| 1. |
- Householder, John Ethan, et al.
(författare)
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One sixth of Amazonian tree diversity is dependent on river floodplains
- 2024
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Ingår i: NATURE ECOLOGY & EVOLUTION. - 2397-334X.
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Tidskriftsartikel (refereegranskat)abstract
- Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function.
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| 2. |
- Luize, Bruno Garcia, et al.
(författare)
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Geography and ecology shape the phylogenetic composition of Amazonian tree communities
- 2024
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Ingår i: JOURNAL OF BIOGEOGRAPHY. - 0305-0270 .- 1365-2699.
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Tidskriftsartikel (refereegranskat)abstract
- Aim: Amazonia hosts more tree species from numerous evolutionary lineages, both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonized multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types. Location: Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods: Data for the abundance of 5082 tree species in 1989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny. Results: In the terra firme and v & aacute;rzea forest types, the phylogenetic composition varies by geographic region, but the igap & oacute; and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R-2 = 19% overall for combined spatial/environmental effects). The phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R-2 = 28%). A greater number of lineages were significant indicators of geographic regions than forest types. Main Conclusion: Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization in specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions.
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| 3. |
- ter Steege, Hans, et al.
(författare)
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Mapping density, diversity and species-richness of the Amazon tree flora
- 2023
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Ingår i: COMMUNICATIONS BIOLOGY. - 2399-3642. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution. A study mapping the tree species richness in Amazonian forests shows that soil type exerts a strong effect on species richness, probably caused by the areas of these forest types. Cumulative water deficit, tree density and temperature seasonality affect species richness at a regional scale.
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| 4. |
- C. Couto, Rafael, 1987-, et al.
(författare)
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Selective gating to vibrational modes through resonant X-ray scattering
- 2017
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Ingår i: Nature Communications. - : Macmillan Publishers Ltd.. - 2041-1723. ; 8, s. 14165-1-14165-7
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Tidskriftsartikel (refereegranskat)abstract
- The dynamics of fragmentation and vibration of molecular systems with a large number of coupled degrees of freedom are key aspects for understanding chemical reactivity and properties. Here we present a resonant inelastic X-ray scattering (RIXS) study to show how it is possible to break down such a complex multidimensional problem into elementary components. Local multimode nuclear wave packets created by X-ray excitation to different core-excited potential energy surfaces (PESs) will act as spatial gates to selectively probe the particular ground-state vibrational modes and, hence, the PES along these modes. We demonstrate this principle by combining ultra-high resolution RIXS measurements for gas-phase water with state-of-the-art simulations.
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| 5. |
- Couto, Rafael C., et al.
(författare)
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Anomalously strong two-electron one-photon X-ray decay transitions in CO caused by avoided crossing
- 2016
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- The unique opportunity to study and control electron-nuclear quantum dynamics in coupled potentials offered by the resonant inelastic X-ray scattering (RIXS) technique is utilized to unravel an anomalously strong two-electron one-photon transition from core-excited to Rydberg final states in the CO molecule. High-resolution RIXS measurements of CO in the energy region of 12-14 eV are presented and analyzed by means of quantum simulations using the wave packet propagation formalism and ab initio calculations of potential energy curves and transition dipole moments. The very good overall agreement between the experimental results and the theoretical predictions allows an in-depth interpretation of the salient spectral features in terms of Coulomb mixing of "dark" with "bright" final states leading to an effective two-electron one-photon transition. The present work illustrates that the improved spectral resolution of RIXS spectra achievable today may call for more advanced theories than what has been used in the past.
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| 6. |
- Couto, Rafael C., et al.
(författare)
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Coupled electron-nuclear dynamics in resonant 1 sigma -> 2 pi x-ray Raman scattering of CO molecules
- 2016
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Ingår i: Physical Review A. - : American Physical Society. - 2469-9926. ; 93:3
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Tidskriftsartikel (refereegranskat)abstract
- We present a detailed experimental-theoretical analysis of O K-edge resonant 1 sigma-2 pi inelastic x-ray scattering (RIXS) from carbon monoxide with unprecedented energy resolution. We employ high-level ab initio calculations to compute the potential energy curves of the states involved in the RIXS process and simulate the measured RIXS spectra using the wave-packet-propagation formalism, including Coulomb coupling in the final-state manifold. The theoretical analysis allows us to explain all the key features of the experimental spectra, including some that were not seen before. First, we clearly show the interference effect between different RIXS channels corresponding to the transition via orthogonal (1)Pi(x) and (1)Pi(y) core-excited states of CO. Second, the RIXS region of 13 eV energy loss presents a triple structure, revealed only by the high-resolution measurement. In previous studies, this region was attributed solely to a valence state. Here we show a strong Coulomb mixing of the Rydberg and valence final states, which opens the forbidden RIXS channels to the "dark" final Rydberg states and drastically changes the RIXS profile. Third, using a combination of high-resolution experiment and high-level theory, we improve the vertical bar 4 sigma(-1)2 pi(1)> final-state potential-energy curve by fitting its bottom part with the experiment. Also, the coupling constants between Rydberg and valence states were refined via comparison with the experiment. Our results illustrate the large potential of the RIXS technique for advanced studies of highly excited states of neutral molecules.
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| 7. |
- Couto, Rafael C., et al.
(författare)
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Coupled electron-nuclear dynamics in resonant 1σ→2π x-ray Raman scattering of CO molecules
- 2016
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Ingår i: Physical Review A (Atomic, Molecular and Optical Physics). - 1050-2947. ; 93:3
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Tidskriftsartikel (refereegranskat)abstract
- We present a detailed experimental-theoretical analysis of O K-edge resonant 1σ-2π inelastic x-ray scattering (RIXS) from carbon monoxide with unprecedented energy resolution. We employ high-level ab initio calculations to compute the potential energy curves of the states involved in the RIXS process and simulate the measured RIXS spectra using the wave-packet-propagation formalism, including Coulomb coupling in the final-state manifold. The theoretical analysis allows us to explain all the key features of the experimental spectra, including some that were not seen before. First, we clearly show the interference effect between different RIXS channels corresponding to the transition via orthogonal Πx1 and Πy1 core-excited states of CO. Second, the RIXS region of 13 eV energy loss presents a triple structure, revealed only by the high-resolution measurement. In previous studies, this region was attributed solely to a valence state. Here we show a strong Coulomb mixing of the Rydberg and valence final states, which opens the forbidden RIXS channels to the "dark" final Rydberg states and drastically changes the RIXS profile. Third, using a combination of high-resolution experiment and high-level theory, we improve the |4σ-12π1) final-state potential-energy curve by fitting its bottom part with the experiment. Also, the coupling constants between Rydberg and valence states were refined via comparison with the experiment. Our results illustrate the large potential of the RIXS technique for advanced studies of highly excited states of neutral molecules.
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| 8. |
- Ignatova, Nina, 1989-, et al.
(författare)
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Gradual collapse of nuclear wave functions regulated by frequency tuned X-ray scattering
- 2017
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Ingår i: Scientific Reports. - London : Nature Publishing Group. - 2045-2322. ; 7:43891
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Tidskriftsartikel (refereegranskat)abstract
- As is well established, the symmetry breaking by isotope substitution in the water molecule results in localisation of the vibrations along one of the two bonds in the ground state. In this study we find that this localisation may be broken in excited electronic states. Contrary to the ground state, the stretching vibrations of HDO are delocalised in the bound core-excited state in spite of the mass difference between hydrogen and deuterium. The reason for this effect can be traced to the narrow “canyon-like” shape of the potential of the state along the symmetric stretching mode, which dominates over the localisation mass-difference effect. In contrast, the localisation of nuclear motion to one of the HDO bonds is preserved in the dissociative core-excited state . The dynamics of the delocalisation of nuclear motion in these core-excited states is studied using resonant inelastic X-ray scattering of the vibrationally excited HDO molecule. The results shed light on the process of a wave function collapse. After core-excitation into the state of HDO the initial wave packet collapses gradually, rather than instantaneously, to a single vibrational eigenstate.
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| 9. |
- Ignatova, Nina, 1989-, et al.
(författare)
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Infrared-pump–x-ray-probe spectroscopy of vibrationally excited molecules
- 2017
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Ingår i: Physical Review A. - 2469-9926 .- 2469-9934. ; 95:4
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Tidskriftsartikel (refereegranskat)abstract
- We develop a theory of infrared (IR)-pump–x-ray-probe spectroscopy for molecular studies. We illustrate advantages of the proposed scheme by means of numerical simulations employing a vibrational wave packet technique applied to x-ray absorption and resonant inelastic x-ray scattering (RIXS) spectra of the water molecule vibrationally excited by a preceding IR field. The promotion of the vibrationally excited molecule to the dissociative 1a−114a1 and bound 1a−112b2 core-excited states with qualitatively different shapes of the potential energy surfaces creates nuclear wave packets localized along and between the OH bonds, respectively. The projection of these wave packets on the final vibrational states, governed by selection and propensity rules, results in spatial selectivity of RIXS sensitive to the initial vibrationally excited state, which makes it possible to probe selectively the ground state properties along different modes. In addition, we propose to use RIXS as a tool to study x-ray absorption from a selected vibrational level of the ground state when the spectral resolution is sufficiently high to resolve vibrational overtones. The proposed technique has potential applications for advanced mapping of multidimensional potential energy surfaces of ground and core-excited molecular states, for symmetry-resolved spectroscopy, and for steering chemical reactions.
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| 10. |
- Vaz da Cruz, Vinicius, 1987-, et al.
(författare)
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A study of the water molecule using frequency control over nuclear dynamics in resonant X-ray scattering
- 2017
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 19:30, s. 19573-19589
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Tidskriftsartikel (refereegranskat)abstract
- In this combined theoretical and experimental study we report a full analysis of the resonant inelastic X-ray scattering (RIXS) spectra of H2O, D2O and HDO. We demonstrate that electronically-elastic RIXS has an inherent capability to map the potential energy surface and to perform vibrational analysis of the electronic ground state in multimode systems. We show that the control and selection of vibrational excitation can be performed by tuning the X-ray frequency across core-excited molecular bands and that this is clearly reflected in the RIXS spectra. Using high level ab initio electronic structure and quantum nuclear wave packet calculations together with high resolution RIXS measurements, we discuss in detail the mode coupling, mode localization and anharmonicity in the studied systems.
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