| 1. |
- Ameur, Adam, et al.
(author)
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SweGen : a whole-genome data resource of genetic variability in a cross-section of the Swedish population
- 2017
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In: European Journal of Human Genetics. - : NATURE PUBLISHING GROUP. - 1018-4813 .- 1476-5438. ; 25:11, s. 1253-1260
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Journal article (peer-reviewed)abstract
- Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.
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| 2. |
- Dahlberg, C. Johan, et al.
(author)
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Correlations between plant climate optima across different spatial scales
- 2020
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In: Environmental and Experimental Botany. - : Elsevier BV. - 0098-8472 .- 1873-7307. ; 170
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Journal article (peer-reviewed)abstract
- Identifying the factors determining the abundance and distribution of species is a fundamental question in ecology. One key issue is how similar the factors determining species' distributions across spatial scales are (here we focus especially on spatial extents). If the factors are similar across extents, then the large scale distribution pattern of a species may provide information about its local habitat requirements, and vice versa. We assessed the relationships between landscape and national optima as well as landscape and continental optima for growing degree days, maximum temperature and minimum temperature for 96 bryophytes and 50 vascular plants. For this set of species, we derived landscape optima from abundance weighted temperature data using species inventories in central Sweden and a fine-grained temperature model (50 m), national optima from niche centroid modelling based on GBIF data from Sweden and the same fine-grained climate model, and continental optima using the same method as for the national optima but from GBIF data from Europe and Worldclim temperatures (c. 1000 m). The landscape optima of all species were positively correlated with national as well as continental optima for maximum temperature (r = 0.45 and 0.46, respectively), weakly so for growing degree days (r = 0.30 and r = 0.28), but sometimes absent for minimum temperature (r = 0.26 and r = 0.04). The regression slopes of national or continental optima on local optima did not differ between vascular plants and bryophytes for GDD and Tmax. However, the relationship between the optima of Tmin differed between groups, being positive in vascular plants but absent in bryophytes. Our results suggest that positive correlations between optima at different spatial scales are present for some climatic variables but not for others. Moreover, our results for vascular plants and bryophytes suggest that correlations might differ between organism groups and depend on the ecology of the focal organisms. This implies that it is not possible to routinely up- or downscale distribution patterns based on environmental correlations, since drivers of distribution patterns might differ across spatial extents.
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| 3. |
- Dahlberg, C. Johan, 1978-, et al.
(author)
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Performance of Forest Bryophytes with Different Geographical Distributions Transplanted across a Topographically Heterogeneous Landscape
- 2014
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:11
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Journal article (peer-reviewed)abstract
- Most species distribution models assume a close link between climatic conditions and species distributions. Yet, we know little about the link between species’ geographical distributions and the sensitivity of performance to local environmental factors. We studied the performance of three bryophyte species transplanted at south- and north-facing slopes in a boreal forest landscape in Sweden. At the same sites, we measured both air and ground temperature. We hypothesized that the two southerly distributed species Eurhynchium angustirete and Herzogiella seligeri perform better on south-facing slopes and in warm conditions, and that the northerly distributed species Barbilophozia lycopodioides perform better on north-facing slopes and in relatively cool conditions. The northern, but not the two southern species, showed the predicted relationship with slope aspect. However, the performance of one of the two southern species was still enhanced by warm temperatures. An important reason for the inconsistent results can be that microclimatic gradients across landscapes are complex and influenced by many climate-forcing factors. Therefore, comparing only north- and south-facing slopes might not capture the complexity of microclimatic gradients. Population growth rates and potential distributions are the integrated results of all vital rates. Still, the study of selected vital rates constitutes an important first step to understand the relationship between population growth rates and geographical distributions and is essential to better predict how climate change influences species distributions.
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| 4. |
- Dahlberg, C. Johan, 1978-, et al.
(author)
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Plant landscape climatic optima correlate with their continental range optima
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Other publication (other academic/artistic)abstract
- Aim Factors determining species’ distributions at smaller scales may inform us about larger scale distributions, and vice versa. We predicted that landscape and continental climatic optima for plants are positively correlated, and that species that have their optima outside a given focal landscape will cluster at the warmest or coldest landscape patches. Also, we predicted that the correlations of temperature optima are stronger for vascular plants than for bryophytes, since bryophytes may be regulated also by air moisture.LocationÅngermanland, Sweden (landscape scale); Europe (continental scale).MethodsWe derived landscape optima from fine-grained temperature models (50 m) and species inventories, and continental optima from MaxEnt niche modelling based on GBIF occurrences and Worldclim temperatures (c. 1000 m), for 96 bryophytes and 50 vascular plants. Optima were derived for growing degree days, and maximum and minimum temperature.ResultsThe landscape and continental optima of all species were positively correlated for growing degree days and maximum temperature (r = 0.19 and r = 0.44), but not for minimum temperature (r = -0.010). Species with their continental optima outside the focal landscape did not clearly cluster in the most extreme parts of the landscape. For vascular plants the correlation was positive for both growing degree days and maximum temperature (r = 0.50 and r = 0.64), but for bryophytes only for maximum temperature (r = 0.34).Main conclusionsThe optima correlations for maximum temperature and growing degree days indicate that we can infer large scale distribution patterns of plants from their local scale distributions, and suggest in which environments species occur if we only know their continental scale optima. The lack of clustering of southern and northern species limits the possibility for conservation actions targeting microrefugia. Lastly, the correlations indicate that the distributions of vascular plants were more influenced by temperature than bryophytes.
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| 5. |
- Dahlberg, C. Johan, 1978-, et al.
(author)
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Population dynamics of moss transplants across microclimatic gradients
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Other publication (other academic/artistic)abstract
- In order to determine the response of a species to climatic change it is important to study how climatic factors influence its vital rates and population growth rate across climatic gradients. We investigated how microclimate influence the population dynamics of transplants from northern and more southern populations of the forest bryophyte Hylocomiastrum umbratum. We predicted that its population growth rate is favored by moist microclimates with colder maximum temperatures, longer snow cover duration and less evaporation, and that annual shoots (segments) will be shorter under drier conditions. We also predicted that northern populations will have higher population growth rate and larger segments than southern populations when transplanted to the northern range. We placed transplants from three northern and three southern populations of H. umbratum at 30 forested sites in central Sweden differing in microclimate. We marked and followed the growth of individual shoots during two years, and calculated population growth rates and stable stage distributions of segment size classes using transition matrix models for northern and southern transplants, respectively, at each locality. Population growth rate was lower and shorter segments developed at sites with higher evaporation, corresponding to our hypothesis. There were no significant difference in population growth rate and stable stage segment length between southern and northern populations. Higher evaporation during the summer result in lower population growth rates of H. umbratum by affecting vital rates, in terms of less segment growth. Both climate change and forestry may alter evaporation conditions across the landscape and, thus, the future distribution of the species.
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| 6. |
- Dahlberg, C. Johan, 1978-
(author)
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The role of microclimate for the performance and distribution of forest plants
- 2016
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Doctoral thesis (other academic/artistic)abstract
- Microclimatic gradients may have large influence on individual vital rates and population growth rates of species, and limit their distributions. Therefore, I focused on the influence of microclimate on individual performance and distribution of species. Further, I examined differences in how microclimate affect species with contrasting distributions or different ecophysiological traits, and populations within species. More specifically, I investigated the performance of northern and southern distributed forest bryophytes that were transplanted across microclimatic gradients, and the timing of vegetative and reproductive development among northern, marginal and more southern populations of a forest herb in a common garden. Also, I compared the landscape and continental distributions across forest bryophytes and vascular plants and, thus, their distribution limiting factors at different spatial scales. Lastly, I examined the population dynamics across microclimatic gradients of transplants from northern and southern populations of a forest moss. The effects of microclimatic conditions on performance differed among bryophytes with contrasting distributions. There were no clear differences between northern and southern populations in the timing of development of a forest herb or in the population dynamics of a moss. However, within each region there was a differentiation of the forest herb populations, related to variation in local climatic conditions and in the south also to proportion of deciduous trees. The continental distributions of species were reflected in their landscape distributions and vice versa, in terms of their occurrence optima for climatic variables. The variation in landscape climatic optima was, however, larger than predicted, which limit the precision for predictions of microrefugia. Probably, the distributions of vascular plants were more affected by temperature than the distributions of bryophytes. Bryophytes are sensitive to moisture conditions, which was demonstrated by a correlation between evaporation and the population growth rate of a forest moss. We might be able to predict species’ landscape scale distributions by linking microclimatic conditions to their population growth rates, via their vital rates, and infer larger scale distribution patterns.
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| 7. |
- Dahlberg, Johan, et al.
(author)
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Arteria : An automation system for a sequencing core facility
- 2019
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In: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 8:12
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Journal article (peer-reviewed)abstract
- Background: In recent years, nucleotide sequencing has become increasingly instrumental in both research and clinical settings. This has led to an explosive growth in sequencing data produced worldwide. As the amount of data increases, so does the need for automated solutions for data processing and analysis. The concept of workflows has gained favour in the bioinformatics community, but there is little in the scientific literature describing end-to-end automation systems. Arteria is an automation system that aims at providing a solution to the data-related operational challenges that face sequencing core facilities.Findings: Arteria is built on existing open source technologies, with a modular design allowing for a community-driven effort to create plug-and-play micro-services. In this article we describe the system, elaborate on the underlying conceptual framework, and present an example implementation. Arteria can be reduced to 3 conceptual levels: orchestration (using an event-based model of automation), process (the steps involved in processing sequencing data, modelled as workflows), and execution (using a series of RESTful micro-services). This creates a system that is both flexible and scalable. Arteria-based systems have been successfully deployed at 3 sequencing core facilities. The Arteria Project code, written largely in Python, is available as open source software, and more information can be found at https://arteria-project.github.io/.Conclusions: We describe the Arteria system and the underlying conceptual framework, demonstrating how this model can be used to automate data handling and analysis in the context of a sequencing core facility.
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| 8. |
- Dahlberg, Lena, 1970-, et al.
(author)
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Ensamhet bland äldre personer i Norden
- 2020
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Reports (other academic/artistic)abstract
- Rapporten presenterar översikter av tidigare forskning och analyser av känslan av ensamhet bland äldre personer. Överlag finns det kunskap om ensamhetens konsekvenser för ohälsa, men det behövs ytterligare forskning där starkare slutsatser kan dras om sambandens riktning, och ett tydligare fokus på ensamhet i gruppen äldre personer. En systematisk översikt visar att det finns god kunskap om en del faktorer som ökar risken för ensamhet, men mer forskning behövs om andra potentiella riskfaktorer. Analyserna visar en relativt låg och stabil förekomst av ensamhet bland äldre personer i Norden, samt att ohälsa och olika indikatorer för social exkludering (t.ex. bristande sociala relationer, otillräcklig inkomst, samt otrygghet i närområdet) har samband med ensamhet. Slutligen konstateras att forskningen om nordiska interventioner för att minska ensamhet bland äldre personer är begränsad.
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