| 1. |
- Caputo, Andrea, 1988-
(författare)
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Genomic and morphological diversity of marine planktonic diatom-diazotroph associations : a continuum of integration and diversification through geological time
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Symbioses between eukaryotes and nitrogen (N2)-fixing cyanobacteria (or diazotrophs) are quite common in the plankton community. A few genera of diatoms (Bacillariophyceae) such as Rhizosolenia, Hemiaulus and Chaetoceros are well known to form symbioses with the heterocystous diazotrophic cyanobacteria Richelia intracellularis and Calothrix rhizosoleniae. The latter are also called diatom-diazotroph associations, or DDAs. Up to now, the prokaryotic partners have been morphologically and genetically characterized, and the phylogenetic reconstruction of the well conserved nifH gene (encodes for the nitrogenase enzyme) placed the symbionts in 3 clusters based on their host-specificity, i.e. het-1 (Rhizosolenia-R. intracellularis), het-2 (Hemiaulus-R. intracellularis), and het-3 (Chaetoceros-C- rhizosoleniae). Conversely, the diatom-hosts, major representative of the phytoplankton community and crucial contributors to the carbon (C) biogeochemical cycle, have been understudied.The first aim of this thesis was to genetically and morphologically characterize the diatom-hosts, and to reconstruct the evolutionary background of the partnerships and the symbiont integration in the host. The molecular-clock analysis reconstruction showed the ancient appearance of the DDAs, and the traits characterizing the ancestors. In addition, diatom-hosts bearing internal symbionts (with more eroded draft genomes) appeared earlier than diatom-hosts with external symbionts. Finally a blast survey highlighted a broader distribution of the DDAs than expected.The second aim of this thesis was to compare genetic and physiological characteristics of the DDAs symbionts with the other eukaryote-diazotroph symbiosis, i.e. prymnesiophyte-UCYN-A (or Candidatus Atelocyanobacterium thalassa). The genome comparison highlighted more genes for transporters in het-3 (external symbiont) and in the UCYN-A based symbiosis, suggesting that symbiont location might be relevant also for metabolic exchanges and interactions with the host and/or environment. Moreover, a summary of methodological biases that brought to an underestimation of the DDAs is reported.The third aim of this thesis was to determine the distribution of the DDAs in the South Pacific Ocean using a quantitative polymerase chain reaction (qPCR) approach and to outline the environmental drivers of such distribution. Among the het-groups, het-1 was the most abundant/detected and co-occurred with the other 2 symbiotic strains, all responding similarly to the influence of abiotic factors, such as temperature and salinity (positive and negative correlation, respectively). Globally, Trichodesmium dominated the qPCR detections, followed by UCYN-B. UCYN-A phylotypes (A-1, A-2) were detected without their proposed hosts, for which new oligonucleotides were designed. The latter suggested a facultative symbiosis. Finally, microscopy observations of the het-groups highlighted a discrepancy with the qPCR counts (i.e. the former were several order of magnitudes lower), leading to the idea of developing a new approach to quantify the DDAs. The fourth aim of this thesis was to develop highly specific in situ hybridization assays (CARD-FISH) to determine the presence of alternative life-stages and/or free-living partners. The new assays were applied to samples collected in the South China Sea and compared with abundance estimates from qPCR assays for the 3 symbiotic strains. Free-living cells were indeed detected along the transect, mainly at deeper depths. Free-living symbionts had two morphotypes: trichomes and single-cells. The latter were interpreted as temporary life-stages. Consistent co-occurrence of the 3 het-groups was also found in the SCS and application of a SEM model predicted positive interactions between the het groups. We interpreted the positive interaction as absence of intra-specific competition, and consistent with the previous study, temperature and salinity were predicted as major drivers of the DDAs distribution.
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| 2. |
- Sernland, Emma
(författare)
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Optimal strategies and information in foraging theory
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis, I present both theoretical and empirical work where we have studied how humans and animals use information in situations where they need to continually update their information on the density of a resource. We have found that the amount of information, and the way the information is presented, are important factors for how well decisions are adapted to current circumstances. In an empirical study on humans, we found that humans seem to have a default idea of the distribution of a resource. This default idea seems to be plastic, i.e. it is adjusted according to incoming information. The way additional information was presented, as well as the information content, was important for how well the default idea was adjusted to current circumstances.By using mathematical models, we have also studied whether access to information from group members, so called public information, is one of the reasons why some species live in groups. When group members aim to maximize its intake rate of food and share both information and food items found equally, and when each individual has to pay all the cost for travelling between foraging patches, the intake rate of food will decrease with increasing group size. The animals will spend a larger proportion of the time on travelling between patches and less time on foraging the larger the group size. In this case, information sharing on food density in patches is not a reason why animals live in groups.We have also used mathematical models to study the information dynamics in a group of foraging animals that cannot both search for food and information at the same time. The animals aim to maximize their survival, and are given three behavioural choices in each time step: stay and search for food, stay and scan for information, or leave the current patch. The results show that the choice of behaviour depends on the energy reserves of the individual. An animal with low energy reserves searches for food and leaves the patch if its assessment of potential patch quality decreases to a certain level. An animal with high energy reserves chooses to stay in the patch and scan for information. In our model we assume that when one individual leaves the patch, the rest of the group also leaves. This means that it is those individuals that have low energy reserves that will make the leaving decisions for the group.In the end, we use these theories on Bayesian foraging, information updating and decision-making in order to develop a new type of effort-based quota for sustainable fisheries management: an effort-based dynamic quota (EDQ). We show that by using information from ongoing fishing combined with fishing data from earlier years, we can reach a higher maximum sustainable yield compared to using a total allowable catch (TAC).
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| 3. |
- Sundblad, Göran
(författare)
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Spatial Modelling of Coastal Fish – Methods and Applications
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Environmental factors influence species and habitats on multiple scales creating a mosaic of distribution patterns. Studying factors shaping these patterns are central to our understanding of population dynamics and ultimately ecosystem functioning. Information on the distribution of resources and conservation values are also highly needed in marine management as coastal areas are increasingly influenced by human activities. In this thesis, large-scale field data is used to explore how strong environmental gradients found on multiple scales in the coastal areas of the Baltic Sea influence fish habitats. The underlying concepts are based in the field of species distribution modelling, whereby habitat maps can be produced using environmental layers in a geographic information system. Distribution modelling is further used to address both ecological and applied questions by examining effects of habitat limitation on fish population sizes and to evaluate management actions aimed at habitat conservation. I show that specific habitat requirements for fish species of both freshwater and marine origin can be described using environmental variables and that species-environment relationships can be used to predict the distribution of early life-stages of fish in the Baltic Sea archipelagos. Further, predicted habitat availability of a specific life-stage was directly related to adult population size of Eurasian perch Perca fluviatilis, signifying that the abundance of large predatory fish can be limited by specific recruitment habitats. Lastly, by predicting the distribution of an assemblage of coastal fish species and their associated habitats, an assessment of a network of marine protected areas was performed. Results revealed large gaps in the current network and identified areas suitable for future protection. By demonstrating how current habitat protection can be improved by including critical habitats for coastal fish population sizes this thesis points to the benefits of integrating nature conservation and fisheries management. Based on these findings I conclude that species distribution modelling provides a suitable analytical framework for assessing the habitat requirements of organisms. An increased understanding of habitat-population relationships and an ability to accurately map ecologically important features will be of great value for an ecosystem-based marine management.
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| 4. |
- Nilsson, R. Henrik, 1976
(författare)
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Fungal taxonomy and systematics in the digital era, with an outlook on the cantharelloid clade (Basidiomycota)
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Fungi form a large and ubiquitous group of organisms where species identification and delimitation on morphological grounds often fall short. DNA sequences have proved an invaluable information source for these pursuits and are now routinely used in most mycological laboratories. Newl generated DNA sequences are typically compared with the entries of the large INSD sequence database for inference of taxonomic affiliations and other properties using the sequence similarity search tool BLAST. This thesis highlights some practical difficulties in using BLAST for these purposes it is for example very sensitive to the length of the sequences - and shows that improper use of BLAST appears to have had considerable repercussion on the general level of taxonomic reliability of the fungal sequences in INSD, more than 10% of which may be incorrectly identified to species level. An initiative to build a new DNA sequence database for taxonomically reliable DNA-based identification of mycorrhizal (plant-mutualistic) fungi is described. The database differs from similar initiatives in that its entries are determined to species level by pertinent experts; it allows for integrative sequence annotations, including photos and morphological descriptions; and it employs new, phylogeny-based tools for sequence identification to alleviate the concerns with simplistic, similarity-based tools as arbiters of taxonomic affiliation. That phylogenetic analyses can be beneficial also to classification and nomenclatural projects is shown in the mor enterprise, which is a weekly automaton of Agaricomycetes (mushroom-forming fungi) phylogeny. All fungal sequences from the nuclear ribosomal large subunit gene are assembled on a weekly basis; automated phylogenetic analyses are undertaken; and the resulting phylogenetic trees are displayed and analyzed for changes in clade topology and inclusiveness. The enigmatic cantharelloid clade of the Agaricomycetes is studied using a four-gene phylogenetic approach. While this heterogeneous assembly of mushroom-like, resupinate, clavarioid, and lichen-forming fungi defies any morphological attempt at indicating a close relatedness for its species, the results from the molecular analyses show that there is indeed strong evidence to support that these fungi form a monophyletic group; a restrictive circumscription of the clade to include the genera Botryobasidium, Sistotrema, Multiclavula, Membranomyces, Hydnum, Clavulina, Cantharellus, and Craterellus is advocated. Stichic basidia, and to a lesser extent parenthesome ultrastructure, are found to be characteristic of the clade, and the previously reported divergent rates of evolution for the genera Cantharellus and Craterellus are shown to be limited to the nuclear ribosomal genes. The largely resupinate, and purportedly wood-decaying, genus Sistotrema is demonstrated to hold mycorrhizal lineages, and the molecular evidence to consider the genus polyphyletic is found to be very convincing.
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| 5. |
- Ekelund Ugge, Gustaf Magnus Oskar, 1990-
(författare)
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Transcriptional biomarkers of toxicity – powerful tools or random noise? : An applied perspective from studies on bivalves
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Aquatic organisms are constantly at risk of being exposed to potentially harmful chemical compounds of natural or anthropogenic origin. Biological life can for instance respond to chemical stressors by changes in gene expression, and thus, certain gene transcripts can potentially function as biomarkers, i.e. early warnings, of toxicity and chemical stress. A major challenge for biomarker application is the extrapolation of transcriptional data to potential effects at the organism level or above. Importantly, successful biomarker use also requires basal understanding of how to distinguish actual responses from background noise. The aim of this thesis is, based on response magnitude and variation, to evaluate the biomarker potential in a set of putative transcriptional biomarkers of general toxicity and chemical stress.Specifically, I addressed a selection of six transcripts involved in cytoprotection and oxidative stress: catalase (cat), glutathione-S-transferase (gst), heat shock proteins 70 and 90 (hsp70, hsp90), metallothionein (mt) and superoxide dismutase (sod). Moreover, I used metal exposures to serve as a proxy for general chemical stress, and due to their ecological relevance and nature as sedentary filter-feeders, I used bivalves as study organisms.In a series of experiments, I tested transcriptional responses in the freshwater duck mussel, Anodonta anatina, exposed to copper or an industrial wastewater effluent, to address response robustness and sensitivity, and potential controlled (e.g. exposure concentration) and random (e.g. gravidness) sources of variation. In addition, I performed a systematic review and meta-analysis on transcriptional responses in metal exposed bivalves to (1) evaluate what responses to expect from arbitrary metal exposures, (2) assess the influence from metal concentration (expressed as toxic unit), exposure time and analyzed tissue, and (3) address potential impacts from publication bias in the scientific literature.Response magnitudes were generally small in relationship to the observed variation, both for A. anatina and bivalves in general. The expected response to an arbitrary metal exposure would generally be close to zero, based on both experimental observations and on the estimated impact from publication bias. Although many of the transcripts demonstrated concentration-response relationships, large background noise might in practice obscure the small responses even at relatively high exposures. As demonstrated in A. anatina under copper exposure, this can be the case already for single species under high resolution exposures to single pollutants. As demonstrated by the meta-regression, this problem can only be expected to increase further upon extrapolation between different species and exposure scenarios, due to increasing heterogeneity and random variation. Similar patterns can also be expected for time-dependent response variation, although the meta-regression revealed a general trend of slightly increasing response magnitude with increasing exposure times.In A. anatina, gravidness was identified as a source of random variability that can potentially affect the baseline of most assessed biomarkers, particularly when quantified in gills. Response magnitudes and variability in this species were generally similar for selected transcripts as for two biochemical biomarkers included for comparison (AChE, GST), suggesting that the transcripts might not capture early warnings more efficiently than other molecular endpoints that are more toxicologically relevant. Overall, high concentrations and long exposure durations presumably increase the likelihood of a detectable transcriptional response, but not to an extent that justifies universal application as biomarkers of general toxicity and chemical stress. Consequently, without a strictly defined and validated application, this approach on its own appears unlikely to be successful for future environmental risk assessment and monitoring. Ultimately, efficient use of transcriptional biomarkers might require additional implementation of complementary approaches offered by current molecular techniques.
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| 6. |
- Pontiller, Benjamin, MSc, 1985-
(författare)
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Molecular mechanisms involved in prokaryotic cycling of labile dissolved organic matter in the sea
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Roughly half of the global primary production originates from microscopic phytoplankton in marine ecosystems, converting carbon dioxide into organic matter. This organic matter pool consists of a myriad of compounds that fuel heterotrophic bacterioplankton. However, knowledge of the molecular mechanisms – particularly the metabolic pathways involved in the degradation and utilization of dissolved organic matter (DOM) – and transcriptional dynamics over spatiotemporal gradients are still scarce. Therefore, we studied the molecular mechanisms of bacterioplankton communities, including archaea, involved in the cycling of DOM, over different spatiotemporal scales in experiments and through field observations.In seawater experiments, we found a divergence of bacterioplankton transcriptional responses to different organic matter compound classes (carbohydrates, nucleic acids, and proteins) and condensation states (monomers or polymers). These responses were associated with distinct bacterial taxa, suggesting pronounced functional partitioning of these compounds in the Sea. Baltic Proper mesocosms amended with two different river loadings (forest versus agriculture river water) revealed a divergence in gene expression patterns between treatments during bloom decay. This was particularly true for genes in phosphorus and nitrogen metabolism, highlighting the importance and sensitivity of interaction effects between river- and phytoplankton-derived DOM in regulating bacterial activity responses to changes in precipitation-induced riverine runoff.In shipboard mesocosms in an Atlantic coastal upwelling system, we found significant changes in bacterioplankton transcription of hydrolyzing enzymes and membrane transporters from phytoplankton bloom development to senescence, primarily driven by phytoplankton-derived DOM and dissolved organic carbon dynamics. These responses differed substantially between bacterial orders, suggesting that functional resource partitioning is dynamically structured by temporal changes in DOM quantity and quality. Further analysis of these gene systems in a stratified fjord revealed pronounced divergence in transcription with depth and between bacterial taxa; moreover, transcription was more variable in the surface waters. This highlights the interplay between functional and physical partitioning of biogeochemical cycles. Collectively, the findings in this thesis contribute novel insights into the interdependency between prokaryotes and DOM by shedding light on the mechanisms involved in DOM cycling over ecologically relevant spatiotemporal scales.
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| 7. |
- Nandakumar, Mridula
(författare)
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Pathogen-mediated selection in the immune system of rodents : Exploring selection targets, functional effects and trade-offs
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Pathogens cause disease and play an important role in shaping evolution of the host immune system. They create pressure on host immunity to evolve in numerous ways, most commonly by increasing divergence between species (positive selection) or increasing polymorphisms within a population (balancing selection). Especially with balancing selection, trade-offs between different traits, for example responses to different pathogens, are essential. Across five papers, questions related to what immune genes are under selection, how this translates to an effect on the immune response and what trade-offs occur, are addressed using rodents as study system. Paper I utilised genomes from 30 rodent species to identify signatures of positive selection in immune genes. In general, function of immune genes was a significant determinant for signs of positive selection. This effect was significant even after accounting for potential confounding factors like gene expression and protein-protein interactions. In Paper II, the focus is on a local population of bank voles in Sweden, to look for signatures of balancing selection in the complement system – a branch of innate immunity. One complement gene, FCNA, was found to be under strong balancing selection. In Paper III, FCNA polymorphism was linked to associations with natural infections of Borrelia afzelii, a common pathogen for bank voles. Papers IV and V look at how the immune response of bank voles of various genotypes differ on stimulation with B. afzelii and the human pathogen Streptococcus pyogenes, captured with transcriptome sequencing of spleen cells. In Paper IV, the analysis is focused on various genotypes of TLR2, an immune gene under balancing selection in bank voles and associated with infection prevalence of B. afzelii in the wild. A stimulation-specific effect of TLR2 on immune response was found, where the magnitude of immune response to B. afzelii, but not S. pyogenes, depends on TLR2 expression level in a TLR2 genotype-specific way. In Paper V, tradeoffs at the cis-regulatory level between the response to B. afzelii and S. pyogenes was tested by searching for polymorphisms where the alleles are expressed differently to these two stimulations. Abundant cis-regulatory variation for responses to the two bacteria was found, but there was no evidence for trade-offs. In summary, this work pushes our knowledge of what immune genes can be expected to be under pathogen-mediated selection, as heretofore understudied categories of immune function showed signs of selection. A novel basis – the combination of genotype and expression – was uncovered for functional effects of polymorphic genes. Finally, there was no evidence for trade-offs between responses to different pathogens. Investigating the nature of trade-offs in the immune system further would be necessary towards understanding the causes and consequences of pathogen-mediated selection.
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| 8. |
- Mattsson, Lina, 1992-
(författare)
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Microalgal solutions in Nordic conditions : industries transition toward resource recovery?
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Microalgal solutions can through photosynthesis recover greenhouse gas (CO2) and nutrients from industrial waste, reducing climate footprint and eutrophication. An added value to the process is algal biomass containing lipids, proteins, and carbohydrates with commercial potential for biofuel, feed, and fertilizer. Microalgal cultivation in Nordic conditions is challenged by strong seasonality in light and temperature that can compromise biomass stability. To make microalgal cultivation sustainable and competitive with conventional feedstock, large-scale outdoor cultivation using waste streams is necessary but limits control over seasonal fluctuations in environmental conditions. In this thesis, I used a polyculture approach in outdoor large-scale cultivations with industrial waste resources, to study biomass production and quality in an annual, seasonal, and diurnal perspective. Research focused on the biomass potential for nutrient recovery and carbon capture from industries, year around stability and quality. Production was tested in the South Baltic Region using a brackish water polyculture grown for five years in a green wall panel (GWP) fed with cement industry flue gas (CO2 source). In a second setup, a freshwater polyculture was cultivated seasonally in raceway ponds (RWP), with an additional waste resource from landfill leachate water (nitrogen source). Stable biomass performance and CO2 recovery up to 10 g m-2 d-1 was achieved for five years over seasons in the GWP with high protein in autumn and winter, whereas lipids remained stable throughout the annual cycle. Laboratory experiments confirmed naturally occurring diurnal shifts in temperature as superior lipid boosters compared to conventional nitrogen limitation. Stability of overall performance could be explained by flue gas recirculation mode, lack of contamination and polyculture complementarity of the two green algal strains that dominated throughout the five years. The use of multiple waste streams in the RWP added complexity to the cultivation as leachate water composition varied, resulting in a diverse green algal polyculture. Seasonality in nitrogen recovery rate was explained by total nitrogen and light. Results indicate stability of biomass and resource recovery in Nordic conditions using local polycultures in large-scale outdoor cultivation and periods of lower biomass production can be compensated by high quality metabolites such as proteins and lipids.
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| 9. |
- Rundlöf, Maj
(författare)
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Biodiversity in Agricultural Landscapes: Landscape and Scale-Dependent Effects of Organic Farming
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Declines in the distribution and abundance of many farmland species during recent decades have been attributed to agricultural intensification. Agri-environment schemes are commonly used in Europe to reduce this loss of farmland biodiversity, but their effectiveness may depend on several external factors. In this thesis, I have used one such scheme, organic faming, as a landscape scale experiment to test if its effect on the species richness and abundance of butterflies, bumble bees and plants differs depending on the surrounding landscape context or on which spatial scale organic farming is applied. In the first studies, including pairs of organic and conventional farms located in either heterogeneous or homogeneous landscapes, I found that the species richness and abundance of both butterflies and bumble bees were enhanced by organic farming compared to conventional farming, partly related to higher abundance of flowers on organically managed farmland. However, the enhancing effect depended on the landscape context, such that the species richness and abundance were only significantly higher on organic farms in intensively farmed homogeneous landscapes, but not on the ones in less intensively farmed heterogeneous landscapes. Bumble bee species were classified into three groups based on their colony sizes, reflecting differences in their landscape perception. The abundances of bumble bees with small and large colonies were positively associated with organic farming, while the ones with medium sized colonies instead were affected by landscape heterogeneity, which may indicate differences between groups in sensitivity to resources fragmentation. For the scale-dependent effect of organic farming, I found that local butterfly and plant species richness and butterfly abundance were enhanced by organic farming at a local scale. In addition, my results showed that, besides the local effect, the amount of organic farming in the surrounding landscape can have an additive (species richness) or interactive effect (abundance). Local species richness was positively affected by a large proportion of organic farming at the landscape scale, while the local farming practice was of larger importance for local butterfly abundance in conventionally managed landscapes compared to organically managed ones. In conclusion, I show that the effectiveness of agri-environment schemes to promote biodiversity may depend on the landscape heterogeneity and on how large proportion of a landscape that are subjected to the scheme. These results consequently imply that to increase their efficiency it may be important to consider the spatial arrangement of schemes and their allocation at a landscape scale.
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| 10. |
- Öckinger, Erik
(författare)
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Butterfly Diversity and Dispersal in Fragmented Grasslands
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- During the last decades, the distribution and abundance of many European species of birds, plants and insects in agricultural landscapes have declined due to agricultural intensification. To be able to mitigate these declines, it is essential to know the relative importance on local and regional ecological processes on population persistence and patterns of species richness. I have studied the effect of landscape composition on local species richness, abundance and dispersal patterns of butterflies, and in one of the papers also on bumblebees. In the first study, I showed that the species richness of butterflies in southern Sweden had declined significantly during the last decades, and that the observed declines could be related to changes in local habitat quality rather that to landscape composition. However, a larger turnover of species also in sites where species richness was constant indicated that metapopulation dynamics might be important. In the second study, I studied butterfly species richness in similar grasslands situated in contrasting landscapes. A high proportion of semi-natural grassland at the landscape scale increased species richness at the local scale. In the third study, I found that the effect of landscape composition on species richness was dependent on the mobility of the species, with intermediately mobile species most strongly affected. By studying species richness and population densities at different distances from semi-natural grasslands and using mark-recapture techniques to study butterfly movements, I found that in intensively farmed agricultural landscapes, semi-natural grassland can act as population sources, contributing to higher species richness and population densities in their surroundings. So called ecological corridors have been suggested to increase dispersal between local populations. I found no evidence of this when studying the dispersal of three grassland butterflies, but there was some evidence of a diffusion of butterflies over shorter distances along the corridors. In conclusion, my results clearly show that population processes at the landscape scale are important for population persistence and species richness. However, they also show that different landscape ecological processes may be important, which implies that both thorough studies and explicit objectives are needed in order to be able to suggest measures to counteract biodiversity loss.
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