Univariate, bivariate, and multivariate methods in corpus-based lexicography : A study of synonymy

In this dissertation, I present an overall methodological framework for studying linguistic alternations, focusing specifically on lexical variation in denoting a single meaning, that is, synonymy. As the practical example, I employ the synonymous set of the four most common Finnish verbs denoting THINK, namely ajatella, miettiä, pohtia and harkita ‘think, reflect, ponder, consider’. As a continuation to previous work, I describe in considerable detail the extension of statistical methods from dichotomous linguistic settings (e.g., Gries 2003; Bresnan et al. 2007) to polytomous ones, that is, concerning more than two possible alternative outcomes. The applied statistical methods are arranged into a succession of stages with increasing complexity, proceeding from univariate via bivariate to multivariate techniques in the end. As the central multivariate method, I argue for the use of polytomous logistic regression and demonstrate its practical implementation to the studied phenomenon, thus extending the work by Bresnan et al. (2007), who applied simple (binary) logistic regression to a dichotomous structural alternation in English. The results of the various statistical analyses confirm that a wide range of contextual features across different categories are indeed associated with the use and selection of the selected think lexemes; however, a substantial part of these features are not exemplified in current Finnish lexicographical descriptions. The multivariate analysis results indicate that the semantic classifications of syntactic argument types are on the average the most distinctive feature category, followed by overall semantic characterizations of the verb chains, and then syntactic argument types alone, with morphological features pertaining to the verb chain and extra-linguistic features relegated to the last position. In terms of overall performance of the multivariate analysis and modeling, the prediction accuracy seems to reach a ceiling at a Recall rate of roughly two-thirds of the sentences in the research corpus. The analysis of these results suggests a limit to what can be explained and determined within the immediate sentential context and applying the conventional descriptive and analytical apparatus based on currently available linguistic theories and models. The results also support Bresnan’s (2007) and others’ (e.g., Bod et al. 2003) probabilistic view of the relationship between linguistic usage and the underlying linguistic system, in which only a minority of linguistic choices are categorical, given the known context – represented as a feature cluster – that can be analytically grasped and identified. Instead, most contexts exhibit degrees of variation as to their outcomes, resulting in proportionate choices over longer stretches of usage in texts or speech.

Quantitative trait loci detection and benefits from marker-assisted selection in dairy cattle

Knowing the chromosomal areas or actual genes affecting the traits under selection would add more information to be used in the selection decisions which would potentially lead to higher genetic response. The first objective of this study was to map quantitative trait loci (QTL) affecting economically important traits in the Finnish Ayrshire population. The second objective was to investigate the effects of using QTL information in marker-assisted selection (MAS) on the genetic response and the linkage disequilibrium between the different parts of the genome. Whole genome scans were carried out on a grand-daughter design with 12 half-sib families and a total of 493 sons. Twelve different traits were studied: milk yield, protein yield, protein content, fat yield, fat content, somatic cell score (SCS), mastitis treatments, other veterinary treatments, days open, fertility treatments, non-return rate, and calf mortality. The average spacing of the typed markers was 20 cM with 2 to 14 markers per chromosome. Associations between markers and traits were analyzed with multiple marker regression. Significance was determined by permutation and genome-wise P-values obtained by Bonferroni correction. The benefits from MAS were investigated by simulation: a conventional progeny testing scheme was compared to a scheme where QTL information was used within families to select among full-sibs in the male path. Two QTL on different chromosomes were modelled. The effects of different starting frequencies of the favourable alleles and different size of the QTL effects were evaluated. A large number of QTL, 48 in total, were detected at 5% or higher chromosome-wise significance. QTL for milk production were found on 8 chromosomes, for SCS on 6, for mastitis treatments on 1, for other veterinary treatments on 5, for days open on 7, for fertility treatments on 7, for calf mortality on 6, and for non-return rate on 2 chromosomes. In the simulation study the total genetic response was faster with MAS than with conventional selection and the advantage of MAS persisted over the studied generations. The rate of response and the difference between the selection schemes reflected clearly the changes in allele frequencies of the favourable QTL. The disequilibrium between the polygenes and QTL was always negative and it was larger with larger QTL size. The disequilibrium between the two QTL was larger with QTL of large effect and it was somewhat larger with MAS for scenarios with starting frequencies below 0.5 for QTL of moderate size and below 0.3 for large QTL. In conclusion, several QTL affecting economically important traits of dairy cattle were detected. Further studies are needed to verify these QTL, check their presence in the present breeding population, look for pleiotropy and fine map the most interesting QTL regions. The results of the simulation studies show that using MAS together with embryo transfer to pre-select young bulls within families is a useful approach to increase the genetic merit of the AI-bulls compared to conventional selection.

The Population Consequences of Sex and Conflict

Natural selection generally operates at the level of the individual, or more specifically at the level of the gene. As a result, individual selection does not always favour traits which benefit the population or species as a whole. The spread of an individual gene may even act to the detriment of the organism in which it finds. Thus selection at the level of the individual can affect processes at the level of the organism, group or even at the level of the species. As most behaviours ultimately affect births, deaths and the distribution of individuals, it seems inevitable that behavioural decisions will have an impact on population dynamics and population densities. Behavioural decisions can often involve costs through allocation of energy into behavioural strategies, such as the investment into armaments involved in fighting over resources or increased mortality due to injury or increased predation risk. Similarly, behaviour may act o to benefit the population, in terms of higher survival and increased fecundity. Examples include increased investment through parental care, choosing a mate based on the nuptial gifts they may supply and choosing territories in the face of competition. Investigating the impact of behaviour on population ecology may seem like a trivial task, but it is likely to have important consequences at different levels. For example, antagonistic behaviour may occasionally become so extreme that it increases the risk of extinction, and such extinction risk may have important implications for conservation. As a corollary, any such behaviour may also act as a macroevolutionary force, weeding out populations with traits which, whilst beneficial to the individuals in the short term, ultimately result in population extinction. In this thesis, I examine how behaviours, specifically conflict and competition over a resource and aspects of behaviour involved in sexual selection, can affect population densities, and what the implications are for the evolution and ecology of the populations in question. It is found that both behaviours related to individual conflict and mating strategies can have an effect at the level of the population, but that various factors, such as a feedback between selection and population densities or macroevolution caused by species extinctions, may act to limit the intensity of conflicts that we observe in nature.

Pre- and post-copulatory sexual selection in the least killifish, Heterandria formosa

It has been only recently realized that sexual selection does not end at copulation but that post-copulatory processes are often important in determining the fitness of individuals. In this thesis, I experimentally studied both pre- and post-copulatory sexual selection in the least killifish, Heterandria formosa. I found that this species suffers from severe inbreeding depression in male reproductive behaviour, offspring viability and offspring maturation times. Neither sex showed pre-copulatory inbreeding avoidance but when females mated with their brothers, less sperm were retrieved from their reproductive system compared to the situation when females mated with unrelated males. Whether the difference in sperm numbers is due to female or male effect could not be resolved. Based on theory, females should be more eager to avoid inbreeding than males in this species, because females invest more in their offspring than males do. Inbreeding seems to be an important part of this species biology and the severe inbreeding depression has most likely selected for the evolution of the post-copulatory inbreeding avoidance mechanism that I found. In addition, I studied the effects of polyandry on female reproductive success. When females mated with more than one male, they were more likely to get pregnant. However, I also found a cost of polyandry. The offspring of females mated to four males took longer to reach sexual maturity compared to the offspring of monandrous females. This cost may be explained by parent-offspring conflict over maternal resource allocation. In another experiment, in which within-brood relatedness was manipulated, offspring sizes decreased over time when within-brood relatedness was low. This result is partly in accordance with the kinship theory of genomic imprinting. When relatedness decreases, offspring are expected to be less co-operative and demand fewer resources from their mother, which leads to impaired development. In the last chapter of my thesis, I show that H. formosa males do not prefer large females as in other Poeciliidae species. I suggest that males view smaller females as more profitable mates because those are more likely virgin. In conclusion, I found both pre- and post-copulatory sexual selection to be important factors in determining reproductive success in H. formosa.

Human genetic variation in the Baltic Sea region: Features of population history and natural selection

In this thesis, the genetic variation of human populations from the Baltic Sea region was studied in order to elucidate population history as well as evolutionary adaptation in this region. The study provided novel understanding of how the complex population level processes of migration, genetic drift, and natural selection have shaped genetic variation in North European populations. Results from genome-wide, mitochondrial DNA and Y-chromosomal analyses suggested that the genetic background of the populations of the Baltic Sea region lies predominantly in Continental Europe, which is consistent with earlier studies and archaeological evidence. The late settlement of Fennoscandia after the Ice Age and the subsequent small population size have led to pronounced genetic drift, especially in Finland and Karelia but also in Sweden, evident especially in genome-wide and Y-chromosomal analyses. Consequently, these populations show striking genetic differentiation, as opposed to much more homogeneous pattern of variation in Central European populations. Additionally, the eastern side of the Baltic Sea was observed to have experienced eastern influence in the genome-wide data as well as in mitochondrial DNA and Y-chromosomal variation – consistent with linguistic connections. However, Slavic influence in the Baltic Sea populations appears minor on genetic level. While the genetic diversity of the Finnish population overall was low, genome-wide and Y-chromosomal results showed pronounced regional differences. The genetic distance between Western and Eastern Finland was larger than for many geographically distant population pairs, and provinces also showed genetic differences. This is probably mainly due to the late settlement of Eastern Finland and local isolation, although differences in ancestral migration waves may contribute to this, too. In contrast, mitochondrial DNA and Y-chromosomal analyses of the contemporary Swedish population revealed a much less pronounced population structure and a fusion of the traces of ancient admixture, genetic drift, and recent immigration. Genome-wide datasets also provide a resource for studying the adaptive evolution of human populations. This study revealed tens of loci with strong signs of recent positive selection in Northern Europe. These results provide interesting targets for future research on evolutionary adaptation, and may be important for understanding the background of disease-causing variants in human populations.

Thyroid Hormone Control of Cardiac Substrate Metabolism

Thyroid hormone (TH) plays an important role in maintaining a homeostasis in all the cells of our body. It also has significant cardiovascular effects, and abnormalities of its concentration can cause cardiovascular disease and even morbidity. Especially development of heart failure has been connected to low levels of thyroid hormone. A decrease in TH levels or TH-receptor binding adversely effects cardiac function. Although, this occurs in part through alterations in excitation-contraction and transport proteins, recent data from our laboratory indicate that TH also mediates changes in myocardial energy metabolism. Thyroid dysfunction may limit the heart s ability to shift substrate pathways and provide adequate energy supply during stress responses. Our goals of these studies were to determine substrate oxidation pattern in systemic and cardiac specific hypothyroidism at rest and at higher rates of oxygen demand. Additionally we investigated the TH mediated mechanisms in myocardial substrate selection and established the metabolic phenotype caused by a thyroid receptor dysfunction. We measured cardiac metabolism in an isolated heart model using 13Carbon isotopomer analyses with MR spectroscopy to determine function, oxygen consumption, fluxes and fractional contribution of acetyl-CoA to the citric acid cycle (CAC). Molecular pathways for changes in cardiac function and substrate shifts occurring during stress through thyroid receptor abnormalities were determined by protein analyses. Our results show that TH modifies substrate selection through nuclear-mediated and rapid posttranscriptional mechanisms. It modifies substrate selection differentially at rest and at higher rates of oxygen demand. Chronic TH deficiency depresses total CAC flux and selectively fatty acid flux, whereas acute TH supplementation decreases lactate oxidation. Insertion of a dominant negative thyroid receptor (Δ337T) alters metabolic phenotype and contractive efficiency in heart. The capability of the Δ337T heart to increase carbohydrate oxidation in response to stress seems to be limited. These studies provided a clearer understanding of the TH role in heart disease and shed light to identification of the molecular mechanisms that will facilitate in finding targets for heart failure prevention and treatment.

Kin selection, social polymorphism, and reproductive allocation in ants

Social groups are common across animal species. The reasons for grouping are straightforward when all individuals gain directly from cooperating. However, the situation becomes more complex when helping entails costs to the personal reproduction of individuals. Kin selection theory has offered a fruitful framework to explain such cooperation by stating that individuals may spread their genes not only through their own reproduction, but also by helping related individuals reproduce. However, kin selection theory also implicitly predicts conflicts when groups consist of non-clonal individuals, i.e. relatedness is less than one. Then, individual interests are not perfectly aligned, and each individual is predicted to favour the propagation of their own genome over others. Social insects provide a solid study system to study the interplay between cooperation and conflict. Breeding systems in social insects range from solitary breeding to eusocial colonies displaying complete division of reproduction between the fertile queen and the sterile worker caste. Within colonies, additional variation is provided by the presence of several reproductive individuals. In many species, the queen mates multiply, which causes the colony to consist of half-sib instead of full-sib offspring. Furthermore, in many species colonies contain multiple breeding queens, which further dilutes relatedness between colony members. Evolutionary biology is thus faced with the challenge to answer why such variation in social structure exists, and what the consequences are on the individual and population level. The main part of this thesis takes on this challenge by investing the dynamics of socially polymorphic ant colonies. The first four chapters investigate the causes and consequences of different social structures, using a combination of field studies, genetic analyses and laboratory experiments. The thesis ends with a theoretical chapter focusing on different social interactions (altruism and spite), and the evolution of harming traits. The main results of the thesis show that social polymorphism has the potential to affect the behaviour and traits of both individuals and colonies. For example, we found that genetic polymorphism may increase the phenotypic variation between individuals in colonies, and that socially polymorphic colonies may show different life history patterns. We also show that colony cohesion may be enhanced even in multiple-queen colonies through patterns of unequal reproduction between queens. However, the thesis also demonstrates that spatial and temporal variation between both populations and environments may affect individual and colony traits, to the degree that results obtained in one place or at one time may not be applicable in other situations. This opens up potential further areas of research to explain these differences.

The influence of eutrophication on sexual selection in sticklebacks

Jordens ekologiska system undergår för tillfället stora förändringar pga. människans aktiviteter. Ett växande antal studier visar att dessa förändringar påverkar naturliga och sexuella urvalet och därmed evolutiva processer. Målet med detta arbete var att undersöka effekterna av omgivningsförändringar på sexuella urvalet genom att använda den ökade övergödningen inom storpiggen Gasterosteus aculeatus lekområden som modell system. Sexuella urvalet är en viktig evolutiv kraft med följder på populations- och artnivå (Kapitel 1). Avhandlingens olika delar fokuserar på övergödningens effekter på upptäckandet av partners, användningen av visuella- och doftsignaler i partnersval, och fördelningen av parningsframgången mellan bobyggande hanar. I Kapitel II och III simuleras hur grumlighet orsakad av fytoplankton påverkar hastigheten med vilken potentiella partners påträffas, genom effekter på synligheten. Resultaten visar att normala algblomningar i Östersjön har en måttlig effekt på finnandet av potentiella partners. Detta tyder på att algblomningarna troligen inte kommer att minska på selektiva parningen pga. ökade sökkostnader. I Kapitel IV visas att storspiggen ändrar relativa användningen av olika signaler när vattnets grumlighet ökar; visuella signaler minskar i betydelse medan doftsignaler ökar i betydelse. Samtidigt underlättas användandet av doftsignaler av ändringar i vattnets kemiska sammansättning då fotosyntesen intensifieras (Kapitel V). Lek i övergödda vatten kan ändå vara kostsamt både på individ- och populationsnivån, då parasiterade hanar, som troligen är dåligt genetiskt anpassade till sin miljö, lyckas få mer ägg i sina bon än friskare hanar som troligen är av högre genetisk kvalitet (Kapitel VI). Övergödningen påverkar således partnersval och konkurrensen om partners genom att påverka upptäckandet av potentiella partners, evalueringen av partners och fördelningen av partners inom lekområdena. De följder detta kan ha för evolutionen av sexuellt selekterad egenskaper och för populationers dynamik och livskraft är dock oklara. Avhandlingen visar på svårigheten att förutse följderna av omgivningsförändringar för sexuella urvalet och effekterna på individ och populationsnivå.

Combined Tevatron upper limit on gg->H->W+W- and constraints on the Higgs boson mass in fourth-generation fermion models

We combine results from searches by the CDF and D0 collaborations for a standard model Higgs boson (H) in the process gg->H->W+W- in p=pbar collisions at the Fermilab Tevatron Collider at sqrt{s}=1.96 TeV. With 4.8 fb-1 of integrated luminosity analyzed at CDF and 5.4 fb-1 at D0, the 95% Confidence Level upper limit on \sigma(gg->H) x B(H->W+W-) is 1.75 pb at m_H=120 GeV, 0.38 pb at m_H=165 GeV, and 0.83 pb at m_H=200 GeV. Assuming the presence of a fourth sequential generation of fermions with large masses, we exclude at the 95% Confidence Level a standard-model-like Higgs boson with a mass between 131 and 204 GeV.

Search for WW and WZ production in lepton plus jets final state at CDF

We present a search for WW and WZ production in final states that contain a charged lepton (electron or muon) and at least two jets, produced in sqrt(s) = 1.96 TeV ppbar collisions at the Fermilab Tevatron, using data corresponding to 1.2 fb-1 of integrated luminosity collected with the CDF II detector. Diboson production in this decay channel has yet to be observed at hadron colliders due to the large single W plus jets background. An artificial neural network has been developed to increase signal sensitivity, as compared with an event selection based on conventional cuts. We set a 95% confidence level upper limit of sigma_{WW}* BR(W->lnu,W->jets)+ sigma_{WZ}*BR(W->lnu,Z->jets)

Search for Long-Lived Massive Charged Particles in 1.96 TeV pp̅ Collisions

We performed a signature-based search for long-lived charged massive particles (CHAMPs) produced in 1.0 $\rm{fb}^{-1}$ of $\bar{p}p$ collisions at $\sqrt{s}=1.96$ TeV, collected with the CDF II detector using a high transverse-momentum ($p_T$) muon trigger. The search used time-of-flight to isolate slowly moving, high-$p_T$ particles. One event passed our selection cuts with an expected background of $1.9 \pm 0.2$ events. We set an upper bound on the production cross section, and, interpreting this result within the context of a stable scalar top quark model, set a lower limit on the particle mass of 249 GeV/$c^2$ at 95% C.L.