| 1. |
- Sernland, Emma
(författare)
-
Optimal strategies and information in foraging theory
- 2005
-
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).
|
|
| 2. |
- Sundblad, Göran
(författare)
-
Spatial Modelling of Coastal Fish – Methods and Applications
- 2010
-
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.
|
|
| 3. |
- Bag, Pushan, 1993-
(författare)
-
How could Christmas trees remain evergreen? : photosynthetic acclimation of Scots pine and Norway spruce needles during winter
- 2022
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Plants and other green organisms harvest sunlight by green chlorophyll pigments and covertit to chemical energy (sugars) and oxygen in a process called photosynthesis providing the foundation for life on Earth. Although it is unanimously believed that oceanic phytoplanktons are the main contributors to the global photosynthesis, the contribution of coniferous boreal forests distributed across vast regions of the northern hemisphere cannot be undermined. Hence boreal forests account signifificantly for social, economical and environmental sustainability. Not only do conifers thrive in the tundra regions with extreme climate, but they also maintain their needles green over the boreal winter. A question remains; what makes them so resilient? In this respect, we aimed to understand the remarkable winter adaptation strategies in two dominant boreal coniferous species,i.e., Pinus sylvestris and Picea abies. First, we mapped the transcriptional landscape in Norway spruce (Picea abies) needles over the annual cycle. Transcriptional changes in the nascent needles reflflected a sequence of developmental processes and active vegetative growth during early summer and summer. Later after maturation, transcriptome reflflected activated defense against biotic factors and acclimationin response to abiotic environmental cues such as freezing temperatures during winter. Secondly, by monitoring the photosynthetic performance of Scot pine needles, we found that the trees face extreme stress during the early spring (Feb-Mar) when sub-zero temperatures are accompanied by high solar radiation. At this time, drastic changes occur in the thylakoid membranes of the chloroplast that allows the mixing of photosystem I and photosystem II that typically remain laterally segregated. This triggers direct energy transfer from PSII to PSI and thus protects PSII from damage. Furthermore, we found that this loss of lateral segregation may be a consequence of triple phosphorylationof Lhcb1 (Light harvesting complex1 of photosystem II). The structural changes in thylakoid membranes also lead to changes inthe thylakoid macro domain organisationand pigment protein composition. Furthermore, we discovered that while PSII is protected by direct energy transfer, the protection of PSI is provided through photoreduction of oxygen by flavodiiron proteins, which in turn allows P700 to stay in an oxidised state necessary for direct energy transfer. These coordinated cascades of changes concomitantly protect both PSI and PSII to maintain the needles green over the winter.
|
|
| 4. |
- Caputo, Andrea, 1988-
(författare)
-
Genomic and morphological diversity of marine planktonic diatom-diazotroph associations : a continuum of integration and diversification through geological time
- 2019
-
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.
|
|
| 5. |
- Norrström, Niclas
(författare)
-
Artificial neural networks in models of specialization and sympatric speciation
- 2009
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis deals with specialization and how it is linked to sympatric speciation. The trait driving specialization is a cue recognition trait modelled with artificial neural networks that exploiters use to discriminate beneficial resources from detrimental resources based on the signals of the resources. Paper I investigates how haploid exploiters and the resources coevolve when the signals of the resources can evolve through mutations. We find that this coevolution can be a cyclic process with saltational changes between different stages and that evolution is only directional and the exploiters are only specialists in parts of this cycle. In simulations underlying Paper II the signals of the resources can not mutate but the exploiters have a diploid genome and the organisms reproduce sexually. We show that the disruptive selection stemming from exploiters specializing on different resources can overcome the homogenizing effect of sexual recombination when exploiters mate randomly and produce a functional genetic polymorphism with specialized exploiters. A functional genetic polymorphism removes the force of reinforcement but we run simulations where the exploiters have a mating gene determining if mating is random or if exploiters should mate assortatively in Paper III. We find that assortative invades the exploiter population and homozygote specialists evolve because the genetic polymorphism pays a cost by having some alleles being silenced (that is they do not contribute to the complete phenotype) in certain genotypes so a mutation in these silenced alleles is not selected against, which cause these alleles to accumulate deleterious mutations. The homozygote specialists, mating assortatively, are much more efficiently removing deleterious mutations from the population and hence can invade the population. Finally, in Paper IV we investigate the effects of resource and resource signal arrangements in the environment. We show that the environment can influence the evolution of specialization and sympatric speciation. By modelling a resource discrimination trait based on the interaction of epistatic genes we find a novel force promoting sympatric speciation over genetic polymorphisms.
|
|
| 6. |
- Bergsten, Anna
(författare)
-
Population Differentiation in Solidago virgaurea along Altitudinal Gradients
- 2009
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Altitudinal gradients offer attractive opportunities for studies of population differentiation in response to environmental heterogeneity. In this thesis, I examined population differentiation along altitudinal gradients by combining common-garden experiments with field studies and experiments in alpine, subalpine and boreal populations of the perennial herb Solidago virgaurea. More specifically, I determined whether leaf physiology in terms of nitrogen concentration and resorption, flowering phenology, flower production and reproductive effort vary along altitudinal gradients. Nitrogen concentration in green leaves were higher in alpine than in subalpine and boreal populations. These differences persisted when plants were grown from seeds in a common-garden experiment at two sites, suggesting that the differences have a genetic component. There was mixed support for a trade-off between maximized carbon gain through the maintenance of high nitrogen concentration, and minimized nitrogen loss through high resorption. In their natural habitats alpine populations began flowering later than subalpine populations, but this difference was reversed when plants were grown in a common environment. This suggests that genetic differences among populations counteract environmental effects and reduce phenotypic variation in flowering time among populations. Flowering time thus shows countergradient genetic variation in S. virgaurea. In a common-garden experiment, boreal populations produced more flowers and had a higher reproductive effort than subalpine and alpine populations indicating habitat-specific genetic differences in reproductive allocation. In a field study, which included three populations, seed set was close to zero in the alpine population, intermediate in the subalpine population, and high in the boreal population. Experimental flower removal showed that seed production was associated with a considerable cost in terms of reduced flowering propensity the following year, but did not support the hypothesis that a large floral display is important for pollination success.
|
|
| 7. |
- Söderberg, Jonas, 1977-
(författare)
-
Surviving the ratchet : Modelling deleterious mutations in asexual populations
- 2011
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- One of the most unforgiving processes in nature is that of Muller's ratchet, a seemingly irreversible accumulation of deleterious mutations that all organisms have to deal with or face extinction. The most obvious way to avoid fitness collapse is recombination, though asexual populations usually do not have the luxury of recombining freely. With the aid of computational and mathematical models, we have studied other situations where this threat is averted and the organism can survive the ratchet. The results show that a ratchet where all mutations have the same deleterious fitness effect is very effectively stalled for large effects. However, if mutations are allowed to have a broad range of effects, the fitness-loss rate can be substantial even with the same mean effect as the one-type ratchet, but we have identified parameter regions where even the broad-range effects are effectively stopped. The fitness-loss from a ratchet is very sensitive to the mutation rate and a mutation that increases the mutation rate (mutator) can easily start an otherwise stalled ratchet. Large effect mutators are heavily counter-selected, but smaller mutators can spread in the population. They can be stopped by reversals (antimutators), but even if the mutation rate is equilibrated in this way, there will be large fluctuations in mutation rate and even larger in the fitness-loss rate due to the feedback amplification in their coupling. Another way of preventing the ratchet is by reversal of the deleterious mutations themselves through back-mutations or compensatory mutations. The rate required to stop the ratchet using only back-mutations before the fitness collapses is very large. A detailed comparison between the deleterious mutations in the ratchet and in a sexual population was made and the difference was found to be greatest for large populations with large genomes. There are obviously many ways to survive the ratchet, but even more ways to drive a species to extinction by enhancing and speeding up the ratchet. By modelling and testing the ratchet for numerous different situations, we show the effects of some of these threats and benefits.
|
|
| 8. |
- den Tex, Robert-Jan, 1969-
(författare)
-
Patterns and Processes of Evolution in Sundaland
- 2011
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Biodiversity in the tropics is disproportionately high compared to other habitats, and also under disproportionate threat from human impact. It is necessary to understand how this diversity evolved and how it is partitioned across space in order to preserve it. In this thesis I construct phylogenies of tropical forest dependent vertebrates from Southeast Asia and the islands of the Sunda shelf, a region referred to as Sundaland. I focus on the tree squirrels (genus Sundasciurus) and Asian barbets (Aves: Family Megalaimidae), two taxa with similar ecological characteristics. I use these phylogenies to test hypotheses that have been put forward to explain high levels of tropical diversity including the Pleistocene pump and museum hypotheses. I also use phylogenies to elucidate phylogeographic patterns within the region. I find no evidence for an increase in speciation in the Pleistocene, but I do find within species structure that dates to this period. Common phylogeographic patterns were identified between many forest dependent vertebrates that suggest that populations on the island of Sumatra are generally more closely related to Malay Peninsula populations than to populations on Borneo. From a methodological viewpoint we propose careful usage of universal primers in ancient DNA studies because of our finding of increased risk of amplifying pseudogenes of the mtDNA.
|
|
| 9. |
- Khalaf, Hazem
(författare)
-
Characterization and environmental influences on inflammatory and physiological responses
- 2010
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Pharmaceuticals are regularly released into the environment, in particular nonsteroidalanti-inflammatory drugs (NSAIDs) and antibiotics. The measuredconcentrations are relatively low and have therefore been considered to be harmless.However, several pharmaceuticals, including naproxen and atenolol, are stable for upto 1 year in the environment, which increases the risk for accumulation. Evaluation ofthe effects of pharmaceuticals on induced inflammatory responses is thereforenecessary for the assessment of potential risks. Since NF-κB and MAPK are the mainpathways known to be critical regulators of inflammatory responses, intracellularsignalling and effects on these systems were examined in vitro using human cell-lines.NSAIDs were shown to significantly reduce NF-κB activity at environmentallyrelevant concentrations. Suppression of immune responses may lead to progressiveinfections since inflammatory responses are controlled by a cooperative activity ofAP-1 and NF-κB. Alterations in the activity of transcription factors and proinflammatorycytokine and chemokine levels such as TNF, IL-6 and CXCL8 areassociated with several human diseases including cystic fibrosis and AIDS. PMAexposure resulted in a rapid NF-κB activation, while extended treatment suppressedNF-κB and activated AP-1. Suppression of NF-κB activity may be due to PKCdependentBcl10 degradation, which decreased in response to PMA and correlatedwith the NF-κB activity. Regulation of cytokine expression revealed that NF-κB wasessential for IL-6 but not CXCL8 expression following specific inhibition of NF-κB,without affecting AP-1 activity. Furthermore, several reports have indicated theimportance of a functional NF-κB complex in zebrafish embryogenesis, whereblockage of NF-κB activation resulted in a deformation of the tail. Our results indicatea suppression of apoptotic pathways following activation of inflammatory mediatorsin response to HK E. coli treatment. These signals acted to direct zebrafish sexdifferentiation towards feminization. NF-κB was shown to regulate zp2 geneexpression, an indicator of oocyte development. Zebrafish sex determination was alsoshown to start early, prior to 16 days post fertilization. The results support thetransition through a juvenile ovary stage and suggests that steriodogenesis is aconsequence of sex differentiation rather than a regulatory mechanism.Control of prescription, use and disposal of pharmaceuticals is therefore importantto preserve human health, biotic processes and to avoid developmental alterations inaquatic organisms. The complexity of regulatory systems involved in inflammationsuggest that there is a need to further evaluate the signalling pathways involved inorder to provide a better understanding of cellular responses to manmade substances,but also to offer an insight into possible development of alternative treatments forhuman diseases with elevated cytokine/chemokine levels.
|
|
| 10. |
- Larsson, Anders, 1977-
(författare)
-
Androgen receptors and endocrine disrupting substances
- 2010
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Throughout the animal kingdom, organisms are dependent on substances such as steroid hormones to help them maintain internal balances. Examples of important tasks that are under regulation of steroid hormones are somatic and gonadal development, sexual performance and behavior (both social and sexual) as well as sex differentiation. Balance in the biology of reproduction is important for all organisms, and is sensitive to alterations and disturbances. If the environment is altered in a manner that lead to higher estrogenic or androgenic levels, the sex ratio of organisms that do not rely on genetic differences in the sex differentiation, will be biased towards more females or males in the population. It has been known for some time that there are pollutants in the environment that affect steroid pathways, such as the estrogenic and thyroid systems, but not much has been known about the androgenic systems. Examples of populations being masculinized have been recorded, and estrogenic compounds have been known to act as antiandrogens, but not until recently the first androgen agonist was identified. We used a combination of in vitro and computational modeling to identify the brominated flame retardant, 1,2-dibromo-4-(1,2-dibromoethyl)cyclohexane, as a potent androgen agonist to the human androgen receptor.In addition to this we cloned and characterized the androgen receptor from, a frequently used model organism, zebrafish (Danio rerio) as a receptor primarily activated by 11-ketotestosterone. This is a feature the zebrafish share with several other teleost fishes, such as the three-spined stickleback. Thus fish androgen receptors differ from most mammalian androgen receptors, where dihydrotestosterone is the most potent activator.
|
|
