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- Graco-Roza, Caio, et al.
(författare)
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Distance decay 2.0 – A global synthesis of taxonomic and functional turnover in ecological communities
- 2022
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Ingår i: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 31:7, s. 1399-1421
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Tidskriftsartikel (refereegranskat)abstract
- Aim: Understanding the variation in community composition and species abundances (i.e., beta-diversity) is at the heart of community ecology. A common approach to examine beta-diversity is to evaluate directional variation in community composition by measuring the decay in the similarity among pairs of communities along spatial or environmental distance. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 148 datasets comprising different types of organisms and environments.Location: Global.Time period: 1990 to present.Major taxa studied: From diatoms to mammals.Method: We measured the strength of the decay using ranked Mantel tests (Mantel r) and the rate of distance decay as the slope of an exponential fit using generalized linear models. We used null models to test whether functional similarity decays faster or slower than expected given the taxonomic decay along the spatial and environmental distance. We also unveiled the factors driving the rate of decay across the datasets, including latitude, spatial extent, realm and organismal features.Results: Taxonomic distance decay was stronger than functional distance decay along both spatial and environmental distance. Functional distance decay was random given the taxonomic distance decay. The rate of taxonomic and functional spatial distance decay was fastest in the datasets from mid-latitudes. Overall, datasets covering larger spatial extents showed a lower rate of decay along spatial distance but a higher rate of decay along environmental distance. Marine ecosystems had the slowest rate of decay along environmental distances.Main conclusions: In general, taxonomic distance decay is a useful tool for biogeographical research because it reflects dispersal-related factors in addition to species responses to climatic and environmental variables. Moreover, functional distance decay might be a cost-effective option for investigating community changes in heterogeneous environments.
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| 2. |
- Prieto, P., et al.
(författare)
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The value of selected in vitro and in silico methods to predict acute oral toxicity in a regulatory context : Results from the European Project ACuteTox
- 2013
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Ingår i: Toxicology in Vitro. - : Elsevier BV. - 0887-2333 .- 1879-3177. ; 27:4, s. 1357-1376
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Tidskriftsartikel (refereegranskat)abstract
- ACuteTox is a project within the 6th European Framework Programme which had as one of its goals to develop, optimise and prevalidate a non-animal testing strategy for predicting human acute oral toxicity. In its last 6 months, a challenging exercise was conducted to assess the predictive capacity of the developed testing strategies and final identification of the most promising ones. Thirty-two chemicals were tested blind in the battery of in vitro and in silico methods selected during the first phase of the project. This paper describes the classification approaches studied: single step procedures and two step tiered testing strategies. In summary, four in vitro testing strategies were proposed as best performing in terms of predictive capacity with respect to the European acute oral toxicity classification. In addition, a heuristic testing strategy is suggested that combines the prediction results gained from the neutral red uptake assay performed in 3T3 cells, with information on neurotoxicity alerts identified by the primary rat brain aggregates test method. Octanol-water partition coefficients and in silico prediction of intestinal absorption and blood-brain barrier passage are also considered. This approach allows to reduce the number of chemicals wrongly predicted as not classified (LD50 > 2000 mg/kg b.w.).
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| 6. |
- Ovaskainen, Otso, et al.
(författare)
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Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA
- 2024
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Ingår i: Scientific Data. - 2052-4463. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition.
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| 8. |
- Sanandaji, Nima, et al.
(författare)
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Unusual crystals of poly(epsilon-caprolactone) by unusual crystallisation : The effects of rapid cooling and fast solvent loss on the morphology, crystal structure and melting
- 2013
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Ingår i: Polymer. - : Elsevier BV. - 0032-3861 .- 1873-2291. ; 54:5, s. 1497-1503
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Tidskriftsartikel (refereegranskat)abstract
- The lateral habit, unit cell structure and melting behaviour of single crystals of poly(epsilon-caprolactone) (PCL) prepared by the rapid expansion of a supercritical solution technique was studied by AFM at ambient and higher temperatures and by grazing-incident X-ray scattering using a synchrotron source. After dissolving PCL in a solution of supercritical CO2 and 0.1 vol.% chloroform, an extremely fast phase transfer from a supercritical to a gas-like state occurred during expansion into atmospheric conditions, leading to a temporary temperature drop to below -;50 degrees C at the silica surface where the crystals were deposited. Single crystals of a hitherto unreported rectangular lateral habit were observed. Six-sided crystals were also observed, but they were fewer than the rectangular crystals and in addition the angles between the lateral faces were different from the theoretical angles between adjacent {110} faces and {110} and {100} faces. X-ray scattering indicated a polymorphic structure also including the orthorhombic (110) and (200) diffraction peaks. Distinct low angle peaks essentially along the c-axis indicated a stacking on a very fine scale (3.7-4.7 nm) within the crystals. The equatorial diffraction peaks indicated a less dense packing of the PCL stems. Rectangular single crystals with a height according to AFM of 11-27 nm melted between 40 and 45 degrees C, which is lower than the melting points (55 degrees C) recorded for the distorted six-sided crystals. The unusual conditions for crystallisation used gave the polymer molecules a severe limitation to rearrange from the initial random coil state. The facetted crystals consisted of a stack of 4 nm thick blocks; these blocks most probably constituted a regular variation in molecular packing, i.e. molecular order. The pronounced changes in the angles between adjacent faces from those observed in mature PCL crystals and the wide-angle X-ray scattering data indicated the presence of conformational disorder in the crystals.
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| 9. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
- 2012
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 4, s. 37-63
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Tidskriftsartikel (refereegranskat)abstract
- Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.
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| 10. |
- Sundell, J., et al.
(författare)
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Predation on two vole species by a shared predator: antipredatory response and prey preference
- 2008
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Ingår i: Population Ecology. - : Wiley. - 1438-3896 .- 1438-390X. ; 50:3, s. 257-266
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Tidskriftsartikel (refereegranskat)abstract
- In prey communities with shared predators, variation in prey vulnerability is a key factor in shaping community dynamics. Conversely, the hunting efficiency of a predator depends on the prey community structure, preferences of the predator and antipredatory behavioural traits of the prey. We studied experimentally, under seminatural field conditions, the preferences of a predator and the antipredatory responses of prey in a system consisting of two Myodes species of voles, the grey-sided vole (M. rufocanus Sund.) and the bank vole (M. glareolus Schreb.), and their specialist predator, the least weasel (Mustela nivalis nivalis L.). To quantify the preference of the weasels, we developed a new modelling framework that can be used for unbalanced data. The two vole species were hypothesised to have different habitat-dependent vulnerabilities. We created two habitats, open and forest, to provide different escape possibilities for the voles. We found a weak general preference of the weasels for the grey-sided voles over the bank voles, and a somewhat stronger preference specifically in open habitats. The weasels clearly preferred male grey-sided voles over females, whereas in bank voles, there was no difference. The activity of voles changed over time, so that voles increased their movements immediately after weasel introduction, but later adjusted their movements to times of lowered predation risk. Females that were more active had an elevated mortality risk, whereas in the case of males, the result was the opposite. We conclude that, in vulnerability to predation, the species- or habitat-specific characteristics of these prey species are playing a minor role compared to sex-specific characteristics.
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