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Inproceedings Reference Doubling the number of high-coverage Neandertal genomes
Over the last few years, the recovery and the analyses of genomes of ancient modern humans, Neandertals, and Denisovans have changed our understanding of the origins, the movements, and the relatedness of archaic and modern human populations. How- ever, in many cases endogenous DNA represents such a small fraction of the DNA extracted from specimens that sequencing of the complete ancient genomes is economically infeasible. Thus, to date, only three Neandertal genomes have been sequenced to high coverage [1-3]. Even though Neandertal genome sequences of low coverage [4] can be used to reconstruct various aspects of Neandertal genetic history, many analyses, for example estimation of population size and levels of inbreeding, rely on the reliable diploid genotypes. Recent studies have shown that certain skeletal elements, such as the inner part of the petrous bone and the ce- mentum layer in teeth [5 and references therein], may preserve DNA better over time. There is also evidence that the preservation of endogenous DNA may vary substantially even within a few millimeters distance in a single specimen [2, 4]. Due to the value and scarcity of ancient hominin remains, it is critical that the smallest possible amount of destructive sampling is involved in the recovery of genetic material. A usual sampling strategy typically involves taking around 50 mg of powder from a single location of a given bone or tooth. We investigated here whether taking multiple smaller samples in a step-wise manner of the Neandertal specimens from the Mezmaiskaya Cave in Russia and the Troisième caverne of Goyet in Belgium may improve the yield of an- cient human DNA. We removed between 8.5 and 27.2 mg of bone powder from a Mezmaiskaya 1 rib fragment, between 2.5 and 35.1 mg from a Mezmaiskaya 2 skull fragment, and between 5.8 and 53.8 mg from the Goyet Q56-1 femur fragment, amounting to between 15 and 38 powder subsets per specimen and an average input of 16.6 mg of powder per extraction. Importantly, to minimize the impact of contamination, we treated each powder aliquot with 0.5\% sodium hypochlorite solution prior to DNA extraction. The DNA extracts from the same specimen varied by several orders of magnitude in their proportion of endogenous DNA (between 0.07\% and 54.7\%), their content of nuclear genomes (between 0.01 and 78-fold coverage), as well as in the levels of present-day human contamination (0.2-50.3\%). There was no significant correlation between the amount of powder used for the extraction and the overall amount of the endogenous DNA or the levels of present-day human DNA contamination. Thus, these results indicate that ancient DNA preservation varies greatly within one specimen and that the removal of multiple, small sub-samples instead of one larger sample, here coupled with a decontamination procedure, can drastically improve the likelihood of isolating large enough amounts of DNA to make whole genome sequencing feasible. This approach allowed us to identify extracts with exceptionally high endogenous DNA content and low levels of present-day human DNA contamination (2\%), enabling us to generate three additional high-coverage Neandertal genomes. The high-quality genome sequences of multiple Neandertals form a unique reference resource for the scientific community and are valuable for analyses that require reliable diploid genotypes and haplotype information. For example, these data open new opportunities to investigate Neandertal population history, to identify genetic variants that arose uniquely on the Neandertal lineage and might have changed through time, and to determine those that may underlie archaic-specific traits or adaptations.
Located in Library / RBINS Staff Publications 2019
Inproceedings Reference Palaeogenomic investigations at the Troisième caverne of Goyet, Belgium
The main excavations at the Troisième caverne of Goyet in Belgium were conducted by Edouard Dupont in 1868 who identified Palaeolithic human occupations later attributed to the Middle and Upper Palaeolithic. These are represented by an archaeologi- cal record that spans the Mousterian, Lincombian-Ranisian-Jerzmanowician, Aurignacian, Gravettian, and Magdalenian, and then extends into the Neolithic and historic periods. Due to the lack of detailed documentation of the excavated materials, their asso- ciation to a specific chronocultural context has been challenging. Morphometric and taphonomic analyses, combined with direct radiocarbon dating as well as isotopic and genetic analyses, were used to assign human remains to either late Neanderthals or an- cient modern humans from different chronocultural groups. In 2016 the first palaeogenetic investigation of Neanderthal specimens from Goyet was published [1]. Taxonomic assignment was confirmed by performing hybridization capture of the mitochondrial DNA (mtDNA) and later inspecting diagnostic mutations at nucleotide positions that distinguish modern humans from Nean- derthals. Moreover, a phylogenetic reconstruction placed seven nearly complete mtDNA sequences from Goyet within the diver- sity of late Neanderthal mtDNA. An around two-fold coverage nuclear genome was later sequenced from one of those individuals (Goyet Q56-1) [2], revealing a high genetic similarity to other late Neanderthals that is well correlated to their geographical dis- tance. Analyzing modern human remains retrieved at Goyet, mtDNA genomes were initially reported for two specimens directly dated to the Aurignacian, five to the Gravettian, and one to the Magdalenian [3]. Aurignacian-related individuals were particu- larly intriguing as they were found to carry mtDNA haplogroup M, which is almost entirely absent in present-day Europeans. For Gravettian- to Magdalenian-related individuals, the shift from U2/U5 to U8 haplogroups was detected locally - as in other regions of Central Europe - likely influenced by the genetic bottleneck during the Last Glacial Maximum (LGM). Furthermore, nuclear sequences of five modern human individuals from Goyet were produced through genome-wide targeted enrichment [4] revealing local replacement between Aurignacian- and Gravettian-related populations. However, the genetic component associated with a 35,000-year-old individual (Goyet Q116-1) reappeared after the LGM, first in Spain and then in other European regions includ- ing in a Magdalenian-related individual from Goyet (Goyet Q-2). This individual was later found to be the best proxy for a genetic component that was largely displaced in Europe from around 14,000 years ago onwards while surviving in high proportion among Mesolithic individuals from Iberia [5]. Here we present new palaeogenetic data of Neanderthal and modern human individuals from this iconic site. First, we expand the molecular taxonomic identifications with three additional Neanderthal specimens and reconstruct their partial mtDNA genomes. Those confirm the general picture of a limited genetic diversity for late Neanderthals, which is also apparent among the Goyet Neanderthals. Second, working on modern human remains, we produced new mtDNA and nuclear data from four Gravettian specimens. They belong to mtDNA haplogroups U2 and U5, further extending the observa- tion of both mtDNA types being largely present in pre-LGM Europe. Moreover, their nuclear genomes provide additional evidence for the genetic affinity between Gravettian-related groups across Europe, from the present-day regions of the Czech Republic to Belgium and Southern Italy. In conclusion, the deep temporal range covered by the human remains from the Troisième caverne of Goyet provides the unique opportunity to describe within a single archaeological site the major genetic transformations that took place in Europe throughout the Middle and Upper Palaeolithic.
Located in Library / RBINS Staff Publications 2019
Inproceedings Reference New Neandertal remains from Trou Magrite, Belgium
Trou Magrite is a cave site located at Pont-à-Lesse in the Lesse Valley, commune of Dinant, Belgium. It has been known since E. Dupont conducted excavations at the site in 1867 [1]. The most recent fieldwork was done by L. Straus and M. Otte in 1991-92 [2]. Trou Magrite yielded rich lithic assemblages, osseous artifacts, mobiliary art, and numerous faunal remains. Several human re- mains were also recovered and identified as Palaeolithic humans by E. Dupont but have been only partially published thus far. The archaeological record covers a broad time range spanning from the Middle and Upper Palaeolithic to the Mesolithic, Neolithic, and Iron Age. An important Middle Palaeolithic collection is present, probably representing several occupation phases during the Late Pleistocene [2]. Unfortunately, although E. Dupont conducted excavations that can be characterized as modern for that time, the materials from the different so-called “fauna-bearing levels” that he defined in the field were mixed post-excavation [3]. In 2015, we initiated a multidisciplinary re-assessment of the human and faunal collections from Trou Magrite in order to update the inven- tory of human remains already identified, check for the presence of human remains that may have been previously overlooked, and verify their chronocultural context. We revised the already known human collection, conducted a systematic sorting of the faunal material, and combined the use of morphometrics, taphonomy, stable isotopes, dating, and genetic analyses to perform taxonomic and chronocultural identifications. Here we present two previously unidentified Neandertal fossils that we isolated from the Trou Magrite faunal material excavated by E. Dupont in the 19th century. They represent two different individuals: an adult/adolescent, represented by an upper right permanent canine, and a neonate, represented by the diaphysis of a left femur. Whereas no endoge- nous DNA was recovered from the tooth, the palaeogenetic analyses of the neonate femur confirmed its Neandertal status and indicate its sex to be male. We will present the biological characteristics and mitochondrial DNA phylogenetic position of the Trou Magrite Neandertals, in particular with regard to the other Northern European Neandertals. Our project adds Trou Magrite to the list of Belgian sites that have yielded Neandertal fossils and helps to emphasize the importance of the Mosan Basin in Neandertal studies.
Located in Library / RBINS Staff Publications 2019
Inproceedings Reference When diet became diverse: Isotopic tracking of subsistence strategies among Gravettian hunters in Europe
Subsistence strategies are key paleoecological features of Paleolithic hunter-gatherers and their deeper understanding provides crit- ical insights into essential aspects of human evolution. In this study, we discuss new collagen stable isotopic values (C, N, S) rep- resenting seven Gravettian individuals from the Troisième caverne of Goyet in Belgium. The dietary strategies of the Gravettian humans from Goyet are in line with the general trends observed among Western European Gravettian populations. These pop- ulations show both a low intake of mammoth and a high consumption of other terrestrial mammals as well as aquatic resources, such as at the sites Arene Candide and La Rochette. This is different for more eastern Gravettian hunter-gatherers, for example in Kostenki, Brno-Francouzska, Mal’ta, Předmostí, and Dolní Věstonice where the dietary contribution of mammoth meat was sig- nificantly higher. The stable isotopic data of the Gravettian humans from Goyet indicate that their dietary ecology was essentially based on terrestrial resources like reindeer, horse, and, to a lesser extent, mammoth. However, they yielded δ15N values that are substantially lower than those of the earlier modern humans and Neandertals from the same site [1-2]. We hypothesize that the Gravettian humans had much less mammoth in their diet than all earlier humans from the same region. It was previously shown that in northwestern Europe a decline of mammoth, a key prey species, could already be detected at the onset of the Upper Paleolithic [2]. This trend appears to continue into the Gravettian, despite the persistence of the typical mammoth ecological niche, which is represented by a grassland with high δ15N values. Interestingly, through isotopic analysis, we are able to track the spread of the horse from the local ecosystem (represented by specimens from Walou Cave, Belgium) into this niche now under-occupied by the mammoth. Radiocarbon dates obtained from several mammoth skeletal remains from the Troisième caverne of Goyet showed that this megaherbivore was indeed part of the ecosystem during pre-LGM periods. However, from the Gravettian in Goyet and the surrounding region we have only one mammoth specimen represented by a long bone, and interestingly, its sulphur isotopic signal indicates that this individual was not of local origin. We propose that the local mammoth population was under intensive hunting pressure or may even have been no longer present in the region. Instead, single individuals from other regions may have made it into the area and ended up as prey animals. While the δ15N values of all Goyet Gravettian humans are relatively homogeneous, their δ13C values are variable. This indicates significant dietary differences among the seven individuals, an observation that has not been described before for hunter-gatherers pre-dating the Gravettian. The human δ34S values also support substantial differences in life mobility history between different individuals, which were not observed for the Goyet Neandertals. The result that different mem- bers of the same chrono-group had various individual mobility histories has implications for land use procurement strategies of those hunter-gatherer groups. In conclusion, our new isotopic results demonstrate a broad ecological flexibility among Gravettian humans, which can be seen in different human ecosystem interactions across Europe. The Goyet individuals contribute substan- tially to a more complete understanding of hunter-gatherer’s ecology during this particular phase of the European Late Pleistocene. Our study shows that the Gravettian cannot be depicted as a uniform entity from an ecological perspective. It instead indicates that during this period, and not earlier, both inter- and intra-group diversity in subsistence strategies can be tracked through stable isotopic analysis.
Located in Library / RBINS Staff Publications 2019
Inproceedings Reference Ammonoids and anoxia from the Belgian Frasnian: the Carrière de Lompret section
Located in Library / RBINS Staff Publications 2018
Inproceedings Reference A double whammy for dinosaurs and ammonites: fake news or the real deal
Located in Library / RBINS Staff Publications 2018
Article Reference Synopsis of Central Andean Orthalicoid land snails (Gastropoda, Stylommatophora), excluding Bulimulidae
Located in Library / RBINS Staff Publications 2016
Article Reference First inventory of Ants (Hymenoptera: Formicidae) with detection of potentially invasive species in National Park of Ehotilés islands, Côte d’Ivoire
Estuarine and wetland ecosystems are becoming increasingly altered by the concentration of human population near the coastline. A major threat to biodiversity related to this is the introduction of invasive alien species. This is particularly the case for isolated ecosystems like islands where the invasion of non-native species is often harmful. The National Park of Ehotilés Islands is an archipelago of 6 islands and a RAMSAR site subjected to disturbances, namely agriculture, illegal fisheries, and tourism. These factors often act as an accelerator for the introduction of invasive species. However, there is a lack of research on insects, specifically ants, on these islands. This study aimed to inventory the present ant fauna and estimate the vulnerability to tramp and potential invasive ant species. Ants were collected using Winkler, pitfall, and funnel traps on five islands. In total, 76 ant species were recorded. These species are distributed into 20 genera and five subfamilies: Dolichoderinae (5 species), Formicinae (11 species), Myrmicinae (49 species), Ponerinae (11 species) and Proceratiinae (1 species). We also detected two tramp and potentially invasive species: the ghost ant Tapinoma melanocephalum and the big-headed ant Pheidole megacephala. Ant communities are dominated by six species, namely Odontomachus troglodytes, Oecophylla longinoda, Nylanderia lepida, Pheidole sp.2, Monomorium invidium, and the invasive ghost ant Tapinoma melanocephalum. This work is the first to inventory ants on the Islands of Ehotilés National Park and may serve as a basis for conservation decisions as it demonstrates that this park is not spared from the introduction of invasive ant species.
Located in Library / RBINS Staff Publications 2024
Article Reference Soil‑litter arthropod communities under pasture land use in southern Rwanda
Land use change caused by human activities is the main driver of biodiversity loss and changes in ecosystem functioning. However, less is known about how the conversion of a natural to pasture land favour the biological diversity of soil-litter arthropods to advance efective conservation plans and management systems. To fll the gap, this study focussed on soil-litter arthropod communities under a pasture land use in southern Rwanda. Data have been collected using pitfall traps and hand collection between April and June 2021. Sampled specimens of soil-litter arthropods have been identifed to order and family levels by using dichotomous keys. Further, the species name was given when the identifcation key was available, while the morphological description was provided in absence of the identifcation keys. Results indicated a total of 3013 individuals of soil-litter arthropods grouped into 3 classes, 13 orders, 46 families and 87 morpho-species. Coleoptera showed a high number of families, while higher abundance and the number of morpho-species were found for ants (Hymenoptera: Formicidae). Higher abundance of sampled soil-litter arthropods is a sign that the studied area ofers suitable habitat for soil-litter arthropods. However, less abundance found for some groups of soil-litter arthropods might be infuenced by the used sampling techniques which were not appropriate for them. We recommend surveys using multiple sampling techniques to maximize chances of capturing a wide range of soil-litter arthropods
Located in Library / RBINS Staff Publications 2022
Article Reference Recent and old records of the rare myrmecophilous beetle Haeterius ferrugineus (Olivier 1789) in Belgium, Luxembourg and North-East of France
Haeterius ferrugineus (Olivier 1789) is a rarely observed histerid beetle which lives permanently in ant nests. We provide the first records of this species in Flanders, the northern part of Belgium, and give an overview of the scattered records for this species in Belgium, Grand-Duché of Luxembourg and the border region in the North of France gathered over the past 150 years.
Located in Library / RBINS Staff Publications 2023