| 1. |
- Groenen, M. A., et al.
(author)
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Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
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Journal article (peer-reviewed)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. |
- ter Steege, Hans, et al.
(author)
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Mapping density, diversity and species-richness of the Amazon tree flora
- 2023
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In: COMMUNICATIONS BIOLOGY. - 2399-3642. ; 6:1
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Journal article (peer-reviewed)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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| 3. |
- Hudson, Lawrence N., et al.
(author)
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The PREDICTS database : a global database of how local terrestrial biodiversity responds to human impacts
- 2014
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In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 4:24, s. 4701-4735
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Journal article (peer-reviewed)abstract
- Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - ). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
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| 4. |
- Tavares, Julia, et al.
(author)
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Basin-wide variation in tree hydraulic safety margins predicts the carbon balance of Amazon forests
- 2023
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In: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 617:7959, s. 111-117
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Journal article (peer-reviewed)abstract
- Tropical forests face increasing climate risk(1,2), yet our ability to predict their response to climate change is limited by poor understanding of their resistance to water stress. Although xylem embolism resistance thresholds (for example, ?(50)) and hydraulic safety margins (for example, HSM50) are important predictors of drought-induced mortality risk(3-5), little is known about how these vary across Earth's largest tropical forest. Here, we present a pan-Amazon, fully standardized hydraulic traits dataset and use it to assess regional variation in drought sensitivity and hydraulic trait ability to predict species distributions and long-term forest biomass accumulation. Parameters ?(50) and HSM50 vary markedly across the Amazon and are related to average long-term rainfall characteristics. Both ?(50) and HSM50 influence the biogeographical distribution of Amazon tree species. However, HSM50 was the only significant predictor of observed decadal-scale changes in forest biomass. Old-growth forests with wide HSM50 are gaining more biomass than are low HSM(50 )forests. We propose that this may be associated with a growth-mortality trade-off whereby trees in forests consisting of fast-growing species take greater hydraulic risks and face greater mortality risk. Moreover, in regions of more pronounced climatic change, we find evidence that forests are losing biomass, suggesting that species in these regions may be operating beyond their hydraulic limits. Continued climate change is likely to further reduce HSM50 in the Amazon(6,7), with strong implications for the Amazon carbon sink.
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| 5. |
- Stone, D., et al.
(author)
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A method of establishing a transect for biodiversity and ecosystem function monitoring across Europe
- 2016
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In: Applied Soil Ecology. - : Elsevier BV. - 0929-1393 .- 1873-0272. ; 97, s. 3-11
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Journal article (peer-reviewed)abstract
- The establishment of the range of soil biodiversity found within European soils is needed to guide EU policy development regarding the protection of soil. Such a base-line should be collated from a wide-ranging sampling campaign to ensure that soil biodiversity from the majority of soil types, land-use or management systems, and European climatic (bio-geographical zones) were included. This paper reports the design and testing of a method to achieve the large scale sampling associated with the establishment of such a baseline, carried out within the remit of the EcoFINDERS project, and outlines points to consider when such a task is undertaken. Applying a GIS spatial selection process, a sampling campaign was undertaken by 13 EcoFINDERS partners across 11 countries providing data on the range of indicators of biodiversity and ecosystem functions including; micro and meso fauna biodiversity, extracellular enzyme activity, PLEA and community level physiological profiling (MicroResp (TM) and Biolog (TM)). Physical, chemical and bio-geographical parameters of the 81 sites sampled were used to determine whether the model predicted a wide enough range of sites to allow assessment of the biodiversity indicators tested. Discrimination between the major bio-geographical zones of Atlantic and Continental was possible for all land-use types. Boreal and Alpine zones only allowed discrimination in the most common land-use type for that area e.g. forestry and grassland sites, respectively, while the Mediterranean zone did not have enough sites sampled to draw conclusions across all land-use types. The method used allowed the inclusion of a range of land-uses in both the model prediction stage and the final sites sampled. The establishment of the range of soil biodiversity across Europe is possible, though a larger targeted campaign is recommended. The techniques applied within the EcoFINDERS sampling would be applicable to a larger campaign. (C) 2015 Elsevier B.V. All rights reserved.
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| 6. |
- Hansen, Lea B.S., et al.
(author)
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A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults
- 2018
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 9:1
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Journal article (peer-reviewed)abstract
- © 2018, The Author(s). Adherence to a low-gluten diet has become increasingly common in parts of the general population. However, the effects of reducing gluten-rich food items including wheat, barley and rye cereals in healthy adults are unclear. Here, we undertook a randomised, controlled, cross-over trial involving 60 middle-aged Danish adults without known disorders with two 8-week interventions comparing a low-gluten diet (2 g gluten per day) and a high-gluten diet (18 g gluten per day), separated by a washout period of at least six weeks with habitual diet (12 g gluten per day). We find that, in comparison with a high-gluten diet, a low-gluten diet induces moderate changes in the intestinal microbiome, reduces fasting and postprandial hydrogen exhalation, and leads to improvements in self-reported bloating. These observations suggest that most of the effects of a low-gluten diet in non-coeliac adults may be driven by qualitative changes in dietary fibres.
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| 7. |
- Munch Roager, Henrik, et al.
(author)
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Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: A randomised cross-over trial
- 2019
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In: Gut. - : BMJ. - 1468-3288 .- 0017-5749. ; 68:1, s. 83-93
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Journal article (peer-reviewed)abstract
- Objective T o investigate whether a whole grain diet alters the gut microbiome and insulin sensitivity, as well as biomarkers of metabolic health and gut functionality. Design 60 Danish adults at risk of developing metabolic syndrome were included in a randomised cross-over trial with two 8-week dietary intervention periods comprising whole grain diet and refined grain diet, separated by a washout period of =6 weeks. The response to the interventions on the gut microbiome composition and insulin sensitivity as well on measures of glucose and lipid metabolism, gut functionality, inflammatory markers, anthropometry and urine metabolomics were assessed. Results 50 participants completed both periods with a whole grain intake of 179±50 g/day and 13±10 g/day in the whole grain and refined grain period, respectively. Compliance was confirmed by a difference in plasma alkylresorcinols (p<0.0001). Compared with refined grain, whole grain did not significantly alter glucose homeostasis and did not induce major changes in the faecal microbiome. Also, breath hydrogen levels, plasma short-chain fatty acids, intestinal integrity and intestinal transit time were not affected. The whole grain diet did, however, compared with the refined grain diet, decrease body weight (p<0.0001), serum inflammatory markers, interleukin (IL)-6 (p=0.009) and C-reactive protein (p=0.003). The reduction in body weight was consistent with a reduction in energy intake, and IL-6 reduction was associated with the amount of whole grain consumed, in particular with intake of rye. Conclusion C ompared with refined grain diet, whole grain diet did not alter insulin sensitivity and gut microbiome but reduced body weight and systemic lowgrade inflammation.
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| 8. |
- Vedovato, Laura B., et al.
(author)
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Ancient fires enhance Amazon forest drought resistance
- 2023
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In: Frontiers in Forests and Global Change. - : Frontiers Media SA. - 2624-893X. ; 6
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Journal article (peer-reviewed)abstract
- Drought and fire reduce productivity and increase tree mortality in tropical forests. Fires also produce pyrogenic carbon (PyC), which persists in situ for centuries to millennia, and represents a legacy of past fires, potentially improving soil fertility and water holding capacity and selecting for the survival and recruitment of certain tree life-history (or successional) strategies. We investigated whether PyC is correlated with physicochemical soil properties, wood density, aboveground carbon (AGC) dynamics and forest resistance to severe drought. To achieve our aim, we used an Amazon-wide, long-term plot network, in forests without known recent fires, integrating site-specific measures of forest dynamics, soil properties and a unique soil PyC concentration database. We found that forests with higher concentrations of soil PyC had both higher soil fertility and lower wood density. Soil PyC was not associated with AGC dynamics in non-drought years. However, during extreme drought events (10% driest years), forests with higher concentrations of soil PyC experienced lower reductions in AGC gains (woody growth and recruitment), with this drought-immunizing effect increasing with drought severity. Forests with a legacy of ancient fires are therefore more likely to continue to grow and recruit under increased drought severity. Forests with high soil PyC concentrations (third quartile) had 3.8% greater AGC gains under mean drought, but 33.7% greater under the most extreme drought than forests with low soil PyC concentrations (first quartile), offsetting losses of up to 0.68 Mg C ha–1yr–1 of AGC under extreme drought events. This suggests that ancient fires have legacy effects on current forest dynamics, by altering soil fertility and favoring tree species capable of continued growth and recruitment during droughts. Therefore, mature forest that experienced fires centuries or millennia ago may have greater resistance to current short-term droughts.
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