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- Edger, Patrick P., et al.
(författare)
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The butterfly plant arms-race escalated by gene and genome duplications
- 2015
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 112:27, s. 8362-8366
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Tidskriftsartikel (refereegranskat)abstract
- Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race. Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. Furthermore, we show that the origins of both chemical defenses and of molecular counter adaptations were associated with shifts in diversification rates during the arms-race. These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits.
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- Hendriks, Kasper P., et al.
(författare)
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Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset
- 2023
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Ingår i: Current Biology. - : Elsevier. - 0960-9822 .- 1879-0445. ; 33:19, s. 4052-4068
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Tidskriftsartikel (refereegranskat)abstract
- The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Bras-sicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To eval-uate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moder-ate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
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- Zhang, Yu, et al.
(författare)
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Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis
- 2024
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Ingår i: Plant communications. - 2590-3462. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- Plant root-nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. Nodulating species share many commonalities, explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period. Regardless, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation-what must be acquired or cannot be lost for a functional symbiosis-and the latitude for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here, we employed a large-scale phylogenomic analysis across 88 species, complemented by 151 RNA-seq libraries, to elucidate the evolution of RNS. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key mutations that affect its function across the NFNC. Comparative transcriptomic assessment revealed nodulespecific upregulated genes across diverse nodulating plants, while also identifying nodule-specific and nitrogen-response genes. Approximately 70% of symbiosis-related genes are highly conserved in the four representative species, whereas defense-related and host-range restriction genes tend to be lineage specific. Our study also identified over 900 000 conserved non-coding elements (CNEs), over 300 000 of which are unique to sampled NFNC species. NFNC-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions, thus representing a pool of candidate regulatory elements for genes involved in RNS. Collectively, our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.
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- Hansmann, Georg, et al.
(författare)
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2019 updated consensus statement on the diagnosis and treatment of pediatric pulmonary hypertension: The European Pediatric Pulmonary Vascular Disease Network (EPPVDN), endorsed by AEPC, ESPR and ISHLT
- 2019
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Ingår i: The Journal of Heart and Lung Transplantation. - : Elsevier BV. - 1053-2498. ; 38:9, s. 879-901
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Forskningsöversikt (refereegranskat)abstract
- © 2019 The European Pediatric Pulmonary Vascular Disease Network is a registered, non-profit organization that strives to define and develop effective, innovative diagnostic methods and treatment options in all forms of pediatric pulmonary hypertensive vascular disease, including pulmonary hypertension (PH) associated with bronchopulmonary dysplasia, PH associated with congenital heart disease (CHD), persistent PH of the newborn, and related cardiac dysfunction. The executive writing group members conducted searches of the PubMed/MEDLINE bibliographic database (1990–2018) and held face-to-face and web-based meetings. Ten section task forces voted on the updated recommendations, based on the 2016 executive summary. Clinical trials, meta-analyses, guidelines, and other articles that include pediatric data were searched using the term “pulmonary hypertension” and other keywords. Class of recommendation (COR) and level of evidence (LOE) were assigned based on European Society of Cardiology/American Heart Association definitions and on pediatric data only, or on adult studies that included >10% children or studies that enrolled adults with CHD. New definitions by the World Symposium on Pulmonary Hypertension 2018 were included. We generated 10 tables with graded recommendations (COR/LOE). The topics include diagnosis/monitoring, genetics/biomarkers, cardiac catheterization, echocardiography, cardiac magnetic resonance/chest computed tomography, associated forms of PH, intensive care unit/lung transplantation, and treatment of pediatric PH. For the first time, a set of specific recommendations on the management of PH in middle- and low-income regions was developed. Taken together, these executive, up-to-date guidelines provide a specific, comprehensive, detailed but practical framework for the optimal clinical care of children and young adults with PH.
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- Lee, Cheng-Ruei, et al.
(författare)
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Young inversion with multiple linked QTLs under selection in a hybrid zone
- 2017
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Ingår i: NATURE ECOLOGY & EVOLUTION. - : Springer Science and Business Media LLC. - 2397-334X. ; 1:5
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Tidskriftsartikel (refereegranskat)abstract
- Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.
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- van de Kerke, Sara J., et al.
(författare)
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Capturing variation in floral shape : a virtual3D based morphospace for Pelargonium
- 2020
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundVariation in floral shapes has long fascinated biologists and its modelling enables testing of evolutionary hypotheses. Recent comparative studies that explore floral shape have largely ignored 3D floral shape. We propose quantifying floral shape by using geometric morphometrics on a virtual3D model reconstructed from 2D photographical data and demonstrate its performance in capturing shape variation.MethodsThis approach offers unique benefits to complement established imaging techniques (i) by enabling adequate coverage of the potential morphospace of large and diverse flowering-plant clades; (ii) by circumventing asynchronicity in anthesis of different floral parts; and (iii) by incorporating variation in copy number of floral organs within structures. We demonstrate our approach by analysing 90 florally-diverse species of the Southern African genus Pelargonium (Geraniaceae). We quantify Pelargonium floral shapes using 117 landmarks and show similarities in reconstructed morphospaces for nectar tube, corolla (2D datasets), and a combined virtual3D dataset.ResultsOur results indicate that Pelargonium species differ in floral shape, which can also vary extensively within a species. PCA results of the reconstructed virtual3D floral models are highly congruent with the separate 2D morphospaces, indicating it is an accurate, virtual, representation of floral shape. Through our approach, we find that adding the third dimension to the data is crucial to accurately interpret the manner of, as well as levels of, shape variation in flowers.
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- Vinck, Ken, et al.
(författare)
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Advanced in-situ and laboratory characterisation of the ALPACA chalk research site
- 2022
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Ingår i: Geotechnique. - : ICE Publishing. - 0016-8505 .- 1751-7656.
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Tidskriftsartikel (refereegranskat)abstract
- Low-to-medium density chalk at St Nicholas at Wade, UK, is characterised by intensive testing to inform the interpretation of axial and lateral tests on driven piles. The chalk de-structures when taken to large strains, especially under dynamic loading, leading to remarkably high pore pressures beneath penetrating CPT and driven pile tips, weak putty annuli around their shafts and degraded responses in full-displacement pressuremeter tests. Laboratory tests on carefully formed specimens explore the chalk’s unstable structure and markedly time and rate-dependent mechanical behaviour. A clear hierarchy is found between profiles of peak strength with depth of Brazilian tension (BT), drained and undrained triaxial and direct simple shear (DSS) tests conducted from in-situ stress conditions. Highly instrumented triaxial tests reveal the chalk’s unusual effective stress paths, markedly brittle failure behaviour from small strains and the effects of consolidating to higher than in-situ stresses. The chalk’s mainly sub-vertical jointing and micro-fissuring leads to properties depending on specimen scale, with in-situ mass stiffnesses falling significantly below high-quality laboratory measurements and vertical Young’s moduli exceeding horizontal stiffnesses. While compressive strength and stiffness appear relatively insensitive to effective stress levels, consolidation to higher pressures closes micro-fissures, increases stiffness and reduces anisotropy.
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