and mollusc datasets for this lower part of the sequence. They are also consistent with regional loess studies in Belgium and with previous work performed on small mammals from MIS 3 in Belgium and elsewhere in Europe. Grant Information: Generalitat de Catalunya projects, Synthesis Grants, PhD grant of the Erasmus Mundus Programme - International Doctorate in Quaternary and Prehistory.
Located in Library / RBINS Staff Publications 2017
Inproceedings Reference Climate change impact on wind, waves and surges
Located in Library / RBINS Staff Publications 2019