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  • Disputation: 2018-01-24 13:00 Lilla Hörsalen. Nod building, Kista
    Rahman, Hasibur
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Institutionen för data- och systemvetenskap.
    Distributed Intelligence-Assisted Autonomic Context-Information Management: A context-based approach to handling vast amounts of heterogeneous IoT data2018Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    As an implication of rapid growth in Internet-of-Things (IoT) data, current focus has shifted towards utilizing and analysing the data in order to make sense of the data. The aim of which is to make instantaneous, automated, and informed decisions that will drive the future IoT. This corresponds to extracting and applying knowledge from IoT data which brings both a substantial challenge and high value. Context plays an important role in reaping value from data, and is capable of countering the IoT data challenges. The management of heterogeneous contextualized data is infeasible and insufficient with the existing solutions which mandates new solutions. Research until now has mostly concentrated on providing cloud-based IoT solutions; among other issues, this promotes real-time and faster decision-making issues. In view of this, this dissertation undertakes a study of a context-based approach entitled Distributed intelligence-assisted Autonomic Context Information Management (DACIM), the purpose of which is to efficiently (i) utilize and (ii) analyse IoT data.

    To address the challenges and solutions with respect to enabling DACIM, the dissertation starts with proposing a logical-clustering approach for proper IoT data utilization. The environment that the number of Things immerse changes rapidly and becomes dynamic. To this end, self-organization has been supported by proposing self-* algorithms that resulted in 10 organized Things per second and high accuracy rate for Things joining. IoT contextualized data further requires scalable dissemination which has been addressed by a Publish/Subscribe model, and it has been shown that high publication rate and faster subscription matching are realisable. The dissertation ends with the proposal of a new approach which assists distribution of intelligence with regard to analysing context information to alleviate intelligence of things. The approach allows to bring few of the application of knowledge from the cloud to the edge; where edge based solution has been facilitated with intelligence that enables faster responses and reduced dependency on the rules by leveraging artificial intelligence techniques. To infer knowledge for different IoT applications closer to the Things, a multi-modal reasoner has been proposed which demonstrates faster response. The evaluations of the designed and developed DACIM gives promising results, which are distributed over seven publications; from this, it can be concluded that it is feasible to realize a distributed intelligence-assisted context-based approach that contribute towards autonomic context information management in the ever-expanding IoT realm.

  • Disputation: 2018-01-26 10:00 Södertörns högskola, rum MA 624, Flemingsberg
    Petrusenko, Nadezda
    Stockholms universitet, Humanistiska fakulteten, Historiska institutionen. Institutionen för historia och samtidsstudier, Södertörns högskola.
    Creating the Revolutionary Heroines: The Case of Female Terrorists of the PSR (Russia, Beginning of the 20th Century)2017Doktorsavhandling, monografi (Övrigt vetenskapligt)
    Abstract [en]

    Representing revolutionary terrorists as heroes and martyrs was a typical feature of the mythology of the Russian revolutionary underground at the beginning of the 20th century. This mythology described Underground Russia, the world of the revolutionaries, as an ideal country inhabited by ideal people. The purpose of that epos was to represent the revolutionary struggle, and individual revolutionaries in such a way that they would gain sympathy from the wider public and become role models for other revolutionary fighters. Sympathetic representations of women who committed political violence seem to be especially shocking in the context of Russia at the beginning of the twentieth century, since female violent behavior contradicted the existing gender order.

    Employing theoretical perspectives of Critical Discourse Analysis, gender history and intersectionality, the dissertation analyzes the way narratives about the individual life paths of female terrorists of the Party of Socialist Revolutionaries (the PSR), the biggest socialist party in Russia at the beginning of the 20th century, were constructed in their revolutionary auto/biographies. It analyzes how the lives of women from different social and ethnic origins, of different ages, with different life paths, who happened to be united only by their participation in the political terrorism of the PSR, were recounted with the help of narratives used in the Russian revolutionary underground.

    The research findings demonstrate that the accounts of the lives of female PSR terrorists were constructed with the help of the dominant narrative that was formed as a conversion story. Within the framework of that narrative, the lives of individual women were adapted to the dominant discourse of heroism and martyrdom, and at the same time were contextualized within the dominant discourse on “good” femininity that existed in the Russian society, and even within the discourse on Jews as perpetual “Others” in the Russian empire in case of Jewish women. Social and ethnic backgrounds as well as individual circumstances of the terrorist women, however, transformed the dominant narrative, and thus created diversity of representations. The discursive practice of writing a revolutionary life accepted by Bolsheviks influenced the discursive practice employed in revolutionary auto/biographies of female terrorists written during the early Soviet period.

  • Disputation: 2018-01-31 10:00 Magnélisalen, Kemiska övningslaboratoriet, Stockholm
    Rabten, Wangchuk
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    The Use of N,P-Iridium and N,P-Palladium Complexes in Asymmetric Synthesis2018Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    The work presented in this thesis concerns asymmetric catalysis using chiral N,P-ligands and iridium or palladium transition metals. The first part  (Chapters 2 and 3) highlights the N,P-iridium catalyzed asymmetric hydrogenation of 1,4-cyclohexadienes having functionalized or unfunctionalized substituents, including allylsilane side chains. A series of N,P-iridium catalysts were synthesized and screened on a number of cyclohexadienes. The developed N,P-iridium catalysts have provided excellent chemo-, regio- and enantioselectivity for most of the products obtained. For substrates having an allylsilane sidechain, the chiral cyclic allylsilane products were used to induce stereocontrol in a subsequent Hosomi-Sakurai reaction using TiCl4 as Lewis acid and aldehydes as electrophiles. The corresponding homoallylic alcohols were obtained in good to excellent diastereoselectivity. 

    The second part (Chapter 4) describes the N,P-iridium catalyzed asymmetric hydrogenation of various vinyl fluorides. A number of tri- and tetrasubstituted vinyl fluorides were synthesized and evaluated for the asymmetric hydrogenation. The corresponding saturated chiral fluoro compounds were obtained in very high enantioselectivity (up to 99% ee). The defluorination, usually known to occur under the catalytic hydrogenation conditions, were not observed for the majority of the substrates. 

    Finally, Chapter 5 describes the application of N,P-ligands in the asymmetric cycloisomerization of 1,6-enynes using a palladium precatalyst. The enantioselectivities for the products were found to depend both on the substrate as well as the hydrogen source. These developed catalytic reactions provide attractive methods to create multiple stereogenic centers in a molecule in relatively few steps from readily available starting materials.

  • Disputation: 2018-01-31 13:00 FB52, AlbaNova Universitetscentrum, Stockholm
    Wolf, Michael
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Energetic processing of complex molecules in the gas phase2018Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Collisions between molecules and gas phase targets often lead to various intriguing processes. Such collisions may induce fragmentation of molecules that can be divided into different subsets depending on the projectile, target, and collision energy. One major part of the present research is the exploration of astrophysical relevant collision mechanisms. In collisions between polycyclic aromatic hydrocarbon (PAH) molecules or fullerenes with, for example, helium, nuclear stopping can lead to the prompt knockout of a carbon atom from the molecule. Such a vacancy in the molecular carbon backbone can be highly reactive, and lead to the formation of larger molecules. The energy dependencies of such processes are important for the understanding of astrochemical molecular growth processes, which in turn may lead to the formation of larger and more complex molecules in space. In addition, hydrogenation of PAHs changes their structures and internal properties, including their resistance against fragmentation. To better understand the effects of hydrogenation on the fragmentation of PAHs, low energy photofragmentation experiments are presented along with the collision experiments, and a detailed comparison is made between the effects of these different types of energy transfer processes.

    Besides astrophysically relevant research, studies on the response of biomolecules to collisions with gas phase targets are presented. Here, the energy dependence for formation of the protonated n-butyl β-ionone Schiff base through electrocyclization of the protonated n-butylamine Schiff base of all-trans-retinal in collisions is presented. The latter is a model compound for all-trans-retinal, the chromophore of the light sensitive opsin proteins, and such studies are essential for the understanding of the operation of mammal vision.

    While our collision studies are very successful, they are sometimes also limited by the experimental timescale. Therefore, we have constructed an experimental setup for ion storage and fragmentation analysis. The goal of this new experiment is to store internally hot fragments to investigate their behavior on extended timescales and as functions of internal excitation energies.

  • Disputation: 2018-02-02 10:00 Magnélisalen, Kemiska övningslaboratoriet, Stockholm
    Koistinen, Niina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi.
    The amyloid-β precursor protein (APP)-binding protein Fe65 and APP processing2018Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by abnormal deposition of neurotoxic amyloid-β (Aβ) peptide. Aβ is generated by sequential cleavage of the amyloid-β precursor protein (APP) by β- and then γ-secretase. However, APP can also be processed by α- and γ-secretase, instead resulting in generation of neuroprotective sAPPα. Increased APP phosphorylation and altered expression levels of the brain enriched Fe65 protein have been observed in the brains of AD patients. Fe65 can not only interact with membrane tethered APP, but can also localized into the nucleus and act as a transcriptional regulator together with the APP intracellular domain (AICD), generated after γ-secretase processing. How APP processing, APP/Fe65 interaction, and the nuclear AICD/Fe65 complex is regulated has not yet been fully understood. The aim of this thesis was therefore to further elucidate how Fe65 is regulated and how APP Ser675 phosphorylation affects APP processing.

    We could identify several factors regulating Fe65. First, we identified that neuronal differentiation induces Fe65 phosphorylation (paper I), and that phosphorylated forms of Fe65 were preferentially localized outside the nucleus (paper II). Second, we found that the APP binding PTB2 domain of Fe65, rather than the previously proposed N-terminal WW domain, is important for the nuclear localization of Fe65 (paper II). In addition, we surprisingly found that mutation of S228 in the Fe65 N-terminus could increase the APP/Fe65 interaction (paper III). Third, both α- and γ-secretase inhibitors decreased Fe65 nuclear localization similarly, indicating an important role of α-secretase in regulating Fe65 nuclear localization (papers II and III). Lastly, we could in paper IV for the first time show that phosphorylation of APP at Ser675 regulates APP processing at the plasma membrane, resulting in reduced levels of sAPPα. These results, together with the observation that APP Ser675 phosphorylation occur in AD brains, suggest that Ser675 phosphorylation could contribute to AD pathology by decreasing α-secretase processing and instead increasing the levels of Aβ.

    In summary these studies have contributed to understanding of APP processing and the interplay between Fe65 and APP, two suggested key players in AD. 

  • Disputation: 2018-02-02 13:00 Nordenskiöldsalen, Geovetenskapens hus, Stockholm
    Josefson, Mie
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Barn- och ungdomsvetenskapliga institutionen.
    Det ansvarsfulla mötet: En närhetsetisk analys av omsorgens innebörder i förskolan2018Doktorsavhandling, monografi (Övrigt vetenskapligt)
    Abstract [en]

    This doctoral thesis embraces Care in the discipline of Early Childhood Education. In this thesis, the concept of responsibility is used to analyze the meaning of care in preschool. The scientific problem can be expressed as follows: How is it possible to grasp the aspects of responsibility in relation to the preschool and preschool teachers’ and staff’s mission in general, and as an expression of meaning of care and practices in particular?

    In order to construct new knowledge on this particular care responsibility in preschool, a theory of ethics is required. Such a theory of ethics cannot be derived solely from general ethical principles or rules, but need to put the emphasis on how people's relationships and mutual dependencies develop and can be maintained in a manner as to uphold that what is good and works in the relationship (Henriksen & Vetlesen, 2013). Against this background, the proximity ethical theory is particularly suitable as an analytical tool box for this thesis. It is represented in my work by Arne Johan Vetlesen, Zygmunt Bauman and Per Nortvedt. The proximity ethics is referred to as an experience-based ethics based on interpersonal practice. It is in this interpersonal practice that we meet the notions of duty and responsibility, respect and care.

    The thesis reflects a specific socio-historical era in preschool history: two breaking points, one in the 1990s and the other in the early 2000s. The thesis’ empirical material consists of analyses, partly from individual interviews that were collected during the period 1993-1995, and partly from focus group interviews gathered in the period 2004-2006.

    The purpose of this study is, by using a proximity ethical approach, to generate knowledge about meaning of care and practices by studying preschool teacher’s speech concerning responsibility during two different time periods: the period just before and just after the introduction of the Curriculum for the Preschool in Sweden (Lpfö98). The following research questions have been formulated for the work: How do preschool staff speak about the expressions of responsibility and the boundaries of responsibility in the preschool’s everyday life? In what way does a theory of care and the proximity ethical perspective contribute to a broader understanding of the meaning of care in preschool and the teaching profession’s ethical dimension, during the current periods of time and in a contemporary perspective?

    The interviews 1993-1995 reveals the following themes as examples of expressions of responsibility and boundaries of responsibility: Control and safety, Flexibility respectively Division of responsibility between preschool and parents, Family support: Information, solidarity and relief. Focus group interview 2004-2006 reveals the following themes as examples of expressions of responsibility and boundaries of responsibility: Peace and quiet, To pay attention to the children respectively The tension between service and educational activity, Family support: To maintain good relationships.

    In conclusion, the challenges that emerge when making the concept of care more visible in pre-school practice are discussed. These challenges are reflected on the basis of an analytical idea of responsibility in the encounter with the other. Furthermore, it is examined how the proximity ethical perspective can be used as a springboard for a contemporary and forward-looking discussion of the meaning of care in preschool and the pedagogical profession’s ethical dimensions.

  • Disputation: 2018-02-05 14:00 FA32, AlbaNova universitetscentrum, Stockholm
    Lindén, Fredrik
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Mechanisms of Anion Reactions from the lab to ionospheres2018Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    A multitude of heavy neutral and ionic molecules have been discovered by the Cassini Plasma Spectrometer in the ionosphere of Saturn's largest moon Titan. However, only three cyano anions were explicitly identified there, namely CN-, C3N- and C5N-.  The identity of the heavier anions, which show an abundance maximum at m/z 1000, could, however, not be elucidated and   there is, so far, no clear explanation how these were generated.

    We investigated the reaction of the cyanide anion with methyl iodide using a velocity map imaging spectrometer setup and ab initio calculations. The data indicate a dominant direct rebound mechanism and a high internal excitation of the neutral product. According to the ab initio calculation two possible reaction pathways were expected, but in the experiment the two channels turned out to be indistinguishable due to low resolution.

    We also studied the reaction between C3N- and acetylene using three different experimental setups: a triple quadrupole mass spectrometer, a tandem quadrupole mass spectrometer, and the ''CERISES'' guided ion beam apparatus.

    The reaction showed three primary reaction pathways leading to C2H-, CN-, and C5N-. The production of C2H- could either happen via proton transfer or via formation of an adduct. The appearance of CN- could be explained by a reaction sequence involving an intermediate adduct but also via collision induced dissociation. Even though ab initio calculations predict two exoergic pathways leading to CN- and C5N-, all products are only accessible via energy barriers above 1 eV.

    In addition, we investigated the reaction between C5N- and acetylene. Also in this case the experimental and theoretical studies revealed that all reaction pathways proceed via energy barriers well above 1 eV. The sole exoergic pathway leading to C7N- has an energy barrier of 1.91 eV.  Since the chemistry in dark interstellar clouds and planetary ionospheres is restricted to exoergic reactions with energy barriers less than 20 meV or proceed in a barrier-less manner (Vuitton et al. Planetary and Space Science 57, 1558-1572 (2009)), none of the observed pathways are feasible growth mechanism in those environments.

    We also performed investigations of reactions between charged clusters with and without barriers using electrostatic models.  This led to the development of both approximate and exact expressions, which describe the sphere-sphere interaction and the electron transfer from a (neutral or charged) dielectric sphere to another charged dielectric sphere.  The exact solutions include sums that describe polarization effects to infinite orders. However, we have shown that these infinite sums can be simplified, and that these approximations can be applied to calculate the charge transfer cross-sections and Langevin-type cross-sections.


  • Disputation: 2018-02-09 10:00 sal FA32, AlbaNova universitetscentrum, Stockholm
    Li, Liang
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Interpretation of gamma-ray burst X-ray and optical afterglow emission: From the central engine to the circumburst interaction2018Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Gamma-ray bursts are the largest electromagnetic explosions known to happen in the Universe and are associated with the collapse of stellar progenitors into blackholes. After an energetic prompt emission phase, lasting typically less than a minute and emitted in the gamma-rays, a long-lived afterglow phase starts. During this phase strong emission is observed at longer wavelengths, e.g., in the X-ray and optical bands. This phase can last several weeks and carries important information about the energetics and structure of the burst as well as about  the circumburst medium (CBM) and its density profile. The standard afterglow model includes a single emission component which comes from synchrotron emission in a blast wave moving into the CBM. Additional factors that could give observable features include prolonged energy injection from the central engine, effects of the jet geometry, and viewing angle effects, which thus constitute an extended standard model.

    In this thesis, I study the afterglow emission in a global approach by analysing large samples of bursts in search for general trends and characteristics. In paper I, I compare the light curves in the X-rays and in the optical bands in a sample of 87 bursts. I find that 62% are consistent with the standard afterglow model. Among these, only 9 cases have a pure single power law flux decay in all bands, and are therefore fully described by the model within the observed time window. Including the additional factors described above, I find that 91% are consistent with the extended standard model. An interesting finding is that in nearly half of all cases the plateau phase (energy injection phase) changes directly into the jet decay phase.  In paper II, I study the afterglow by analysing the temporal evolution of color indices (CI), defined as the magnitude difference between two filters. They can be used to study the energy spectrum with a good temporal resolution, even when high-resolution spectra are not available. I find that a majority of the CI do not vary with time, which means that the spectral slope does not change, even between different emission episodes. For the other cases, the variation is found to occur during limited periods. We suggest that they are due to the cooling frequency passing over the observed filter bands and, in other cases, due to the emergence of the underlying supernova emission. In paper III, I study the energetics of the GRBs that can be inferred from the afterglow observations. Using this information I analyse the limits it sets on what the central engine can be, if it is a magnetar or a spinning black hole. Assuming that the magnetar energy is emitted isotropically, I find that most bursts are consistent with a BH central engine and only around 20% are consistent with a magnetar central engine. As a consistency check, we derive the rotational energy and the spin period of the blackhole sample and the initial spin period and surface polar cap magnetic field for the magnetar sample and find them to be consistent to the expected values. We find that 4 of 5 of the short burst belong to the magnetar sample which supports the hypothesis that short GRB come from neutron star mergers.

  • Disputation: 2018-02-09 10:00 De Geersalen, Geovetenskapens hus, Stockholm
    Krzymowska, Adriana
    Stockholms universitet, Juridiska fakulteten, Juridiska institutionen.
    Skattepliktiga överlåtelser i inkomstslaget kapital2018Doktorsavhandling, monografi (Övrigt vetenskapligt)
    Abstract [en]

    Capital gains and losses are taxed under the Income Tax Act (ITA) and occur when an asset is divested. The concept of divestment, which is regulated in §§ 3-10 in chapter 44 of the ITA, creates the scope of taxable events. Only those transactions that fall into the definition of divestments in accordance with §§ 3-10 in chapter 44 of the ITA are considered taxable events. Gifts, inheritance etc. are not considered divestments and are accordingly not taxed under the ITA.

    The objective of this doctoral project is to examine and analyze the concept of divestment in regards to the taxation of capital gains and losses. The purpose is to identify (a) what components, or requirements are necessary in order to form at transaction that is a divestment and (b) how those requirements are defined. This purpose requires an inventory of applicable law and practice as well as a study of the context of capital gains taxation. 

    The study shows that an divestment is an act through which the former owner disposes of the asset in a definitive manner while directly or indirectly receiving sufficient compensation. The definitive disposal is characterized by that the rights and obligations associated with a particular asset are suspended in such a way that the ownership of the asset expires. This can occur if the asset is modified in such a way that the characteristic components of the asset are changed. If that happens the old asset is considered to have been exchanged for the new one. A divestment typically requires at least two parties.

    Legal certainty sets boundaries for the interpretation of the concept of divestment. The taxation should as far as possible be neutral, take into account if the transaction creates an (at least theoretical) ability to pay tax and if possible avoid solutions that create unnecessary lock-in effects. The context in which an assessment problem has occurred, principles of reciprocity, continuity, symmetry and consistency in the tax system should be taken into account when assessing unclear cases. In the assessment of whether there has been a divestment, the transaction should be broken up into segments and analyzed. In an unclear situation the assessment of whether a divestment was made or not must always be based on the motives of capital gains and loss taxation.

  • Disputation: 2018-02-09 13:00 Vivi Täckholmsalen (Q-salen), NPQ-huset, Stockholm
    van der Bijl, Wouter
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Why and how brain size evolves: Sociality, predation and allometry2018Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    The evolution of the vertebrate brain has remained a topic of intense interest from biologists over many decades. Evolutionary biologists have seen it as an intriguing example of how the size and structure of a trait evolves across large phylogenies and under body size constraints, with both large shifts in deep evolutionary time and continuous smaller scale adaptation. Behavioral ecologists, on the other hand, have put great effort in trying to understand the costs and benefits of brain size and structural variation, usually assuming that the brain morphology of species is the result of a balance between energetic costs and cognitive benefits.

    I discuss two hypotheses that aim to explain under what circumstances a higher cognitive ability yields fitness benefits. The predation avoidance hypothesis states that large brains help to avoid predators. The social brain hypothesis predicts that cognition is especially beneficial for animals living in complex social environments. In practice these hypotheses are difficult to differentiate (paper I), as sociality often evolves in response to predation pressure. Comparative studies on either hypothesis should therefore aim to control for effects of the other hypothesis, and experiments may be especially useful in testing more explicit mechanistic explanations.

    I put the predation hypothesis to the test using two approaches, a comparative analysis and a within-species experiment. The comparative analysis (paper II) used published data on hawk predation and related it to both relative brain size and relative telencephalon size. While sparrowhawk predation was unrelated to brain morphology, birds that experience more goshawk predation had larger brains and telencephali. Next, I performed an experiment (paper III) on guppies that had been artificially selected for relative brain size. The selection lines have demonstrated differences in cognitive ability, as well as a marked survival difference under predation in females. I exposed fish to either a predator model or a novel object control, varying both sex and group size. Large-brained females performed fewer and shorter predator inspections than small-brained females, while keeping a larger distance from the predator model.

    I performed another experiment (paper IV) to investigate differences in social competence. I calculated the duration of contests between random pairs of small- and large-brained males, using movement data. When the loser was large-brained, contests were decided almost 40 minutes earlier than when the loser was small-brained, indicating that the decision for the loser to give up is made quicker with a larger brain.

    This thesis ends with an exploration of variation in the scaling relationship between brain and body size across vertebrates (paper V). The observed scaling between brain and body depends on what taxonomic level is under investigation. This effect, however, exclusively occurs in the two classes with the largest brains, mammals and birds. This indicates that strong developmental constraints have been alleviated in the two highly encephalized classes, but not elsewhere.

    In conclusion, I find evidence that both predator avoidance and social factors may contribute to the evolution of brain size. Further work on explicit behavioral frameworks for cognitive benefit hypotheses is likely to yield significant insight. Constraints in brain size may be hard to overcome and play an especially large role at a larger taxonomic scale.

  • Disputation: 2018-02-13 10:00 Vivi Täckholmssalen, Stockholm
    Pečnerová, Patrícia
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Swedish Museum of Natural History.
    Genomic analysis of the process leading up to the extinction of the woolly mammoth2018Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Species worldwide are subject to contractions in both abundance and geographical range, and their persistence in a changing environment may thus depend on the ability to survive in small and fragmented populations. Despite the urgent need to understand how extinction works, our knowledge of pre-extinction genetic processes is limited because techniques allowing population and conservation genomics to be studied in wild threatened populations have become available only recently. In this thesis, I used the last surviving population of the woolly mammoth (Mammuthus primigenius) as a model for studying pre-extinction population dynamics. I used ancient DNA as a tool to study microevolutionary processes in real time, analysing genetic changes in response to environmental shifts at the end of the last Ice Age and exploring impacts of genetic drift and inbreeding as woolly mammoths became isolated on Wrangel Island and survived for 6000 years at small population size. Using mitochondrial genomes, I found evidence of a founder effect that decreased the maternal diversity to a single lineage at the time when mammoths became trapped on Wrangel Island (~10,500 years ago). Moreover, a two- to three-fold higher mitochondrial mutation rate in Holocene and a fixed, potentially detrimental mutation in the ATP6 gene encoding for one of the key enzymes of the oxidative phosphorylation pathway, is consistent with the hypothesis that selection is less effective in removing deleterious mutations in small populations. A loss of diversity was also observed in an immunity gene that belongs to the major histocompatibility complex (MHC), even though the MHC is considered to be under balancing selection. Low-coverage genomic data was analysed in order to estimate endogenous DNA content and molecular sex of the mammoth samples. The observation of a male bias (69%) in the sex ratio led to the conclusion that male mammoths were more likely to die in a way that ensured good preservation. Another potential way of getting information about life history strategies of extinct species, which was explored here, is by measuring testosterone levels in mammoth hair shafts in connection with molecular sex inference. Finally, given that previous estimates have suggested a very small Holocene effective population size on Wrangel Island and thus that the population may have been too small to avoid genome erosion, four mammoths were sequenced to a high coverage in order to look for genomic consequences of small population size. When compared to mammoths from the Pleistocene mainland population, Wrangel Island mammoths had lower levels of genome-wide diversity and had a higher proportion of their genomes allocated in runs of homozygosity, which are large fragments completely depleted of diversity. Importantly, genome erosion appears to have accelerated in the last ten generations before the extinction, resulting in the last known woolly mammoth having almost 40% of its genome without any genetic diversity. Overall, these results highlight how genetic drift and inbreeding triggered genomic deterioration in the last surviving woolly mammoth population. Although Wrangel Island was a refugium, where mammoths survived for thousands of years after the last Ice Age, and the causal factors of the final extinction are not yet clear, isolation and small population size without any possibility of new gene flow may have contributed to reduced fitness, and thus to extinction.