Climate forcing on avian life history

In the 21st century, human-induced global climate change has been highlighted as one of the most serious threats to ecosystems worldwide. According to global climate scenarios, the mean temperature in Finland is expected to increase by 1.8 4.0°C by the end of the century. The regional and seasonal change in temperature has predicted to be spatially and temporally asymmetric, where the High-Arctic and Antarctic areas and winter and spring seasons have been projected to face the highest temperature increase. To understand how species respond to the ongoing climate change, we need to study how climate affects species in different phases of their life cycle. The impact of climate on breeding and migration of eight large-sized bird species was studied in this thesis, taking food availability into account. The findings show that climatic variables have considerable impact on the life-history traits of large-sized birds in northern Europe. The magnitude of climatic effects on migration and breeding was comparable with that of food supply, conventionally regarded as the main factor affecting these life-history traits. Based on the results of this thesis and the current climate scenarios, the following not mutually exclusive responses are possible in the near future. Firstly, asymmetric climate change may result in a mistiming of breeding because mild winters and early spring may lead to earlier breeding, whereas offspring are hatching into colder conditions which elevate mortality. Secondly, climate induced responses can differ between species with different breeding tactics (income vs. capital breeding), so that especially capital breeders can gain advantage on global warming as they can sustain higher energy resources. Thirdly, increasing precipitation has the potential to reduce the breeding success of many species by exposing nestlings to more severe post-hatching conditions and hampering the hunting conditions of parents. Fourthly, decreasing ice cover and earlier ice-break in the Baltic Sea will allow earlier spring migration in waterfowl. In eiders, this can potentially lead to more productive breeding. Fifthly, warming temperatures can favour parents preparing for breeding and increase nestling survival. Lastly, the climate-induced phenological changes in life history events will likely continue. Furthermore, interactions between climate and food resources can be complex and interact with each other. Eiders provide an illustrative example of this complexity, being caught in the crossfire between more benign ice conditions and lower salinity negatively affecting their prime food resource. The general conclusion is that climate is controlling not only the phenology of the species but also their reproductive output, thus affecting the entire population dynamics.

Conceptual and statistical modelling of environmental effects in population dynamics

Population dynamics are generally viewed as the result of intrinsic (purely density dependent) and extrinsic (environmental) processes. Both components, and potential interactions between those two, have to be modelled in order to understand and predict dynamics of natural populations; a topic that is of great importance in population management and conservation. This thesis focuses on modelling environmental effects in population dynamics and how effects of potentially relevant environmental variables can be statistically identified and quantified from time series data. Chapter I presents some useful models of multiplicative environmental effects for unstructured density dependent populations. The presented models can be written as standard multiple regression models that are easy to fit to data. Chapters II IV constitute empirical studies that statistically model environmental effects on population dynamics of several migratory bird species with different life history characteristics and migration strategies. In Chapter II, spruce cone crops are found to have a strong positive effect on the population growth of the great spotted woodpecker (Dendrocopos major), while cone crops of pine another important food resource for the species do not effectively explain population growth. The study compares rate- and ratio-dependent effects of cone availability, using state-space models that distinguish between process and observation error in the time series data. Chapter III shows how drought, in combination with settling behaviour during migration, produces asymmetric spatially synchronous patterns of population dynamics in North American ducks (genus Anas). Chapter IV investigates the dynamics of a Finnish population of skylark (Alauda arvensis), and point out effects of rainfall and habitat quality on population growth. Because the skylark time series and some of the environmental variables included show strong positive autocorrelation, the statistical significances are calculated using a Monte Carlo method, where random autocorrelated time series are generated. Chapter V is a simulation-based study, showing that ignoring observation error in analyses of population time series data can bias the estimated effects and measures of uncertainty, if the environmental variables are autocorrelated. It is concluded that the use of state-space models is an effective way to reach more accurate results. In summary, there are several biological assumptions and methodological issues that can affect the inferential outcome when estimating environmental effects from time series data, and that therefore need special attention. The functional form of the environmental effects and potential interactions between environment and population density are important to deal with. Other issues that should be considered are assumptions about density dependent regulation, modelling potential observation error, and when needed, accounting for spatial and/or temporal autocorrelation.

Electron cryo-microscopy studies of bacteriophage phi8 and archaeal virus SH1

Symmetry is a key principle in viral structures, especially the protein capsid shells. However, symmetry mismatches are very common, and often correlate with dynamic functionality of biological significance. The three-dimensional structures of two isometric viruses, bacteriophage phi8 and the archaeal virus SH1 were reconstructed using electron cryo-microscopy. Two image reconstruction methods were used: the classical icosahedral method yielded high resolution models for the symmetrical parts of the structures, and a novel asymmetric in-situ reconstruction method allowed us to resolve the symmetry mismatches at the vertices of the viruses. Evidence was found that the hexameric packaging enzyme at the vertices of phi8 does not rotate relative to the capsid. The large two-fold symmetric spikes of SH1 were found not to be responsible for infectivity. Both virus structures provided insight into the evolution of viruses. Comparison of the phi8 polymerase complex capsid with those of phi6 and other dsRNA viruses suggests that the quaternary structure in dsRNA bacteriophages differs from other dsRNA viruses. SH1 is unusual because there are two major types of capsomers building up the capsid, both of which seem to be composed mainly of single beta-barrels perpendicular to the capsid surface. This indicates that the beta-barrel may be ancestral to the double beta-barrel fold.

Fine-tuning of the signalling network controlling morphogenesis and stem cell development in teeth

Tooth development is regulated by sequential and reciprocal interactions between epithelium and mesenchyme. The molecular mechanisms underlying this regulation are conserved and most of the participating molecules belong to several signalling families. Research focusing on mouse teeth has uncovered many aspects of tooth development, including molecular and evolutionary specifi cs, and in addition offered a valuable system to analyse the regulation of epithelial stem cells. In mice the spatial and temporal regulation of cell differentiation and the mechanisms of patterning during development can be analysed both in vivo and in vitro. Follistatin (Fst), a negative regulator of TGFβ superfamily signalling, is an important inhibitor during embryonic development. We showed the necessity of modulation of TGFβ signalling by Fst in three different regulatory steps during tooth development. First we showed that tinkering with the level of TGFβ signalling by Fst may cause variation in the molar cusp patterning and crown morphogenesis. Second, our results indicated that in the continuously growing mouse incisors asymmetric expression of Fst is responsible for the labial-lingual patterning of ameloblast differentiation and enamel formation. Two TGFβ superfamily signals, BMP and Activin, are required for proper ameloblast differentiation and Fst modulates their effects. Third, we identifi ed a complex signalling network regulating the maintenance and proliferation of epithelial stem cells in the incisor, and showed that Fst is an essential modulator of this regulation. FGF3 in cooperation with FGF10 stimulates proliferation of epithelial stem cells and transit amplifying cells in the labial cervical loop. BMP4 represses Fgf3 expression whereas Activin inhibits the repressive effect of BMP4 on the labial side. Thus, Fst inhibits Activin rather than BMP4 in the cervical loop area and limits the proliferation of lingual epithelium, thereby causing the asymmetric maintenance and proliferation of epithelial stem cells. In addition, we detected Lgr5, a Wnt target gene and an epithelial stem cell marker in the intestine, in the putative epithelial stem cells of the incisor, suggesting that Lgr5 is a marker of incisor stem cells but is not regulated by Wnt/β-catenin signalling in the incisor. Thus the epithelial stem cells in the incisor may not be directly regulated by Wnt/β-catenin signalling. In conclusion, we showed in the mouse incisors that modulating the balance between inductive and inhibitory signals constitutes a key mechanism regulating the epithelial stem cells and ameloblast differentiation. Furthermore, we found additional support for the location of the putative epithelial stem cells and for the stemness of these cells. In the mouse molar we showed the necessity of fi ne-tuning the signalling in the regulation of the crown morphogenesis, and that altering the levels of an inhibitor can cause variation in the crown patterning.

Phospholipids of lipid-containing bacteriophages and their transbilayer distribution

In this study we used electro-spray ionization mass-spectrometry to determine phospholipid class and molecular species compositions in bacteriophages PM2, PRD1, Bam35 and phi6 as well as their hosts. To obtain compositional data of the individual leaflets, phospholipid transbilayer distribution in the viral membranes was studied. We found that 1) the membranes of all studied bacteriophage are enriched in PG as compared to the host membranes, 2) molecular species compositions in the phage and host membranes are similar, and 3) phospholipids in the viral membranes are distributed asymmetrically with phosphatidylglycerol enriched in the outer leaflet and phosphatidylethanolamine in the inner one (except Bam35). Alternative models for selective incorporation of phospholipids to phages and for the origins of the asymmetric phospholipid transbilayer distribution are discussed. Notably, the present data are also useful when constructing high resolution structural models of bacteriophages, since diffraction methods cannot provide a detailed structure of the membrane due to high motility of the lipids and lack of symmetric organization of membrane proteins.

Exploiting ground-based measurements of the Global Positioning System for numerical weather prediction

Data assimilation provides an initial atmospheric state, called the analysis, for Numerical Weather Prediction (NWP). This analysis consists of pressure, temperature, wind, and humidity on a three-dimensional NWP model grid. Data assimilation blends meteorological observations with the NWP model in a statistically optimal way. The objective of this thesis is to describe methodological development carried out in order to allow data assimilation of ground-based measurements of the Global Positioning System (GPS) into the High Resolution Limited Area Model (HIRLAM) NWP system. Geodetic processing produces observations of tropospheric delay. These observations can be processed either for vertical columns at each GPS receiver station, or for the individual propagation paths of the microwave signals. These alternative processing methods result in Zenith Total Delay (ZTD) and Slant Delay (SD) observations, respectively. ZTD and SD observations are of use in the analysis of atmospheric humidity. A method is introduced for estimation of the horizontal error covariance of ZTD observations. The method makes use of observation minus model background (OmB) sequences of ZTD and conventional observations. It is demonstrated that the ZTD observation error covariance is relatively large in station separations shorter than 200 km, but non-zero covariances also appear at considerably larger station separations. The relatively low density of radiosonde observing stations limits the ability of the proposed estimation method to resolve the shortest length-scales of error covariance. SD observations are shown to contain a statistically significant signal on the asymmetry of the atmospheric humidity field. However, the asymmetric component of SD is found to be nearly always smaller than the standard deviation of the SD observation error. SD observation modelling is described in detail, and other issues relating to SD data assimilation are also discussed. These include the determination of error statistics, the tuning of observation quality control and allowing the taking into account of local observation error correlation. The experiments made show that the data assimilation system is able to retrieve the asymmetric information content of hypothetical SD observations at a single receiver station. Moreover, the impact of real SD observations on humidity analysis is comparable to that of other observing systems.

Studies on the Cell Wall Structure and on the Mechanical Properties of Norway Spruce

The structure and the mechanical properties of wood of Norway spruce (Picea abies [L.] Karst.) were studied using small samples from Finland and Sweden. X-ray diffraction (XRD) was used to determine the orientation of cellulose microfibrils (microfibril angle, MFA), the dimensions of cellulose crystallites and the average shape of the cell cross-section. X-ray attenuation and x-ray fluorescence measurements were used to study the chemical composition and the trace element content. Tensile testing with in situ XRD was used to characterise the mechanical properties of wood and the deformation of crystalline cellulose within the wood cell walls. Cellulose crystallites were found to be 192 284 Å long and 28.9 33.4 Å wide in chemically untreated wood and they were longer and wider in mature wood than in juvenile wood. The MFA distribution of individual Norway spruce tracheids and larger samples was asymmetric. In individual cell walls, the mean MFA was 19 30 degrees, while the mode of the MFA distribution was 7 21 degrees. Both the mean MFA and the mode of the MFA distribution decreased as a function of the annual ring. Tangential cell walls exhibited smaller mean MFA and mode of the MFA distribution than radial cell walls. Maceration of wood material caused narrowing of the MFA distribution and removed contributions observed at around 90 degrees. In wood of both untreated and fertilised trees, the average shape of the cell cross-section changed from circular via ambiguous to rectangular as the cambial age increased. The average shape of the cell cross-section and the MFA distribution did not change as a result of fertilisation. The mass absorption coefficient for x-rays was higher in wood of fertilised trees than in that of untreated trees and wood of fertilised trees contained more of the elements S, Cl, and K, but a smaller amount of Mn. Cellulose crystallites were longer in wood of fertilised trees than in that of untreated trees. Kraft cooking caused widening and shortening of the cellulose crystallites. Tensile tests parallel to the cells showed that if the mean MFA is initially around 10 degrees or smaller, no systematic changes occur in the MFA distribution due to strain. The role of mean MFA in defining the tensile strength or the modulus of elasticity of wood was not as dominant as that reported earlier. Crystalline cellulose elongated much less than the entire samples. The Poisson ratio νca of crystalline cellulose in Norway spruce wood was shown to be largely dependent on the surroundings of crystalline cellulose in the cell wall, varying between -1.2 and 0.8. The Poisson ratio was negative in kraft cooked wood and positive in chemically untreated wood. In chemically untreated wood, νca was larger in mature wood and in latewood compared to juvenile wood and earlywood.

Making sense of a transnational merger: Media texts and the (re)construction of power relations

In this study of symbolic power relations in a transnational merger, we suggest that the popular media can provide a significant arena for (re)constructing national identities and power in this kind of dramatic industrial restructuring, and are an under-utilized source of empirical data in research studies. Focusing on the press coverage of a recent Swedish-Finnish merger, we specify and illustrate a particular feature of discursive (re)construction of asymmetric power relations; superior (Swedish) and inferior (Finnish) national identities, which, we argue, are embedded in the history of colonization and domination between the two nations. The findings of the present study lead us to suggest that a lens taken from post-colonial theory is particularly useful in understanding the wider symbolic power implications of international industrial restructuring.

Intraday Dynamics of International Equity Markets

The increased availability of high frequency data sets have led to important new insights in understanding of financial markets. The use of high frequency data is interesting and persuasive, since it can reveal new information that cannot be seen in lower data aggregation. This dissertation explores some of the many important issues connected with the use, analysis and application of high frequency data. These include the effects of intraday seasonal, the behaviour of time varying volatility, the information content of various market data, and the issue of inter market linkages utilizing high frequency 5 minute observations from major European and the U.S stock indices, namely DAX30 of Germany, CAC40 of France, SMI of Switzerland, FTSE100 of the UK and SP500 of the U.S. The first essay in the dissertation shows that there are remarkable similarities in the intraday behaviour of conditional volatility across European equity markets. Moreover, the U.S macroeconomic news announcements have significant cross border effect on both, European equity returns and volatilities. The second essay reports substantial intraday return and volatility linkages across European stock indices of the UK and Germany. This relationship appears virtually unchanged by the presence or absence of the U.S stock market. However, the return correlation among the U.K and German markets rises significantly following the U.S stock market opening, which could largely be described as a contemporaneous effect. The third essay sheds light on market microstructure issues in which traders and market makers learn from watching market data, and it is this learning process that leads to price adjustments. This study concludes that trading volume plays an important role in explaining international return and volatility transmissions. The examination concerning asymmetry reveals that the impact of the positive volume changes is larger on foreign stock market volatility than the negative changes. The fourth and the final essay documents number of regularities in the pattern of intraday return volatility, trading volume and bid-ask spreads. This study also reports a contemporaneous and positive relationship between the intraday return volatility, bid ask spread and unexpected trading volume. These results verify the role of trading volume and bid ask quotes as proxies for information arrival in producing contemporaneous and subsequent intraday return volatility. Moreover, asymmetric effect of trading volume on conditional volatility is also confirmed. Overall, this dissertation explores the role of information in explaining the intraday return and volatility dynamics in international stock markets. The process through which the information is incorporated in stock prices is central to all information-based models. The intraday data facilitates the investigation that how information gets incorporated into security prices as a result of the trading behavior of informed and uninformed traders. Thus high frequency data appears critical in enhancing our understanding of intraday behavior of various stock markets’ variables as it has important implications for market participants, regulators and academic researchers.

Modeling and Forecasting Implied Volatility: Implications for Trading, Pricing, and Risk Management

Modeling and forecasting of implied volatility (IV) is important to both practitioners and academics, especially in trading, pricing, hedging, and risk management activities, all of which require an accurate volatility. However, it has become challenging since the 1987 stock market crash, as implied volatilities (IVs) recovered from stock index options present two patterns: volatility smirk(skew) and volatility term-structure, if the two are examined at the same time, presents a rich implied volatility surface (IVS). This implies that the assumptions behind the Black-Scholes (1973) model do not hold empirically, as asset prices are mostly influenced by many underlying risk factors. This thesis, consists of four essays, is modeling and forecasting implied volatility in the presence of options markets’ empirical regularities. The first essay is modeling the dynamics IVS, it extends the Dumas, Fleming and Whaley (DFW) (1998) framework; for instance, using moneyness in the implied forward price and OTM put-call options on the FTSE100 index, a nonlinear optimization is used to estimate different models and thereby produce rich, smooth IVSs. Here, the constant-volatility model fails to explain the variations in the rich IVS. Next, it is found that three factors can explain about 69-88% of the variance in the IVS. Of this, on average, 56% is explained by the level factor, 15% by the term-structure factor, and the additional 7% by the jump-fear factor. The second essay proposes a quantile regression model for modeling contemporaneous asymmetric return-volatility relationship, which is the generalization of Hibbert et al. (2008) model. The results show strong negative asymmetric return-volatility relationship at various quantiles of IV distributions, it is monotonically increasing when moving from the median quantile to the uppermost quantile (i.e., 95%); therefore, OLS underestimates this relationship at upper quantiles. Additionally, the asymmetric relationship is more pronounced with the smirk (skew) adjusted volatility index measure in comparison to the old volatility index measure. Nonetheless, the volatility indices are ranked in terms of asymmetric volatility as follows: VIX, VSTOXX, VDAX, and VXN. The third essay examines the information content of the new-VDAX volatility index to forecast daily Value-at-Risk (VaR) estimates and compares its VaR forecasts with the forecasts of the Filtered Historical Simulation and RiskMetrics. All daily VaR models are then backtested from 1992-2009 using unconditional, independence, conditional coverage, and quadratic-score tests. It is found that the VDAX subsumes almost all information required for the volatility of daily VaR forecasts for a portfolio of the DAX30 index; implied-VaR models outperform all other VaR models. The fourth essay models the risk factors driving the swaption IVs. It is found that three factors can explain 94-97% of the variation in each of the EUR, USD, and GBP swaption IVs. There are significant linkages across factors, and bi-directional causality is at work between the factors implied by EUR and USD swaption IVs. Furthermore, the factors implied by EUR and USD IVs respond to each others’ shocks; however, surprisingly, GBP does not affect them. Second, the string market model calibration results show it can efficiently reproduce (or forecast) the volatility surface for each of the swaptions markets.