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| 2. |
- Abel, I, et al.
(författare)
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Overview of the JET results with the ITER-like wall
- 2013
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 53:10, s. 104002-
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Tidskriftsartikel (refereegranskat)abstract
- Following the completion in May 2011 of the shutdown for the installation of the beryllium wall and the tungsten divertor, the first set of JET campaigns have addressed the investigation of the retention properties and the development of operational scenarios with the new plasma-facing materials. The large reduction in the carbon content (more than a factor ten) led to a much lower Z(eff) (1.2-1.4) during L- and H-mode plasmas, and radiation during the burn-through phase of the plasma initiation with the consequence that breakdown failures are almost absent. Gas balance experiments have shown that the fuel retention rate with the new wall is substantially reduced with respect to the C wall. The re-establishment of the baseline H-mode and hybrid scenarios compatible with the new wall has required an optimization of the control of metallic impurity sources and heat loads. Stable type-I ELMy H-mode regimes with H-98,H-y2 close to 1 and beta(N) similar to 1.6 have been achieved using gas injection. ELM frequency is a key factor for the control of the metallic impurity accumulation. Pedestal temperatures tend to be lower with the new wall, leading to reduced confinement, but nitrogen seeding restores high pedestal temperatures and confinement. Compared with the carbon wall, major disruptions with the new wall show a lower radiated power and a slower current quench. The higher heat loads on Be wall plasma-facing components due to lower radiation made the routine use of massive gas injection for disruption mitigation essential.
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| 3. |
- Antonelli, Alexandre, 1978, et al.
(författare)
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Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics
- 2019
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 2019:2
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Tidskriftsartikel (refereegranskat)abstract
- Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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| 4. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Time to a single hybridization event in a group of species with unknown ancestral history
- 2013
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 322, s. 1-6
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Tidskriftsartikel (refereegranskat)abstract
- We consider a stochastic process for the generation of species which combines a Yule process with a simple model for hybridization between pairs of co-existent species. We assume that the origin of the process, when there was one species, occurred at an unknown time in the past, and we condition the process on producing n species via the Yule process and a single hybridization event. We prove results about the distribution of the time of the hybridization event. In particular we calculate a formula for all moments, and show that under various conditions, the distribution tends to an exponential with rate twice that of the birth rate for the Yule process.
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| 5. |
- Jones, Robert Graham, 1959, et al.
(författare)
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Statistical Inference of Allopolyploid Species Networks in the Presence of Incomplete Lineage Sorting.
- 2013
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 62:3, s. 467-478
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Tidskriftsartikel (refereegranskat)abstract
- Polyploidy is an important speciation mechanism, particularly in land plants. Allopolyploid species are formed after hybridization between otherwise intersterile parental species. Recent theoretical progress has led to successful implementation of species tree models that take population genetic parameters into account. However, these models have not included allopolyploid hybridization and the special problems imposed when species trees of allopolyploids are inferred. Here, two new models for the statistical inference of the evolutionary history of allopolyploids are evaluated using simulations and demonstrated on two empirical data sets. It is assumed that there has been a single hybridization event between two diploid species resulting in a genomic allotetraploid. The evolutionary history can be represented as a species network or as a multi-labeled species tree, in which some pairs of tips are labeled with the same species. In one of the models (AlloppMUL), the multi-labeled species tree is inferred directly. This is the simplest model and the most widely applicable, since fewer assumptions are made. The second model (AlloppNET) incorporates the hybridization event explicitly which means that fewer parameters need to be estimated. Both models are implemented in the BEAST framework. Simulations show that both models are useful and that AlloppNET is more accurate if the assumptions it is based on are valid. The models are demonstrated on previously analyzed data from the genus Pachycladon (Brassicaceae) and from the genus Silene (Caryophyllaceae).
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