| 1. |
- Schoch, Conrad L., et al.
(författare)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Tidskriftsartikel (refereegranskat)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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| 2. |
- Schoville, Sean D., et al.
(författare)
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A model species for agricultural pest genomics : The genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.
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| 3. |
- Franic, Iva, et al.
(författare)
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Climate, host and geography shape insect and fungal communities of trees
- 2023
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Non-native pests, climate change, and their interactions are likely to alter relationships between trees and tree-associated organisms with consequences for forest health. To understand and predict such changes, factors structuring tree-associated communities need to be determined. Here, we analysed the data consisting of records of insects and fungi collected from dormant twigs from 155 tree species at 51 botanical gardens or arboreta in 32 countries. Generalized dissimilarity models revealed similar relative importance of studied climatic, host-related and geographic factors on differences in tree-associated communities. Mean annual temperature, phylogenetic distance between hosts and geographic distance between locations were the major drivers of dissimilarities. The increasing importance of high temperatures on differences in studied communities indicate that climate change could affect tree-associated organisms directly and indirectly through host range shifts. Insect and fungal communities were more similar between closely related vs. distant hosts suggesting that host range shifts may facilitate the emergence of new pests. Moreover, dissimilarities among tree-associated communities increased with geographic distance indicating that human-mediated transport may serve as a pathway of the introductions of new pests. The results of this study highlight the need to limit the establishment of tree pests and increase the resilience of forest ecosystems to changes in climate.
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| 4. |
- Franic, Iva, et al.
(författare)
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Worldwide diversity of endophytic fungi and insects associated with dormant tree twigs
- 2022
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Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- International trade in plants and climate change are two of the main factors causing damaging tree pests (i.e. fungi and insects) to spread into new areas. To mitigate these risks, a large-scale assessment of tree-associated fungi and insects is needed. We present records of endophytic fungi and insects in twigs of 17 angiosperm and gymnosperm genera, from 51 locations in 32 countries worldwide. Endophytic fungi were characterized by high-throughput sequencing of 352 samples from 145 tree species in 28 countries. Insects were reared from 227 samples of 109 tree species in 18 countries and sorted into taxonomic orders and feeding guilds. Herbivorous insects were grouped into morphospecies and were identified using molecular and morphological approaches. This dataset reveals the diversity of tree-associated taxa, as it contains 12,721 fungal Amplicon Sequence Variants and 208 herbivorous insect morphospecies, sampled across broad geographic and climatic gradients and for many tree species. This dataset will facilitate applied and fundamental studies on the distribution of fungal endophytes and insects in trees.
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| 5. |
- Walsh, Roddy, et al.
(författare)
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Enhancing rare variant interpretation in inherited arrhythmias through quantitative analysis of consortium disease cohorts and population controls
- 2021
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Ingår i: Genetics in Medicine. - : Nature Publishing Group. - 1098-3600 .- 1530-0366. ; 23:1, s. 47-58
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Stringent variant interpretation guidelines can lead to high rates of variants of uncertain significance (VUS) for genetically heterogeneous disease like long QT syndrome (LQTS) and Brugada syndrome (BrS). Quantitative and disease-specific customization of American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines can address this false negative rate.Methods: We compared rare variant frequencies from 1847 LQTS (KCNQ1/KCNH2/SCN5A) and 3335 BrS (SCN5A) cases from the International LQTS/BrS Genetics Consortia to population-specific gnomAD data and developed disease-specific criteria for ACMG/AMP evidence classes-rarity (PM2/BS1 rules) and case enrichment of individual (PS4) and domain-specific (PM1) variants.Results: Rare SCN5A variant prevalence differed between European (20.8%) and Japanese (8.9%) BrS patients (p = 5.7 x 10(-18)) and diagnosis with spontaneous (28.7%) versus induced (15.8%) Brugada type 1 electrocardiogram (ECG) (p = 1.3 x 10(-13)). Ion channel transmembrane regions and specific N-terminus (KCNH2) and C-terminus (KCNQ1/KCNH2) domains were characterized by high enrichment of case variants and >95% probability of pathogenicity. Applying the customized rules, 17.4% of European BrS and 74.8% of European LQTS cases had (likely) pathogenic variants, compared with estimated diagnostic yields (case excess over gnomAD) of 19.2%/82.1%, reducing VUS prevalence to close to background rare variant frequency.Conclusion: Large case-control data sets enable quantitative implementation of ACMG/AMP guidelines and increased sensitivity for inherited arrhythmia genetic testing.
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| 6. |
- Harrison, Paula A., et al.
(författare)
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Identifying and prioritising services in European terrestrial and freshwater ecosystems
- 2010
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Ingår i: Biodiversity and Conservation. - : Springer Science and Business Media LLC. - 0960-3115 .- 1572-9710. ; 19:10, s. 2791-2821
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Tidskriftsartikel (refereegranskat)abstract
- Ecosystems are multifunctional and provide humanity with a broad array of vital services. Effective management of services requires an improved evidence base, identifying the role of ecosystems in delivering multiple services, which can assist policy-makers in maintaining them. Here, information from the literature and scientific experts was used to systematically document the importance of services and identify trends in their use and status over time for the main terrestrial and freshwater ecosystems in Europe. The results from this review show that intensively managed ecosystems contribute mostly to vital provisioning services (e.g. agro-ecosystems provide food via crops and livestock, and forests provide wood), while semi-natural ecosystems (e.g. grasslands and mountains) are key contributors of genetic resources and cultural services (e.g. aesthetic values and sense of place). The most recent European trends in human use of services show increases in demand for crops from agro-ecosystems, timber from forests, water flow regulation from rivers, wetlands and mountains, and recreation and ecotourism in most ecosystems, but decreases in livestock production, freshwater capture fisheries, wild foods and virtually all services associated with ecosystems which have considerably decreased in area (e.g. semi-natural grasslands). The condition of the majority of services show either a degraded or mixed status across Europe with the exception of recent enhancements in timber production in forests and mountains, freshwater provision, water/erosion/natural hazard regulation and recreation/ecotourism in mountains, and climate regulation in forests. Key gaps in knowledge were evident for certain services across all ecosystems, including the provision of biochemicals and natural medicines, genetic resources and the regulating services of seed dispersal, pest/disease regulation and invasion resistance.
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| 7. |
- Luck, Gary W., et al.
(författare)
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Quantifying the Contribution of Organisms to the Provision of Ecosystem Services
- 2009
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Ingår i: BioScience. - : Oxford University Press (OUP). - 0006-3568 .- 1525-3244. ; 59:3, s. 223-235
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Tidskriftsartikel (refereegranskat)abstract
- Research on ecosystem services has grown rapidly over the last decade. Two conceptual frameworks have been published to guide ecological assessments of organisms that deliver services-the concepts of service-providing units (SPUs) and ecosystem service providers (ESPs). Here, we unite these frameworks and present an SPU-ESP continuum that offers a coherent conceptual approach for synthesizing the latest developments in ecosystem service research, and can direct future studies at all levels of organization. In particular, we show how the service-provider concept call be applied tit the population, functional group, and community levels, We strongly emphasize the need to identify and quantify the organisms and their characteristics (e.g., functional traits) that provide services, and to assess service provision relative to the demands of human beneficiaries. We use key examples from the literature to illustrate the new approach and to highlight gaps in knowledge, particularly in relation to the impact of species interactions and ecosystem dynamics on service provision.
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| 8. |
- Walker, Anthony P., et al.
(författare)
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Comprehensive ecosystem model-data synthesis using multiple data sets at two temperate forest free-air CO2 enrichment experiments: Model performance at ambient CO2 concentration
- 2014
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Ingår i: Journal of Geophysical Research - Biogeosciences. - 2169-8953 .- 2169-8961. ; 119:5, s. 937-964
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Tidskriftsartikel (refereegranskat)abstract
- Free-air CO2 enrichment (FACE) experiments provide a remarkable wealth of data which can be used to evaluate and improve terrestrial ecosystem models (TEMs). In the FACE model-data synthesis project, 11 TEMs were applied to two decadelong FACE experiments in temperate forests of the southeastern U.S.the evergreen Duke Forest and the deciduous Oak Ridge Forest. In this baseline paper, we demonstrate our approach to model-data synthesis by evaluating the models' ability to reproduce observed net primary productivity (NPP), transpiration, and leaf area index (LAI) in ambient CO2 treatments. Model outputs were compared against observations using a range of goodness-of-fit statistics. Many models simulated annual NPP and transpiration within observed uncertainty. We demonstrate, however, that high goodness-of-fit values do not necessarily indicate a successful model, because simulation accuracy may be achieved through compensating biases in component variables. For example, transpiration accuracy was sometimes achieved with compensating biases in leaf area index and transpiration per unit leaf area. Our approach to model-data synthesis therefore goes beyond goodness-of-fit to investigate the success of alternative representations of component processes. Here we demonstrate this approach by comparing competing model hypotheses determining peak LAI. Of three alternative hypotheses(1) optimization to maximize carbon export, (2) increasing specific leaf area with canopy depth, and (3) the pipe modelthe pipe model produced peak LAI closest to the observations. This example illustrates how data sets from intensive field experiments such as FACE can be used to reduce model uncertainty despite compensating biases by evaluating individual model assumptions.
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| 9. |
- Moss, Brian D., et al.
(författare)
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Climate change and the future of freshwater biodiversity in Europe : a primer for policy-makers
- 2009
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Ingår i: Freshwater Reviews. - : Freshwater Biological Association. - 1755-084X. ; 2:2, s. 103-130
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Tidskriftsartikel (refereegranskat)abstract
- Earth's climate is changing, and by the end of the 21st century in Europe, average temperatures are likely to have risen by at least 2 °C, and more likely 4 °C with associated effects on patterns of precipitation and the frequency of extreme weather events. Attention among policy-makers is divided about how to minimise the change, how to mitigate its effects, how to maintain the natural resources on which societies depend and how to adapt human societies to the changes. Natural systems are still seen, through a long tradition of conservation management that is largely species-based, as amenable to adaptive management, and biodiversity, mostly perceived as the richness of plant and vertebrate communities, often forms a focus for planning. We argue that prediction of particular species changes will be possible only in a minority of cases but that prediction of trends in general structure and operation of four generic freshwater ecosystems (erosive rivers, depositional floodplain rivers, shallow lakes and deep lakes) in three broad zones of Europe (Mediterranean, Central and Arctic-Boreal) is practicable. Maintenance and rehabilitation of ecological structures and operations will inevitably and incidentally embrace restoration of appropriate levels of species biodiversity. Using expert judgement, based on an extensive literature, we have outlined, primarily for lay policy makers, the pristine features of these systems, their states under current human impacts, how these states are likely to alter with a warming of 2 °C to 4 °C and what might be done to mitigate this. We have avoided technical terms in the interests of communication, and although we have included full referencing as in academic papers, we have eliminated degrees of detail that could confuse broad policy-making
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| 10. |
- De Kauwe, Martin G., et al.
(författare)
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Forest water use and water use efficiency at elevated CO2: a model-data intercomparison at two contrasting temperate forest FACE sites
- 2013
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 19:6, s. 1759-1779
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Tidskriftsartikel (refereegranskat)abstract
- Predicted responses of transpiration to elevated atmospheric CO2 concentration (eCO2) are highly variable amongst process-based models. To better understand and constrain this variability amongst models, we conducted an intercomparison of 11 ecosystem models applied to data from two forest free-air CO2 enrichment (FACE) experiments at Duke University and Oak Ridge National Laboratory. We analysed model structures to identify the key underlying assumptions causing differences in model predictions of transpiration and canopy water use efficiency. We then compared the models against data to identify model assumptions that are incorrect or are large sources of uncertainty. We found that model-to-model and model-to-observations differences resulted from four key sets of assumptions, namely (i) the nature of the stomatal response to elevated CO2 (coupling between photosynthesis and stomata was supported by the data); (ii) the roles of the leaf and atmospheric boundary layer (models which assumed multiple conductance terms in series predicted more decoupled fluxes than observed at the broadleaf site); (iii) the treatment of canopy interception (large intermodel variability, 215%); and (iv) the impact of soil moisture stress (process uncertainty in how models limit carbon and water fluxes during moisture stress). Overall, model predictions of the CO2 effect on WUE were reasonable (intermodel =approximately 28%+/- 10%) compared to the observations (=approximately 30%+/- 13%) at the well-coupled coniferous site (Duke), but poor (intermodel =approximately 24%+/- 6%; observations =approximately 38%+/- 7%) at the broadleaf site (Oak Ridge). The study yields a framework for analysing and interpreting model predictions of transpiration responses to eCO2, and highlights key improvements to these types of models.
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