A system of logic, ratiocinative and inductive; being a connected view of the principles of evidence and the methods of scientific investigation.

Mode of access: Internet.

A system of logic, ratiocinative and inductive, being a connected view of the principles of evidence and the methods of scientific investigation.

Mode of access: Internet.

Genetic variation and inference of demographic histories in non-model species

Both long-term environmental changes such as those driven by the glacial cycles and more recent anthropogenic impacts have had major effects on the past demography in wild organisms. Within species, these changes are reflected in the amount and distribution of neutral genetic variation. In this thesis, mitochondrial and microsatellite DNA was analysed to investigate how environmental and anthropogenic factors have affected genetic diversity and structure in four ecologically different animal species. Paper I describes the post-glacial recolonisation history of the speckled-wood butterfly (Pararge aegeria) in Northern Europe. A decrease in genetic diversity with latitude and a marked population structure were uncovered, consistent with a hypothesis of repeated founder events during the postglacial recolonisation. Moreover, Approximate Bayesian Computation analyses indicate that the univoltine populations in Scandinavia and Finland originate from recolonisations along two routes, one on each side of the Baltic. Paper II aimed to investigate how past sea-level rises affected the population history of the convict surgeonfish (Acanthurus triostegus) in the Indo-Pacific. Assessment of the species’ demographic history suggested a population expansion that occurred approximately at the end of the last glaciation. Moreover, the results demonstrated an overall lack of phylogeographic structure, probably due to the high dispersal rates associated with the species’ pelagic larval stage. Populations at the species’ eastern range margin were significantly differentiated from other populations, which likely is a consequence of their geographic isolation. In Paper III, we assessed the effect of human impact on the genetic variation of European moose (Alces alces) in Sweden. Genetic analyses revealed a spatial structure with two genetic clusters, one in northern and one in southern Sweden, which were separated by a narrow transition zone. Moreover, demographic inference suggested a recent population bottleneck. The inferred timing of this bottleneck coincided with a known reduction in population size in the 19th and early 20th century due to high hunting pressure. In Paper IV, we examined the effect of an indirect but well-described human impact, via environmental toxic chemicals (PCBs), on the genetic variation of Eurasian otters (Lutra lutra) in Sweden. Genetic clustering assignment revealed differentiation between otters in northern and southern Sweden, but also in the Stockholm region. ABC analyses indicated a decrease in effective population size in both northern and southern Sweden. Moreover, comparative analyses of historical and contemporary samples demonstrated a more severe decline in genetic diversity in southern Sweden compared to northern Sweden, in agreement with the levels of PCBs found.

Multilevel modelling for inference of genetic regulatory networks

Time-course experiments with microarrays are often used to study dynamic biological systems and genetic regulatory networks (GRNs) that model how genes influence each other in cell-level development of organisms. The inference for GRNs provides important insights into the fundamental biological processes such as growth and is useful in disease diagnosis and genomic drug design. Due to the experimental design, multilevel data hierarchies are often present in time-course gene expression data. Most existing methods, however, ignore the dependency of the expression measurements over time and the correlation among gene expression profiles. Such independence assumptions violate regulatory interactions and can result in overlooking certain important subject effects and lead to spurious inference for regulatory networks or mechanisms. In this paper, a multilevel mixed-effects model is adopted to incorporate data hierarchies in the analysis of time-course data, where temporal and subject effects are both assumed to be random. The method starts with the clustering of genes by fitting the mixture model within the multilevel random-effects model framework using the expectation-maximization (EM) algorithm. The network of regulatory interactions is then determined by searching for regulatory control elements (activators and inhibitors) shared by the clusters of co-expressed genes, based on a time-lagged correlation coefficients measurement. The method is applied to two real time-course datasets from the budding yeast (Saccharomyces cerevisiae) genome. It is shown that the proposed method provides clusters of cell-cycle regulated genes that are supported by existing gene function annotations, and hence enables inference on regulatory interactions for the genetic network.

Bayesian inference for wind field retrieval

In many problems in spatial statistics it is necessary to infer a global problem solution by combining local models. A principled approach to this problem is to develop a global probabilistic model for the relationships between local variables and to use this as the prior in a Bayesian inference procedure. We show how a Gaussian process with hyper-parameters estimated from Numerical Weather Prediction Models yields meteorologically convincing wind fields. We use neural networks to make local estimates of wind vector probabilities. The resulting inference problem cannot be solved analytically, but Markov Chain Monte Carlo methods allow us to retrieve accurate wind fields.

Efficient Bayesian inference for learning in the Ising linear perceptron and signal detection in CDMA

Efficient new Bayesian inference technique is employed for studying critical properties of the Ising linear perceptron and for signal detection in code division multiple access (CDMA). The approach is based on a recently introduced message passing technique for densely connected systems. Here we study both critical and non-critical regimes. Results obtained in the non-critical regime give rise to a highly efficient signal detection algorithm in the context of CDMA; while in the critical regime one observes a first-order transition line that ends in a continuous phase transition point. Finite size effects are also studied. © 2006 Elsevier B.V. All rights reserved.

Improved message passing for inference in densely connected systems

An improved inference method for densely connected systems is presented. The approach is based on passing condensed messages between variables, representing macroscopic averages of microscopic messages. We extend previous work that showed promising results in cases where the solution space is contiguous to cases where fragmentation occurs. We apply the method to the signal detection problem of Code Division Multiple Access (CDMA) for demonstrating its potential. A highly efficient practical algorithm is also derived on the basis of insight gained from the analysis. © EDP Sciences.

Bayesian inference for wind field retrieval

In many problems in spatial statistics it is necessary to infer a global problem solution by combining local models. A principled approach to this problem is to develop a global probabilistic model for the relationships between local variables and to use this as the prior in a Bayesian inference procedure. We show how a Gaussian process with hyper-parameters estimated from Numerical Weather Prediction Models yields meteorologically convincing wind fields. We use neural networks to make local estimates of wind vector probabilities. The resulting inference problem cannot be solved analytically, but Markov Chain Monte Carlo methods allow us to retrieve accurate wind fields.

An investigation into children’s inductive reasoning strategies:What drives the development of category induction?

In a series of studies, I investigated the developmental changes in children’s inductive reasoning strategy, methodological manipulations affecting the trajectory, and driving mechanisms behind the development of category induction. I systematically controlled the nature of the stimuli used, and employed a triad paradigm in which perceptual cues were directly pitted against category membership, to explore under which circumstances children used perceptual or category induction. My induction tasks were designed for children aged 3-9 years old using biologically plausible novel items. In Study 1, I tested 264 children. Using a wide age range allowed me to systematically investigate the developmental trajectory of induction. I also created two degrees of perceptual distractor – high and low – and explored whether the degree of perceptual similarity between target and test items altered children’s strategy preference. A further 52 children were tested in Study 2, to examine whether children showing a perceptual-bias were in fact basing their choice on maturation categories. A gradual transition was observed from perceptual to category induction. However, this transition could not be due to the inability to inhibit high perceptual distractors as children of all ages were equally distracted. Children were also not basing their strategy choices on maturation categories. In Study 3, I investigated category structure (featural vs. relational category rules) and domain (natural vs. artefact) on inductive preference. I tested 403 children. Each child was assigned to either the featural or relational condition, and completed both a natural kind and an artefact task. A further 98 children were tested in Study 4, on the effect of using stimuli labels during the tasks. I observed the same gradual transition from perceptual to category induction preference in Studies 3 and 4. This pattern was stable across domains, but children developed a category-bias one year later for relational categories, arguably due to the greater demands on executive function (EF) posed by these stimuli. Children who received labels during the task made significantly more category choices than those who did not receive labels, possibly due to priming effects. Having investigated influences affecting the developmental trajectory, I continued by exploring the driving mechanism behind the development of category induction. In Study 5, I tested 60 children on a battery of EF tasks as well as my induction task. None of the EF tasks were able to predict inductive variance, therefore EF development is unlikely to be the driving factor behind the transition. Finally in Study 6, I divided 252 children into either a comparison group or an intervention group. The intervention group took part in an interactive educational session at Twycross Zoo about animal adaptations. Both groups took part in four induction tasks, two before and two a week after the zoo visits. There was a significant increase in the number of category choices made in the intervention condition after the zoo visit, a result not observed in the comparison condition. This highlights the role of knowledge in supporting the transition from perceptual to category induction. I suggest that EF development may support induction development, but the driving mechanism behind the transition is an accumulation of knowledge, and an appreciation for the importance of category membership.