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Article Reference Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
The highly diverse snake superfamily Elapoidea is considered to be a classic example of ancient, rapid radiation. Such radiations are challenging to fully resolve phylogenetically, with the highly diverse Elapoidea a case in point. Previous attempts at inferring a phylogeny of elapoids produced highly incongruent estimates of their evolutionary relationships, often with very low statistical support. We sought to resolve this situation by sequencing over 4,500 ultraconserved element loci from multiple representatives of every elapoid family/subfamily level taxon and inferring their phylogenetic relationships with multiple methods. Concatenation and multispecies coalescent based species trees yielded largely congruent and well-supported topologies. Hypotheses of a hard polytomy were not retained for any deep branches. Our phylogenies recovered Cyclocoridae and Elapidae as diverging early within Elapoidea. The Afro-Malagasy radiation of elapoid snakes, classified as multiple subfamilies of an inclusive Lamprophiidae by some earlier authors, was found to be monophyletic in all analyses. The genus Micrelaps was consistently recovered as sister to Lamprophiidae. We establish a new family, Micrelapidae fam. nov., for Micrelaps and assign Brachyophis to this family based on cranial osteological synapomorphy. We estimate that Elapoidea originated in the early Eocene and rapidly diversified into all the major lineages during this epoch. Ecological opportunities presented by the post-Cretaceous-Paleogene mass extinction event may have promoted the explosive radiation of elapoid snakes.
Located in Library / RBINS Staff Publications 2023
Article Reference Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.
Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4\% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.
Located in Library / RBINS Staff Publications 2019
Article Reference Optimal timing of multiple investment decisions in a wood value chain: A real options approach
Located in Library / RBINS Staff Publications 2021
Article Reference Economic feasibility studies for Carbon Capture and Utilization technologies: a tutorial review
Carbon Capture and Utilization (CCU) involves the capture and use of CO2 as a resource to create valuable products. The competitiveness of various CCU technologies has been investigated frequently resulting in a variety of economic feasibility studies and economic indicators. This study performs a tutorial review, in which practical guidance is given on the implementation of Techno-Economic Assessments (TEAs) for chemical CCU technologies. The tutorial review maps the differences in the methods and assumptions of economic feasibility studies for CCU technologies and advises how these studies can be improved in the future. A TEA framework, drafted by the CCU research community, is used as a benchmark in this review, to allow for objective comparisons between various economic feasibility studies. The four phases of an exhaustive TEA are (I) goal and scope, (II) data inventory, (III) calculation of indicators and (IV) interpretation. The tutorial review reveals that economic feasibility studies for chemical CCU technologies can and should be improved in various manners. Phases I and II are often skipped or incomplete. In Phase III, a very diverse indicator set is observed, which hampers comparability across CCU technologies. Phase IV, the interpretation of results, is often missing in the literature set or lacks thorough uncertainty and sensitivity analyses. The comparison with the TEA framework revealed the diversity in assumptions and methodological choices in the literature set. These findings suggest that future economic feasibility studies should be made in a more standardized way to improve both the quality and comparability of economic feasibility studies. Four improvements to the TEA framework are suggested: (i) focussing more on the impact of technical parameters in sensitivity analyses, (ii) adapting the assessment to the TRL of the technology, (iii) implementing ROA in the TEA and (iv) integrating an environmental assessment or LCA with the TEA. Further research is needed to investigate how Real Options Theory can be integrated into conventional TEA frameworks to analyse the investment decision in CCU technologies in a dynamic setting.
Located in Library / RBINS Staff Publications 2021 OA
Article Reference Explaining Uncertainty Avoidance in Meciaprojects: Resource Constraints, Strategic Behaviour, or Institutions?
Located in Library / RBINS Staff Publications 2021
Article Reference Leasing out unused meeting room capacity to reduce future office space needs: A case study of The Hague, Netherlands
Located in Library / RBINS Staff Publications 2021
Article Reference Investment Decisions with Two-Factor Uncertainty
Located in Library / RBINS Staff Publications 2021
Article Reference New insights into Late Devonian vertebrates and associated fauna from the Cuche Formation (Floresta Massif, Colombia)
Located in Library / RBINS Staff Publications 2019
Article Reference Scheenstia bernissartensis (Actinopterygii: Ginglymodi) from the Early Cretaceous of Bernissart, Belgium, with an appraisal of the ginglymodians evolutionary history
Located in Library / RBINS Staff Publications 2019
Article Reference Dietary reconstruction of Spy I using dental microwear texture analysis
Spy I from the Meuse River Basin of Belgium is among the most recent Neandertals. This adult lived at the terminus of Marine Isotope Stage (MIS) 3 in cold steppe environments at the northern edge of the habitable zone for Neandertals where plants were relatively scarce. The dietary proclivities of Spy I are reconstructed using dental microwear texture analysis and compared to 33 Neandertals from western Eurasia, MIS 5 to MIS 3. Spy I has an elevated enamel surface complexity suggesting the consumption of course dietary items such as wild seeds, acorns, nuts, and underground storage organs laden with particles of grit. Unlike the young and old individuals from Hortus with low values for anisotropy, Spy I is closest to the adults from this site suggesting a common pattern of masticatory behavior typified this life cycle stage. Like many other Neandertals, Spy I probably consumed plant foods at appreciable levels, some of which were hard and brittle or poorly processed.
Located in Library / RBINS Staff Publications 2019