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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
Article Reference Dr Claude Massin (25/08/1948—04/09/2021), in Memoriam
This contribution provides an overview of the scientific career of the late Dr Claude Massin (1948–2021), listing his scientific activities (academic career, participation to and organization of expeditions and scientific conferences, publications) as well as the taxa he described as new to science and the eponyms that were dedicated to him. The scientific career of Claude Massin is briefly sketched against the background of the personal family-life.
Located in Library / RBINS Staff Publications 2021
Article Reference Dragonflies of Cusuco National Park, Honduras; checklist, new country records and the description of a new species of Palaemnema Selys, 1860 (Odonata: Platystictidae)
The odonate fauna of Honduras is poorly documented. Based on 10 years of observations and collections we present an overview of dragonflies from cloud forests in Cusuco National Park, northwestern Honduras. A total of 44 species were reported including at least seven new country records for Honduras we include ecological observations for most species. A new species of Platystictidae (Palaemnema lorae Jocque & Garrison, n. sp. Holotype ♂: HONDURAS: Cortés Dept., CNP, Cantiles, Trail 5, small river close to camp, N15.513457 W88.241681; 1846m, 23 June 2012 collected by Merlijn Jocque, field code: BINCO_HON_12_047, in RBINS) is described and illustrated.
Located in Library / RBINS Staff Publications 2022
Inbook Reference Dredging and dumping
Located in Library / RBINS Staff Publications 2018
Inbook Reference Dredging and dumping
Located in Library / RBINS Staff Publications
Inproceedings Reference Drivers affecting habitat use in Afrotropical hipposiderid and pteropodid bats
Located in Library / RBINS Staff Publications 2023
Article Reference Drivers of morphological evolution in the toothed whale jaw
Located in Library / RBINS Staff Publications 2023
Article Reference Early and Middle Holocene human occupation of the Egyptian Eastern Desert: Sodmein Cave
In this paper, we discuss human occupation during the Early and Middle Holocene in the Eastern Desert of Egypt, based mainly on the data provided by excavated deposits from the Sodmein Cave, which produced an important Holocene stratigraphic sequence. This sequence is dated by a large number of conventional and AMS 14C dates. It appears that the area was empty of human occupation during the Late Glacial Maximum (LGM) and the earliest Holocene. With improved climatic conditions, humans arrived in the area, as hunter-gatherers using no ceramics, from around 7.1 to 6.4 Ka cal BC. Humans were absent from the cave during the Holocene 8.2 Ka event (ca. 6.3 Ka cal BC). From 6.2 to 5.0 Ka cal BC, herders visited the site on a regular basis importing caprines. The bone evidence for domesticated small stock is very limited at Sodmein but is nevertheless extremely important, as it contains the oldest known specimens for Africa to date. After 5.0 Ka cal BC, the area was almost entirely deserted.
Located in Library / RBINS Staff Publications
Article Reference Early and Middle Holocene human occupation of the Egyptian Eastern Desert: Sodmein Cave
Located in Library / RBINS Staff Publications
Article Reference Early Bronze Age population substructure in the Khabur basin: preliminary evidence from Tell Brak, Tell Arbid and Tell Barri (Syria)
Bioarchaeological studies of human remains examine past populations through their mortuary, biological, and socio-cultural contexts. Biological distance, or biodistance, analyses use both genetic and phenetic data to investigate biological relatedness. Biodistance studies frequently employ phenotypic characteristics, or the physical expression of genetic traits that can serve as a proxy for aDNA, to understand evolution, migration, kinship and social organisation. We used phenotypic variation in dental morphology to investigate the population history of the Khabur basin in Syria, during an important period of urbanisation in the Early Bronze Age (EBA, circa 3000-2100 BCE) that shaped the political, social, and economic history of ancient Mesopotamia. Non-metric dental traits from three EBA sites, Tell Brak (n=77), Tell Barri (n=16) and Tell Arbid (n=17), were recorded using the Arizona State University Dental Anthropology System (ASUDAS). Individuals from the sites were compared using the Gower distance matrix and Mean Measure of Divergence (MMD) to examine the difference between sites as population groups. The results suggest that while sites were ancestrally similar, the observed heterogeneity between sites and was related to the socio-political nature of the community. The greatest variation was observed for the samples from Tell Brak and Tell Barri, the capital and the second-rank administrative centre, respectively. Although Tell Arbid showed less variability, some population segmentation was observed between different burial loci.
Located in Associated publications / … / ANTHROPOLOGICA ET PREHISTORICA / Bibliographic references