Search publications of the members of the Royal Belgian institute of natural Sciences
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The Merksplas Formation
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Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing
- Abstract Background Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. Results In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Conclusions Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
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Preference for fish in a Neolithic hunter-gatherer community of the upper Tigris, elucidated by amino acid δ15N analysis
- We report here the stable nitrogen isotope composition (d15N) of individual amino acids and the d15N and d13C content of collagen from human and faunal remains collected from Hasankeyf H€oyük, an early Neolithic site in the upper Tigris valley. Based on the d15N of collagen only, the contributions of freshwater resources to the diet of the hunter-gatherers were difficult to clearly identify relative to terrestrial resources. However, analysis of the nitrogen isotope composition of individual amino acids enabled the identification of minor contributions from freshwater resources to the diet in a community primarily dependent on terrestrial resources. Individual variability suggested that some individuals at Hasankeyf H€oyük used freshwater resources, whereas others probably depended primarily on terrestrial food resources. The importance of freshwater resources as food for this hunter-gatherer community was variable among groups and depended on burial location and time of burial.
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More animal burials from the Predynastic elite cemetery of Hierakonpolis (Upper Egypt): the 2008 season
- Three animal burials from the Predynastic elite cemetery HK6 at Hierakonpolis are described. Recent excavations at this site have revealed large tomb compounds and a precinct of funerary temples dating to the Naqada IC–IIB (ca. 3800–3600 BC), all of which included animal burials. Shallow pits discovered by the enclosure wall of the cemetery and near the northeast corner of the temple precinct yielded the articulated skeletons of nine dogs, a baboon and six cats. A description of the finds is provided and special attention is given to the size reconstruction and possible breeds of the dogs, the pathology seen on the baboon skeleton and its interpretation in terms of conditions of keeping, and the status of the cats (wild, tamed or domestic).
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An unusual cattle burial at Dayr al-Barshā (Late Period, Middle Egypt)
- During excavations in the desert plain near Dayr al-Barshā in Middle Egypt, a circular pit filled with cattle bones was found. The pit, with a diameter of about 1.5m, contained the almost complete skeletons of 15 Egyptian Longhorns, dated to 410–360 cal BC. The material was in a remarkably good state of preservation, but few elements were found in articulation. Apart from the more-or-less complete skeletons, some fragmentary remains of at least three additional individuals have been collected. The age at death, sex and size of the animals has been established and the pathologies and traces on the bones have been recorded. No parallels are known for the cattle burial at Dayr al-Barshā. The animals were probably kept in the context of a local temple economy. In line with common practices at that time, their bodies were macerated and the obtained skeletons ceremonially buried later on.
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Archaeozoology in Sub-Saharan Africa. . In: A. Smith Livingstone, E. Cornelissen, O. Gosselain, S. MacEachern (eds) Field Manual for African Archaeology. Tervuren: RMCA, series ‘Documents on Social Sciences and Humanities’, pp. 210-213
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L’archéozoologie en Afrique subsaharienne. In: A. Smith Livingstone, E. Cornelissen, O. Gosselain, S. MacEachern (eds) Manuel de terrain en Archéologie africaine. Tervuren: MRAC, collection «Documents en Sciences humaines et sociales», pp. 210-213
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De dierenresten
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Final reporting on COMPMON project – MARPOL Annex VI enforcement (2014-16)
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Characterization of the underwater sound emitted during the installation of monopile steel foundation at Nobelwind offshore windfarm and cumulative effects
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Description of three new species of Leptotrophon Houart, 1995 (Gastropoda: Muricidae: Trophoninae) from New Caledonia
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A taxonomic update of the Typhinae (Gastropoda: Muricidae) with a review of New Caledonia species and the description of new species from New Caledonia, the South China Sea and Western Australia
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Glacial melt impacts carbon flows in an Antarctic benthic food web.
- Most coastal glaciers on the West Antarctic Peninsula are in retreat. Glacial ice scouring and lithogenic particle runoff increase turbidity and shape soft sediment benthic communities. This, in turn, has the potential to induce a shift in these systems from an autotrophic to a heterotrophic state. In this study, we investigated the influence of glacial runoff on carbon flows in the softsediment food web of Potter Cove, a well-studied shallow fjord located in the northern region of the West Antarctic Peninsula. We constructed linear inverse food web models using a dataset that includes benthic carbon stocks as well as carbon production and respiration rates. The dataset offers detailed spatial information across three locations and seasonal variations spanning three seasons, reflecting different degrees of disturbance from glacial melt runoff. In these highly resolved food web models, we quantified the carbon flows from various resource compartments (phytoplankton detritus, macroalgae, microphytobenthos, sediment detritus) to consumers (ranging from prokaryotes to various functional groups in meio- and macrofauna). Locations and seasons characterized by high glacial melt runoff exhibited distinct patterns of carbon flow compared to those with low glacial melt runoff. This difference was primarily driven by a less pronounced benthic primary production pathway, an impaired microbial loop and a lower secondary production of the dominant bivalve Aequiyoldia eightsii and other infauna in the location close to the glacier. In contrast, the bivalve Laternula elliptica and meiofauna had the highest secondary production close to the glacier, where they are exposed to high glacial melt runoff. This study shows how the effects of glacial melt propagate from lower to higher trophic levels, thereby affecting the transfer of energy in the ecosystem.
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Review of the Oriental stick insect genus Trachythorax Redtenbacher, 1908 with two new species from Vietnam and comments on egg parasitism and morphological counteradaptations (Phasmida, Lonchodidae, Necrosciinae)
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Noteworthy and New Muricidae (Gastropoda) Collected in the East and South China Seas and off Taiwan
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New species and genera of Muricidae (Mollusca: Gastropoda) from New Zealand
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Ammonite death and nautilus survival at the Chicxulub massacre: here’s what we know so far
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Rapid biological recovery following the Cretaceous-Paleogene boundary catastrophe in the Maastrichtian type area
- Present-day marine biotas are increasingly subject to anthropogenically-forced extinctions. The study of the global mass extinction event at the Cretaceous-Paleogene (K-Pg) boundary can aid in our understanding of the patterns of selective extinction and survival and the dynamics of ecosystem recovery. Outcrops in the Maastrichtian type region (The Netherlands, Belgium) comprise an expanded K-Pg boundary succession, presenting a unique opportunity to study marine ecosystem recovery within the first thousands of years following the Chicxulub impact. We have reevaluated and studied the palynological, micro- and macropalaeontological record of this unique succession. Ecosystem changes across the K-Pg boundary in this region are rather limited, showing a general shift from epibenthic filter feeders to shallow-endobenthic deposit feeders. The fauna of the lowermost Paleocene still has many ‘Maastrichtian’ characteristics, a biological assemblage that survived the first hundreds to thousands of years into the earliest Paleocene. The shallow-marine oligotrophic carbonate sea of the Maastrichtian type area as inhabited by starvation-resistant, low nutrient-adapted taxa, that were seemingly less affected by the shortlived detrimental conditions of the K-Pg boundary catastrophe, such as darkness, cooling, food-starvation, ocean acidification, resulting in relatively high survival rates. The high survival rate allowed for a fast recolonization and rapid recovery of marine faunas in the Maastrichtian type area.
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CO2-enhanced oil recovery and CO2 capture and storage: An environmental economic trade-off analysis
- CO2 enhanced oil recovery can play a significant role in stimulating carbon capture and storage because of additional oil revenues generated. However, it also leads to additional greenhouse gas emissions. We estimate the global warming potential of different CO2 capture scenarios with and without enhanced oil recovery. During a 10 year period in which oil and electricity are produced without CO2 being captured, the global warming potential is 11 MtCO2 equivalents. We show that if CO2 is captured and used for 15 years of enhanced oil recovery, the global warming potential decreases to 3.4 MtCO2 equivalents. This level is 100% higher compared to the scenario in which the captured CO2 would be stored in an offshore aquifer instead. If the capture of CO2 is stopped when the oil reservoir is depleted, the global warming potential resulting from 10 years electricity production is 6 MtCO2 equivalents. However, if CO2 is stored in the depleted reservoir, the global warming potential is six times lower during that period. Electricity production and oil refining are the main contributors to the global warming potential. The net present value analysis indicates that for CO2 prices lower than or equal to 15 €/t and oil prices greater than or equal to 115 €/t, it is most profitable to capture CO2 for enhanced oil recovery only. Because of the low CO2 price considered, large incomes from oil production are required to stimulate CO2 capture. The environmental economic trade-off analysis shows that if CO2-enhanced oil recovery is followed by CO2 capture and storage, costs increase, but the net present value remains positive and the global warming potential is reduced. Authorities could use these outcomes to support the development of economic mechanisms for shared investments in CO2 capture installations and to mandate both oil producer and large CO2 emitting firms to store CO2 in depleted oil fields.
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Reply to Van Peer: Direct radiocarbon dating and ancient genomic analysis reveal the true age of the Neanderthals at Spy Cave
- Van Peer (1) contests the conclusions of our article on Neanderthal disappearance in Northwest Europe (2), but we think his argument may reflect a misunderstanding of the stratigraphy at Spy Cave and/or incomplete reading of our article. We provide here a response to his arguments.The idea that the discovery time of the Neanderthal bones impacts the results is not scientifically valid and indicates an incomplete review of the literature. Among the oldest radiocarbon dates obtained on the Spy Neanderthals are those measured on collagen from material collected on the slope: Spy 737a (OxA-10560) and Spy 94a (GrA-32623) (3, 4). In addition, although found on the slope, the maxillary …
