| 1. |
- Abbasi, Rasha, et al.
(författare)
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IceCube search for neutrinos from GRB 221009A
- 2023
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Ingår i: Proceedings of 38th International Cosmic Ray Conference (ICRC 2023). - : Sissa Medialab Srl.
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Konferensbidrag (refereegranskat)abstract
- GRB 221009A is the brightest Gamma Ray Burst (GRB) ever observed. The observed extremelyhigh flux of high and very-high-energy photons provide a unique opportunity to probe the predictedneutrino counterpart to the electromagnetic emission. We have used a variety of methods to searchfor neutrinos in coincidence with the GRB over several time windows during the precursor, promptand afterglow phases of the GRB. MeV scale neutrinos are studied using photo-multiplier ratescalers which are normally used to search for galactic core-collapse supernovae neutrinos. GeVneutrinos are searched starting with DeepCore triggers. These events don’t have directionallocalization, but instead can indicate an excess in the rate of events. 10 GeV - 1 TeV and >TeVneutrinos are searched using traditional neutrino point source methods which take into accountthe direction and time of events with DeepCore and the entire IceCube detector respectively. The>TeV results include both a fast-response analysis conducted by IceCube in real-time with timewindows of T0 − 1 to T0 + 2 hours and T0 ± 1 day around the time of GRB 221009A, as well asan offline analysis with 3 new time windows up to a time window of T0 − 1 to T0 + 14 days, thelongest time period we consider. The combination of observations by IceCube covers 9 ordersof magnitude in neutrino energy, from MeV to PeV, placing upper limits across the range forpredicted neutrino emission.
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| 2. |
- Bergström, Anders, et al.
(författare)
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Grey wolf genomic history reveals a dual ancestry of dogs
- 2022
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 607:7918, s. 313-320
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Tidskriftsartikel (refereegranskat)abstract
- The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
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| 3. |
- Grüning, Björn, et al.
(författare)
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
- 2017
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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| 4. |
- Larson, Johannes, et al.
(författare)
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Predicting soil moisture conditions across a heterogeneous boreal catchment using terrain indices
- 2022
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Ingår i: Hydrology and Earth System Sciences. - : Copernicus GmbH. - 1027-5606 .- 1607-7938. ; 26, s. 4837-4851
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Tidskriftsartikel (refereegranskat)abstract
- Soil moisture has important implications for drought and flooding forecasting, forest fire prediction and water supply management. However, mapping soil moisture has remained a scientific challenge due to forest canopy cover and small-scale variations in soil moisture conditions. When accurately scaled, terrain indices constitute a good candidate for modelling the spatial variation of soil moisture conditions in many landscapes. In this study, we evaluated seven different terrain indices at varying digital elevation model (DEM) resolutions and user-defined thresholds as well as two available soil moisture maps, using an extensive field dataset (398 plots) of soil moisture conditions registered in five classes from a survey covering a (68 km2) boreal landscape. We found that the variation in soil moisture conditions could be explained by terrain indices, and the best predictors within the studied landscape were the depth to water index (DTW) and a machine-learning-generated map. Furthermore, this study showed a large difference between terrain indices in the effects of changing DEM resolution and user-defined thresholds, which severely affected the performance of the predictions. For example, the commonly used topographic wetness index (TWI) performed best on a resolution of 16 m, while TWI calculated on DEM resolutions higher than 4 m gave inaccurate results. In contrast, depth to water (DTW) and elevation above stream (EAS) were more stable and performed best on 1–2 m DEM resolution. None of the terrain indices performed best on the highest DEM resolution of 0.5 m. In addition, this study highlights the challenges caused by heterogeneous soil types within the study area and shows the need of local knowledge when interpreting the modelled results. The results from this study clearly demonstrate that when using terrain indices to represent soil moisture conditions, modelled results need to be validated, as selecting an unsuitable DEM resolution or user-defined threshold can give ambiguous and even incorrect results.
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| 5. |
- Larson, Johannes
(författare)
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Soil moisture conditions control nutrient accumulation, carbon storage and tree growth in boreal forest landscapes
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Forest and soil properties change across landscapes due to the complex interactions between various environmental factors. In many landscapes, topography exerts a major influence on the variation in soil moisture conditions, which in turn largely affects soil properties and processes. This thesis synthesises the results from four studies (papers I-IV), with the underlying aim to increase the understanding of how environmental factors, in particular, soil moisture, control the variation of nutrient accumulation, carbon storage, and tree growth within boreal landscapes. The four studies were all based on an extensive survey of a 68 km2 boreal forest landscape in northern Sweden. In Paper I, soil moisture conditions were predicted using multiple terrain indices. The results emphasised within-study validation and how digital elevation model resolution together with user-defined thresholds influence prediction accuracy. Paper II focused on how multiple environmental drivers influence the variation in soil carbon-to-nitrogen (C/N) ratios, with a noteworthy result that the ratio decreases as soil moisture conditions increase. Paper III presented how, soil moisture conditions significantly controls the distribution and partitioning of carbon stocks, with large increases in total carbon stock observed as soil moisture conditions increases, which was observed at both plot and landscape scale. The results in paper IV showed that, estimates of forest site quality decrease in response to increased soil moisture conditions. In conclusion, the research discussed in this thesis emphasises the importance of studying forest ecosystems on a landscape scale, an approach that can provide key insights into the factors that influence variation of different attributes of boreal forest ecosystems.
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| 6. |
- Larson, Johannes, et al.
(författare)
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Soil moisture controls the partitioning of carbon stocks across a managed boreal forest landscape
- 2023
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Ingår i: Scientific Reports. - 2045-2322. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Boreal forests sequester and store vast carbon (C) pools that may be subject to significant feedback effects induced by climatic warming. The boreal landscape consists of a mosaic of forests and peatlands with wide variation in total C stocks, making it important to understand the factors controlling C pool sizes in different ecosystems. We therefore quantified the total C stocks in the organic layer, mineral soil, and tree biomass in 430 plots across a 68 km2 boreal catchment. The organic layer held the largest C pool, accounting for 39% of the total C storage; tree and mineral C pools accounted for 38% and 23%, respectively. The size of the soil C pool was positively related to modelled soil moisture conditions, especially in the organic soil layer (R2 = 0.50). Conversely, the tree C pool exhibited a unimodal relationship: storage was highest under intermediate wetness conditions. The magnitude and variation in the total soil C stocks observed in this work were comparable to those found at the national level in Sweden, suggesting that C accumulation in boreal landscapes is more sensitive to local variation resulting primarily from differences in soil moisture conditions than to regional differences in climate, nitrogen deposition, and parent material.
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| 7. |
- Larson, Johannes, et al.
(författare)
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Tree growth potential and its relationship with soil moisture conditions across a heterogeneous boreal forest landscape
- 2024
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Ingår i: Scientific Reports. - 2045-2322. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Forest growth varies across landscapes due to the intricate relationships between various environmental drivers and forest management. In this study, we analysed the variation of tree growth potential across a landscape scale and its relation to soil moisture. We hypothesised that soil moisture conditions drive landscape-level variation in site quality and that intermediate soil moisture conditions demonstrate the highest potential forest production. We used an age-independent difference model to estimate site quality in terms of maximum achievable tree height by measuring the relative change in Lorey's mean height for a five year period across 337 plots within a 68 km2 boreal landscape. We achieved wall-to-wall estimates of site quality by extrapolating the modelled relationship using repeated airborne laser scanning data collected in connection to the field surveys. We found a clear decrease in site quality under the highest soil moisture conditions. However, intermediate soil moisture conditions did not demonstrate clear site quality differences; this is most likely a result of the nature of the modelled soil moisture conditions and limitations connected to the site quality estimation. There was considerable unexplained variation in the modelled site quality both on the plot and landscape levels. We successfully demonstrated that there is a significant relationship between soil moisture conditions and site quality despite limitations associated with a short study period in a low productive region and the precision of airborne laser scanning measurements of mean height.
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| 8. |
- Larson, Johannes, et al.
(författare)
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Variability in soil carbon-to-nitrogen ratios explained by environmental conditions in a boreal catchment
- 2024
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Ingår i: Forest Ecology and Management. - 0378-1127 .- 1872-7042. ; 568
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Tidskriftsartikel (refereegranskat)abstract
- Forest soil functions are influenced by interactions among trees, other organisms, and environmental factors such as the soil parent material and climate. Tree productivity and potential for forest C sequestration are currently receiving considerable attention. In boreal forests, plant productivity is commonly limited by the supply of N. Trees and other plants integrate the C and N cycles to form plant organs, which provide organic material for soils and subsequently feed the soil biota. Thus, plant growth has profound impacts on soil and ecosystem biogeochemistry. In this context, the soil C/N ratio is a critical parameter, which can display large variation across forest landscapes. This variation is correlated with forest productivity and other ecosystem functions. The aim of this study was to explore how C/N ratios in boreal forest soils are related to topography, dominant tree species, parent material, and soil texture. This was done by using a spatially-intense dataset of soil C/N ratios which included three sampling depths from 391 forest plots located within a 68 km (2) boreal forest catchment. Hydrological conditions related to topography (i.e., Topographic Wetness Index) demonstrated a significant influence on organic layer C/N ratios (R (2) =0.11, p <0.001), which decreased with increaced soil wetness. The topographic control on C/N ratios was strongest in unsorted sediments (R- 2 =0.15, p <0.001), where topography is the main driver of the variation in soil moisture conditions. The topographic influence on C/N ratios in mineral soil decreased with depth and was found to be non-significant at the 10 -20 cm depth. Forests dominated by Scots pine showed higher C/N ratios in the surficial organic layer than forests with other dominant tree species (mainly Norway spruce) or a mixed forests. In contrast, dominant tree species was not found to influence the C/N ratio in mineral soil layers. For mineral soil samples representing sorted sediments, C/N ratios decreased with grain size distribution, while no significant differences in C/N rations were observed in unsorted sediments. The study highlights a large landscape variation in soil C/N ratios within a boreal landscape. It also demonstrates the challenges associated with explaining soil properties, as a sizeable proportion of unexplained variation is caused by the complex interactions between multiple environmental factors linked to the biogeochemistry of forest soils including tree-soil interactions.
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| 9. |
- Larson, Johannes, et al.
(författare)
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What happens to trees and soils during five decades of experimental nitrogen loading?
- 2024
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Ingår i: Forest Ecology and Management. - 0378-1127 .- 1872-7042. ; 553
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Tidskriftsartikel (refereegranskat)abstract
- High deposition of nitrogen was postulated to drive losses of NO3 - and nutrient base cations, causing soil acidification, nutrient deficiencies reducing tree growth and ultimately tree mortality. We tested these predictions in a uniquely long-term study involving three NH4NO3 addition treatments (N1-N3) in a boreal Pinus sylvestris forest. The lowest level (N1), 30 kg N ha− 1 yr− 1 was applied during 50 years. Twice this rate (N2) was added 38 years, followed by 12 years of recovery, while thrice this rate (N3) was added 20 years followed by 30 years of recovery. We compared tree growth, changes in foliar and soil chemistry among treatments including control plots without N additions. As predicted, the N treatments lowered soil pH and reduced soil base saturation by around 50 %. They also lowered foliar levels of Ca, Mg, K, P and B initially, but after 50 years only Ca and Mg remained lower than in the control. Lack of B motivated a single addition of 2.5 kg ha− 1 after ten years of N treatment. Tree stem growth became and then remained higher in N1 than in the other treatments through the 50 years of treatments. In N2 and N3, foliar δ15N increased during the N-loading phase, but declined during the recovery phase, indicating a return of ectomycorrhizal fungi and their role in tightening the N cycle in N-limited forests. In the terminated, initially highest N treatments, N2 and N3, the trees even show signs of returning to Nlimitation. In these treatments, the soil base saturation remains lower, while the pH was only lower at 0–10 depth in the mineral soil, but not in the 10–20 cm depth horizon or in the superficial organic mor-layer. Accurately documenting the effect of N additions on forest growth required a long-term approach, where reasonable rates of application could be compared with extreme rates. Such long-term experiments are necessary to support forest management in achieving goals for developing future forests as they shift in response to major, global-scale changes.
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| 10. |
- MacDougall, Andrew S., et al.
(författare)
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Widening global variability in grassland biomass since the 1980s
- 2024
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Ingår i: Nature Ecology & Evolution. - : Springer Nature. - 2397-334X.
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Tidskriftsartikel (refereegranskat)abstract
- Global change is associated with variable shifts in the annual production of aboveground plant biomass, suggesting localized sensitivities with unclear causal origins. Combining remotely sensed normalized difference vegetation index data since the 1980s with contemporary field data from 84 grasslands on 6 continents, we show a widening divergence in site-level biomass ranging from +51% to −34% globally. Biomass generally increased in warmer, wetter and species-rich sites with longer growing seasons and declined in species-poor arid areas. Phenological changes were widespread, revealing substantive transitions in grassland seasonal cycling. Grazing, nitrogen deposition and plant invasion were prevalent in some regions but did not predict overall trends. Grasslands are undergoing sizable changes in production, with implications for food security, biodiversity and carbon storage especially in arid regions where declines are accelerating.
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