| 11. |
- Dahlqvist, Johanna, 1979-, et al.
(författare)
-
Identification and functional characterization of a novel susceptibility locus for small vessel vasculitis with MPO-ANCA
- 2022
-
Ingår i: Rheumatology. - Oxford, United Kingdom : Oxford University Press (OUP). - 1462-0324 .- 1462-0332. ; 61:8, s. 3461-3470
-
Tidskriftsartikel (refereegranskat)abstract
- Objective To identify and characterize genetic loci associated with the risk of developing ANCA-associated vasculitides (AAV). Methods Genetic association analyses were performed after Illumina sequencing of 1853 genes and subsequent replication with genotyping of selected single nucleotide polymorphisms in a total cohort of 1110 Scandinavian cases with granulomatosis with polyangiitis or microscopic polyangiitis, and 1589 controls. A novel AAV-associated single nucleotide polymorphism was analysed for allele-specific effects on gene expression using luciferase reporter assay. Results PR3-ANCA(+) AAV was significantly associated with two independent loci in the HLA-DPB1/HLA-DPA1 region [rs1042335, P = 6.3 x 10(-61), odds ratio (OR) 0.10; rs9277341, P = 1.5 x 10(-44), OR 0.22] and with rs28929474 in the SERPINA1 gene (P = 2.7 x 10(-10), OR 2.9). MPO-ANCA(+) AAV was significantly associated with the HLA-DQB1/HLA-DQA2 locus (rs9274619, P = 5.4 x 10(-25), OR 3.7) and with a rare variant in the BACH2 gene (rs78275221, P = 7.9 x 10(-7), OR 3.0), the latter a novel susceptibility locus for MPO-ANCA(+) granulomatosis with polyangiitis/microscopic polyangiitis. The rs78275221-A risk allele reduced luciferase gene expression in endothelial cells, specifically, as compared with the non-risk allele. Conclusion We identified a novel susceptibility locus for MPO-ANCA(+) AAV and propose that the associated variant is of mechanistic importance, exerting a regulatory function on gene expression in specific cell types.
|
|
| 12. |
- Dawson, Samantha K., et al.
(författare)
-
Convergence of fungal traits over time in natural and forestry-fragmented patches
- 2020
-
Ingår i: Biological Conservation. - : Elsevier BV. - 0006-3207 .- 1873-2917. ; 251
-
Tidskriftsartikel (refereegranskat)abstract
- Setting aside small remnant patches of high biodiversity forest within managed forest landscapes is often used as conservation measure to provide a refuge and future source population of forest biodiversity, including wood-inhabiting fungal communities. Yet little is known about the long-term fungal community assembly, how these small, isolated patches change through time and how forest management in the surrounding landscape impacts traits and community functionality housed within. We applied a joint species distribution model to compare how fungal traits and communities changed over two survey periods undertaken ~20 years apart in boreal forest set-aside and natural patches. Natural patches in naturally fragmented landscapes were considered reference forests for small, remnant, near-natural forest patches in intensively managed forest landscapes. We found the majority of fungal traits converged over time between set-aside and natural patches, without changes in overall species richness. Red-listed species occurrence was initially lower in set-aside patches, but reached a comparable level of natural patches over time as a result of opposing changes in both patch types. Functional trait changes were larger in set-aside patches, but convergence was also related to opposing changes in natural patches. This is the first study to directly measure and test wood fungal community trait-environment relationships over time in small, high-conservation value forest patches. The long-term functional trait and red-listed species values of set-asides, coupled with their capacity for old-growth recovery, make them valuable focal areas for conservation.
|
|
| 13. |
|
|
| 14. |
- Ekman, Diana, et al.
(författare)
-
Stratified genetic analysis reveals sex differences in MPO-ANCA-associated vasculitis
- 2023
-
Ingår i: Rheumatology. - : Oxford University Press. - 1462-0324 .- 1462-0332. ; 62:9, s. 3213-3218
-
Tidskriftsartikel (refereegranskat)abstract
- Objective: To identify and genetically characterize subgroups of patients with ANCA-associated vasculitides (AAV) based on sex and ANCA subtype. Methods: A previously established SNP dataset derived from DNA sequencing of 1853 genes and genotyping of 1088 Scandinavian cases with AAV and 1589 controls was stratified for sex and ANCA subtype and analysed for association with five top AAV SNPs. rs9274619, a lead variant at the HLA-DQB1/HLA-DQA2 locus previously associated with AAV positive for myeloperoxidase (MPO)-ANCA, was analysed for association with the cumulative disease involvement of ten different organ systems. Results: rs9274619 showed a significantly stronger association to MPO-ANCA-positive females than males [P = 2.0 × 10-4, OR = 2.3 (95% CI 1.5, 3.5)], whereas proteinase 3 (PR3)-ANCA-associated variants rs1042335, rs9277341 (HLA-DPB1/A1) and rs28929474 (SERPINA1) were equally associated with females and males with PR3-ANCA. In MPO-ANCA-positive cases, carriers of the rs9274619 risk allele were more prone to disease engagement of eyes [P = 0.021, OR = 11 (95% CI 2.2, 205)] but less prone to pulmonary involvement [P = 0.026, OR = 0.52 (95% CI 0.30, 0.92)]. Moreover, AAV with both MPO-ANCA and PR3-ANCA was associated with the PR3-ANCA lead SNP rs1042335 [P = 0.0015, OR = 0.091 (95% CI 0.0022, 0.55)] but not with rs9274619. Conclusions: Females and males with MPO-ANCA-positive AAV differ in genetic predisposition to disease, suggesting at least partially distinct disease mechanisms between the sexes. Double ANCA-positive AAV cases are genetically similar to PR3-ANCA-positive cases, providing clues to the clinical follow-up and treatment of these patients.
|
|
| 15. |
- Ekström, Magnus, 1966-, et al.
(författare)
-
Estimating density from presence/absence data in clustered populations
- 2020
-
Ingår i: Methods in Ecology and Evolution. - : John Wiley & Sons. - 2041-210X. ; 11:3, s. 390-402
-
Tidskriftsartikel (refereegranskat)abstract
- Inventories of plant populations are fundamental in ecological research and monitoring, but such surveys are often prone to field assessment errors. Presence/absence (P/A) sampling may have advantages over plant cover assessments for reducing such errors. However, the linking between P/A data and plant density depends on model assumptions for plant spatial distributions. Previous studies have shown, for example, how that plant density can be estimated under Poisson model assumptions on the plant locations. In this study, new methods are developed and evaluated for linking P/A data with plant density assuming that plants occur in clustered spatial patterns. New theory was derived for estimating plant density under Neyman-Scott-type cluster models such as the Matern and Thomas cluster processes. Suggested estimators, corresponding confidence intervals and a proposed goodness-of-fit test were evaluated in a Monte Carlo simulation study assuming a Matern cluster process. Furthermore, the estimators were applied to plant data from environmental monitoring in Sweden to demonstrate their empirical application. The simulation study showed that our methods work well for large enough sample sizes. The judgment of what is' large enough' is often difficult, but simulations indicate that a sample size is large enough when the sampling distributions of the parameter estimators are symmetric or mildly skewed. Bootstrap may be used to check whether this is true. The empirical results suggest that the derived methodology may be useful for estimating density of plants such as Leucanthemum vulgare and Scorzonera humilis. By developing estimators of plant density from P/A data under realistic model assumptions about plants' spatial distributions, P/A sampling will become a more useful tool for inventories of plant populations. Our new theory is an important step in this direction.
|
|
| 16. |
- Ekström, Magnus, 1966-, et al.
(författare)
-
Estimating density from presence/absence data in clustered populations
- 2021
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- 1. Inventories of plant populations are fundamental in ecological research and monitoring, butsuch surveys are often prone to field assessment errors. Presence/ absence (P/A) samplingmay have advantages over plant cover assessments for reducing such errors. However, thelinking between P/A data and plant density depends on model assumptions for plant spatialdistributions. Previous studies have shown, for example, how that plant density can beestimated under Poisson model assumptions on the plant locations. In this study, newmethods are developed and evaluated for linking P/A data with plant density assuming thatplants occur in clustered spatial patterns.2. New theory was derived for estimating plant density under Neyman–Scott-type cluster models such as the Matérn and Thomas cluster processes. Suggested estimators, correspondingconfidence intervals and a proposed goodness-of-fit test were evaluated in a Monte Carlosimulation study assuming a Matérn cluster process. Furthermore, the estimators were applied to plant data from environmental monitoring in Sweden to demonstrate their empiricalapplication.3. The simulation study showed that our methods work well for large enough sample sizes.The judgment of what is ’large enough’ is often difficult, but simulations indicate that asample size is large enough when the sampling distributions of the parameter estimators aresymmetric or mildly skewed. Bootstrap may be used to check whether this is true. Theempirical results suggest that the derived methodology may be useful for estimating densityof plants such as Leucanthemum vulgare and Scorzonera humilis.4. By developing estimators of plant density from P/A data under realistic model assumptions about plants’ spatial distributions, P/A sampling will become a more useful tool forinventories of plant populations. Our new theory is an important step in this direction.
|
|
| 17. |
- Ekström, Magnus, 1966-, et al.
(författare)
-
Model-based estimation and mapping of plant density based on remotesensing and presence/absence data
- 2023
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Inventories of populations are of great importance in ecological research. For monitoring plants,presence/absence (P/A) sampling is simple to conduct, since only presence or absence of aspecies on a plot needs to be registered. Estimates of plant density may be obtained from P/Adata but need to be based on model assumptions about the spatial distribution of plants. Wehave showed, in a model-based setting, how to use P/A and remote sensing data for estimatingand mapping plant density for regions and subregions, where the model assumes plant locationsto follow an inhomogeneous Poisson point process. To guard against model misspecifications,we derived a test for assessing the plausibility of the model assumptions of the inhomogeneousPoisson point process. Using empirical data from the Swedish National Forest Inventory as wellas artificial plant population data, we evaluated the performance of the suggested estimators ofplant density and the proposed test of model assumptions, respectively.
|
|
| 18. |
- Esseen, Per-Anders, et al.
(författare)
-
Long-term dynamics of the iconic old-forest lichen Usnea longissima in a protected landscape
- 2023
-
Ingår i: Forest Ecology and Management. - : Elsevier. - 0378-1127 .- 1872-7042. ; 546
-
Tidskriftsartikel (refereegranskat)abstract
- Long-term data on spatial dynamics of epiphytic lichens associated with old-growth forests are fundamental for understanding how environmental factors drive their extinction and colonization in heterogeneous landscapes. This study focuses on Usnea longissima, a flagship species for biodiversity conservation. By using a long-term data set (37 yr.) of U. longissima in old Picea abies forests in Skuleskogen National Park, Sweden, we examined changes in the number of host trees, population size (sum of thallus length), extinction, colonization, dispersal, and distribution in a protected landscape. We surveyed the lichen in 1984–1985 by applying a line transect inventory and a total population inventory and tagged 355 occupied trees with an aluminium plate buried in the ground. We repeated the survey in 2021 using a metal detector and recorded GPS-position of host trees, tree and lichen population characteristics. We also measured the structure and age (tree-ring data) of the forest to understand how disturbance history influenced lichen populations. Usnea longissima occurred on 66 of the tagged trees and we recorded 141 new host trees. The number of host trees decreased with 41.7% and the population size with 41.9%. One third of the decline was caused by deterministic extinction (treefalls) and two thirds by stochastic extinction on standing trees. The probability of stochastic extinction on live trees decreased with population size in logistic regression. The decline in the sites with largest populations (35–87% loss) was more influenced by limited colonization than extinction. Colonization was highest in humid north-facing hillslopes with multi-layered forests driven by gap dynamics. The lichen was strongly dispersal-limited, with a median effective horizontal dispersal of only 3.8 m in 37 yr., explaining its strong dependence of long continuity of forest cover. The populations were clustered and had substantial local turnover, yet with stable distribution at landscape scale. The tree-ring index, growth releases and gap recruitments indicate extensive harvesting ∼ 1860–1900, but without major disturbances during the last 70–80 yr. Instead, the decline of U. longissima was probably driven by air pollution, climate change (autumn/winter mortality and heatwaves) and denser forests. Our findings highlight that the long-term survival of this lichen may be at risk even in forests having a strong level of protection.
|
|
| 19. |
- Esseen, Per-Anders, et al.
(författare)
-
Multiple drivers of large-scale lichen decline in boreal forest canopies
- 2022
-
Ingår i: Global Change Biology. - : John Wiley & Sons. - 1354-1013 .- 1365-2486. ; 28:10, s. 3293-3309
-
Tidskriftsartikel (refereegranskat)abstract
- Thin, hair-like lichens (Alectoria, Bryoria, Usnea) form conspicuous epiphyte communities across the boreal biome. These poikilohydric organisms provide important ecosystem functions and are useful indicators of global change. We analyse how environmental drivers influence changes in occurrence and length of these lichens on Norway spruce (Picea abies) over 10 years in managed forests in Sweden using data from >6000 trees. Alectoria and Usnea showed strong declines in southern-central regions, whereas Bryoria declined in northern regions. Overall, relative loss rates across the country ranged from 1.7% per year in Alectoria to 0.5% in Bryoria. These losses contrasted with increased length of Bryoria and Usnea in some regions. Occurrence trajectories (extinction, colonization, presence, absence) on remeasured trees correlated best with temperature, rain, nitrogen deposition, and stand age in multinomial logistic regression models. Our analysis strongly suggests that industrial forestry, in combination with nitrogen, is the main driver of lichen declines. Logging of forests with long continuity of tree cover, short rotation cycles, substrate limitation and low light in dense forests are harmful for lichens. Nitrogen deposition has decreased but is apparently still sufficiently high to prevent recovery. Warming correlated with occurrence trajectories of Alectoria and Bryoria, likely by altering hydration regimes and increasing respiration during autumn/winter. The large-scale lichen decline on an important host has cascading effects on biodiversity and function of boreal forest canopies. Forest management must apply a broad spectrum of methods, including uneven-aged continuous cover forestry and retention of large patches, to secure the ecosystem functions of these important canopy components under future climates. Our findings highlight interactions among drivers of lichen decline (forestry, nitrogen, climate), functional traits (dispersal, lichen colour, sensitivity to nitrogen, water storage), and population processes (extinction/colonization).
|
|
| 20. |
- Feng, Shaohong, et al.
(författare)
-
Dense sampling of bird diversity increases power of comparative genomics
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
-
Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
|
|
