| 1. |
- Groenen, M. A., et al.
(författare)
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Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
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Tidskriftsartikel (refereegranskat)abstract
- For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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| 2. |
- Abbott, Benjamin W., et al.
(författare)
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Biomass offsets little or none of permafrost carbon release from soils, streams, and wildfire : an expert assessment
- 2016
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Ingår i: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 11:3
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Tidskriftsartikel (refereegranskat)abstract
- As the permafrost region warms, its large organic carbon pool will be increasingly vulnerable to decomposition, combustion, and hydrologic export. Models predict that some portion of this release will be offset by increased production of Arctic and boreal biomass; however, the lack of robust estimates of net carbon balance increases the risk of further overshooting international emissions targets. Precise empirical or model-based assessments of the critical factors driving carbon balance are unlikely in the near future, so to address this gap, we present estimates from 98 permafrost-region experts of the response of biomass, wildfire, and hydrologic carbon flux to climate change. Results suggest that contrary to model projections, total permafrost-region biomass could decrease due to water stress and disturbance, factors that are not adequately incorporated in current models. Assessments indicate that end-of-the-century organic carbon release from Arctic rivers and collapsing coastlines could increase by 75% while carbon loss via burning could increase four-fold. Experts identified water balance, shifts in vegetation community, and permafrost degradation as the key sources of uncertainty in predicting future system response. In combination with previous findings, results suggest the permafrost region will become a carbon source to the atmosphere by 2100 regardless of warming scenario but that 65%-85% of permafrost carbon release can still be avoided if human emissions are actively reduced.
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| 3. |
- Davies, Stuart J., et al.
(författare)
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ForestGEO: Understanding forest diversity and dynamics through a global observatory network
- 2021
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Ingår i: Biological Conservation. - : Elsevier BV. - 0006-3207. ; 253
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Tidskriftsartikel (refereegranskat)abstract
- ForestGEO is a network of scientists and long-term forest dynamics plots (FDPs) spanning the Earth's major forest types. ForestGEO's mission is to advance understanding of the diversity and dynamics of forests and to strengthen global capacity for forest science research. ForestGEO is unique among forest plot networks in its large-scale plot dimensions, censusing of all stems ≥1 cm in diameter, inclusion of tropical, temperate and boreal forests, and investigation of additional biotic (e.g., arthropods) and abiotic (e.g., soils) drivers, which together provide a holistic view of forest functioning. The 71 FDPs in 27 countries include approximately 7.33 million living trees and about 12,000 species, representing 20% of the world's known tree diversity. With >1300 published papers, ForestGEO researchers have made significant contributions in two fundamental areas: species coexistence and diversity, and ecosystem functioning. Specifically, defining the major biotic and abiotic controls on the distribution and coexistence of species and functional types and on variation in species' demography has led to improved understanding of how the multiple dimensions of forest diversity are structured across space and time and how this diversity relates to the processes controlling the role of forests in the Earth system. Nevertheless, knowledge gaps remain that impede our ability to predict how forest diversity and function will respond to climate change and other stressors. Meeting these global research challenges requires major advances in standardizing taxonomy of tropical species, resolving the main drivers of forest dynamics, and integrating plot-based ground and remote sensing observations to scale up estimates of forest diversity and function, coupled with improved predictive models. However, they cannot be met without greater financial commitment to sustain the long-term research of ForestGEO and other forest plot networks, greatly expanded scientific capacity across the world's forested nations, and increased collaboration and integration among research networks and disciplines addressing forest science.
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| 4. |
- Xiao, K., et al.
(författare)
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Crab bioturbation drives coupled iron-phosphate-sulfide cycling in mangrove and salt marsh soils
- 2022
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Ingår i: Geoderma. - : Elsevier BV. - 0016-7061. ; 424
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Tidskriftsartikel (refereegranskat)abstract
- Coastal wetlands sequestering abundant blue carbon in soils are biogeochemical hotspots and critical habitats for benthic animals like invertebrate fiddler crabs. Here, we reveal how crab bioturbation (i.e., burrowing activity) drives the redox geochemistry of ferrous iron (Fe(II)), phosphate (PO43-), and sulfide (S(-II)) under contrasting vegetation types and hydrological conditions. We used in-situ approaches of diffusive gradients in thin films to perform detailed mm-scale burrow observations in two subtropical wetlands with a vegetation gradient of mudflat-salt marsh-mangrove. Burrow flushing caused a top-down hydrologic connectivity through the crab burrows and thus created a deep depth for the occurrence of Fe(III) reduction and sulfate reduction which were accompanied by P mobilization. The burrow oxidation zone, indicated by lower concentrations of Fe(II), PO43- and S(-II), were shallower in mudflats and salt marshes than in mangroves due to the unique respiratory roots of mangrove plants. The redox of Fe(II), PO(4)(3-)and S(-II) in crab burrow was insensitive to the convection flow induced input of dissolved oxygen through the surrounding soil matrix, indicating the burrow soil is an independent microenvironment. Crab burrowing activities favored Fe-S coupling which is conductive the formation of pyrite and alkalinity generation. Overall, our in-situ high-resolution observations and porewater hydraulic dynamics revealed spatially variable soil geochemistry, active coupled cycling of Fe-P-S in crab burrows, and mm-scale hotspots of redox cycling within burrows.
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| 5. |
- Duan, X. B., et al.
(författare)
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GsSLAH3, a Glycine soja slow type anion channel homolog, positively modulates plant bicarbonate stress tolerance
- 2018
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Ingår i: Physiologia Plantarum. - : Wiley. - 0031-9317. ; 164:2, s. 145-162
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Tidskriftsartikel (refereegranskat)abstract
- Alkaline stress is a major form of abiotic stress that severely inhibits plant growth and development, thus restricting crop productivity. However, little is known about how plants respond to alkali. In this study, a slow-type anion channel homolog 3 gene, GsSLAH3, was isolated and functionally characterized. Bioinformatics analysis showed that the GsSLAH3 protein contains 10 transmembrane helices. Consistently, GsSLAH3 was found to locate on plasma membrane by transient expression in onion epidermal cells. In wild soybeans, GsSLAH3 expression was induced by NaHCO3 treatment, suggesting its involvement in plant response to alkaline stress. Ectopic expression of GsSLAH3 in yeast increased sensitivity to alkali treatment. Dramatically, overexpression of GsSLAH3 in Arabidopsis thaliana enhanced alkaline tolerance during the germination, seedling and adult stages. More interestingly, we found that transgenic lines also improved plant tolerance to KHCO3 rather than high pH treatment. A nitrate content analysis of Arabidopsis shoots showed that GsSLAH3 overexpressing lines accumulated more NO3- than wild-type. In summary, our data suggest that GsSLAH3 is a positive alkali responsive gene that increases bicarbonate resistance specifically.
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| 6. |
- Ruiz-Ramos, Miguel, et al.
(författare)
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Adaptation response surfaces for managing wheat under perturbed climate and CO2 in a Mediterranean environment
- 2018
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Ingår i: Agricultural Systems. - : Elsevier BV. - 0308-521X. ; 159, s. 260-274
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Tidskriftsartikel (refereegranskat)abstract
- Adaptation of crops to climate change has to be addressed locally due to the variability of soil, climate and the specific socio-economic settings influencing farm management decisions. Adaptation of rainfed cropping systems in the Mediterranean is especially challenging due to the projected decline in precipitation in the coming decades, which will increase the risk of droughts. Methods that can help explore uncertainties in climate projections and crop modelling, such as impact response surfaces (IRSs) and ensemble modelling, can then be valuable for identifying effective adaptations. Here, an ensemble of 17 crop models was used to simulate a total of 54 adaptation options for rainfed winter wheat (Triticum aestivum) at Lleida (NE Spain). To support the ensemble building, an ex post quality check of model simulations based on several criteria was performed. Those criteria were based on the "According to Our Current Knowledge" (AOCK) concept, which has been formalized here. Adaptations were based on changes in cultivars and management regarding phenology, vernalization, sowing date and irrigation. The effects of adaptation options under changed precipitation (P), temperature (T), [CO2] and soil type were analysed by constructing response surfaces, which we termed, in accordance with their specific purpose, adaptation response surfaces (ARSs). These were created to assess the effect of adaptations through a range of plausible P, T and [CO2] perturbations. The results indicated that impacts of altered climate were predominantly negative. No single adaptation was capable of overcoming the detrimental effect of the complex interactions imposed by the P, T and [CO2] perturbations except for supplementary irrigation (sI), which reduced the potential impacts under most of the perturbations. Yet, a combination of adaptations for dealing with climate change demonstrated that effective adaptation is possible at Lleida. Combinations based on a cultivar without vernalization requirements showed good and wide adaptation potential. Few combined adaptation options performed well under rainfed conditions. However, a single sI was sufficient to develop a high adaptation potential, including options mainly based on spring wheat, current cycle duration and early sowing date. Depending on local environment (e.g. soil type), many of these adaptations can maintain current yield levels under moderate changes in T and P, and some also under strong changes. We conclude that ARSs can offer a useful tool for supporting planning of field level adaptation under conditions of high uncertainty.
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| 7. |
- Rodríguez, A., et al.
(författare)
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Implications of crop model ensemble size and composition for estimates of adaptation effects and agreement of recommendations
- 2019
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Ingår i: Agricultural and Forest Meteorology. - : Elsevier BV. - 0168-1923 .- 1873-2240. ; 264, s. 351-362
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Tidskriftsartikel (refereegranskat)abstract
- Climate change is expected to severely affect cropping systems and food production in many parts of the world unless local adaptation can ameliorate these impacts. Ensembles of crop simulation models can be useful tools for assessing if proposed adaptation options are capable of achieving target yields, whilst also quantifying the share of uncertainty in the simulated crop impact resulting from the crop models themselves. Although some studies have analysed the influence of ensemble size on model outcomes, the effect of ensemble composition has not yet been properly appraised. Moreover, results and derived recommendations typically rely on averaged ensemble simulation results without accounting sufficiently for the spread of model outcomes. Therefore, we developed an Ensemble Outcome Agreement (EOA) index, which analyses the effect of changes in composition and size of a multi-model ensemble (MME) to evaluate the level of agreement between MME outcomes with respect to a given hypothesis (e.g. that adaptation measures result in positive crop responses). We analysed the recommendations of a previous study performed with an ensemble of 17 crop models and testing 54 adaptation options for rainfed winter wheat (Triticum aestivum L.) at Lleida (NE Spain) under perturbed conditions of temperature, precipitation and atmospheric CO2 concentration. Our results confirmed that most adaptations recommended in the previous study have a positive effect. However, we also showed that some options did not remain recommendable in specific conditions if different ensembles were considered. Using EOA, we were able to identify the adaptation options for which there is high confidence in their effectiveness at enhancing yields, even under severe climate perturbations. These include substituting spring wheat for winter wheat combined with earlier sowing dates and standard or longer duration cultivars, or introducing supplementary irrigation, the latter increasing EOA values in all cases. There is low confidence in recovering yields to baseline levels, although this target could be attained for some adaptation options under moderate climate perturbations. Recommendations derived from such robust results may provide crucial information for stakeholders seeking to implement adaptation measures.
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| 8. |
- Leite, Melina de Souza, et al.
(författare)
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Major axes of variation in tree demography across global forests
- 2024
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Ingår i: Ecography. - 0906-7590 .- 1600-0587.
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Tidskriftsartikel (refereegranskat)abstract
- The future trajectory of global forests is closely intertwined with tree demography, and a major fundamental goal in ecology is to understand the key mechanisms governing spatio-temporal patterns in tree population dynamics. While previous research has made substantial progress in identifying the mechanisms individually, their relative importance among forests remains unclear mainly due to practical limitations. One approach to overcome these limitations is to group mechanisms according to their shared effects on the variability of tree vital rates and quantify patterns therein. We developed a conceptual and statistical framework (variance partitioning of Bayesian multilevel models) that attributes the variability in tree growth, mortality, and recruitment to variation in species, space, and time, and their interactions – categories we refer to as organising principles (OPs). We applied the framework to data from 21 forest plots covering more than 2.9 million trees of approximately 6500 species. We found that differences among species, the species OP, proved a major source of variability in tree vital rates, explaining 28–33% of demographic variance alone, and 14–17% in interaction with space, totalling 40–43%. Our results support the hypothesis that the range of vital rates is similar across global forests. However, the average variability among species declined with species richness, indicating that diverse forests featured smaller interspecific differences in vital rates. Moreover, decomposing the variance in vital rates into the proposed OPs showed the importance of unexplained variability, which includes individual variation, in tree demography. A focus on how demographic variance is organized in forests can facilitate the construction of more targeted models with clearer expectations of which covariates might drive a vital rate. This study therefore highlights the most promising avenues for future research, both in terms of understanding the relative contributions of groups of mechanisms to forest demography and diversity, and for improving projections of forest ecosystems.
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| 9. |
- McKeown, Nicola M., et al.
(författare)
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Comparison of plasma alkylresorcinols (AR) and urinary AR metabolites as biomarkers of compliance in a short-term, whole-grain intervention study
- 2016
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Ingår i: European Journal of Nutrition. - : Springer Science and Business Media LLC. - 1436-6207 .- 1436-6215. ; 55:3, s. 1235-1244
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Tidskriftsartikel (refereegranskat)abstract
- Alkylresorcinols (AR) are phenolic lipids present in the bran of wheat and rye. Plasma AR and their urinary metabolites may be suitable biomarkers of whole-grain (WG) wheat and rye consumption. The objective of this study was to examine plasma AR and urinary AR metabolites in response to WG wheat consumption. In a randomized crossover study, 19 subjects (10 males, 9 females; BMI 22.0 kg/m(2); age 26 years) incorporated either 3 servings (48 g) or 6 servings (96 g) of WG wheat daily into their regular diet for 1 week. Subjects completed a 2-week washout period, abstaining from all WG consumption, before each intervention. Fasting blood and 24-h urine were collected before and after each intervention. Plasma AR homologues (C19:0, C21:0, C23:0) were quantified by GC-MS after diethyl ether and solid phase extraction and derivatization. Urinary AR metabolites [3,5-dihydroxybenzoic acid and 3-(3,5-dihydroxyphenyl)-propanoic acid] were determined using HPLC with electrochemical detection after enzymatic deconjugation and ethyl acetate extraction. Urinary total AR metabolites were significantly higher after 6 compared with 3 servings of WG wheat (56 vs. 32 mu mol/day, P < 0.001). This dose-response relationship was independent of age, sex, energy intake, and baseline urinary AR metabolite concentration. Plasma total AR tended to be higher after 6 compared with 3 servings of WG wheat (103.0 vs. 86.9 nmol/L), but this difference was not significant (P = 0.42). The results suggest that urinary AR metabolites from 24-h urine collections may be useful as biomarkers of compliance in intervention studies of WG wheat.
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