The rapid accumulation of numerous sequenced genomes has provided a golden opportunity for ancestral state reconstruction studies, especially in the whole genome reconstruction area. However, most ancestral genome reconstruction methods developed so far only focus on gene or replicon sequences instead of whole genomes. They rely largely on either detailed modeling of evolutionary events or edit distance computation, both of which can be computationally prohibitive for large data sets. Hence, most of these methods can only be applied to a small number of features and species. In this dissertation, we describe the design, implementation, and evaluation of an ancestral genome reconstruction system (REGEN) for bacteria. It is the first bacterial genome reconstruction tool that focuses on ancestral state reconstruction at the genome scale instead of the gene scale. It not only reconstructs ancestral gene content and contiguous gene runs using either a maximum parsimony or a maximum likelihood criterion but also replicon structures of each ancestor. Based on the reconstructed genomes, it can infer all major events at both the gene scale, such as insertion, deletion, and translocation, and the replicon scale, such as replicon gain, loss, and merge. REGEN finishes by producing a visual representation of the entire evolutionary history of all genomes in the study. With a model-free reconstruction method at its core, the computational requirement for ancestral genome reconstruction is reduced sufficiently for the tool to be applied to large data sets with dozens of genomes and thousands of features. To achieve as accurate a reconstruction as possible, we also develop a homologous gene family prediction tool for preprocessing. Furthermore, we build our in-house Prokaryote Genome Evolution simulator (PEGsim) for evaluation purposes. The homologous gene family prediction refinement module can refine homologous gene family predictions generated by third party de novo prediction programs by combining phylogeny and local gene synteny. We show that such refinement can be accomplished for up to 80% of homologous gene family predictions with ambiguity (mixed families). The genome evolution simulator, PEGsim, is the first random events based high level bacteria genome evolution simulator with models for all common evolutionary events at the gene, replicon, and genome scales. The concepts of conserved gene runs and horizontal gene transfer (HGT) are also built in. We show the validation of PEGsim itself and the evaluation of the last reconstruction component with simulated data produced by it. REGEN, REconstruction of GENomes, is an ancestral genome reconstruction tool based on the concept of neighboring gene pairs (NGPs). Although it does not cover the reconstruction of actual nucleotide sequences, it is capable of reconstructing gene content, contiguous genes runs, and replicon structure of each ancestor using either a maximum parsimony or a maximum likelihood criterion. Based on the reconstructed genomes, it can infer all major events at both the gene scale, such as insertion, deletion, and translocation, and the replicon scale, such as replicon gain, loss, and merge. REGEN finishes by producing a visual representation of the entire evolutionary history of all genomes in the study. / Ph. D.

This thesis focuses on the storage location assignment problem using modern meta-heuristic techniques combined with realistic simulation. A graphical tool implemented as part of this work is capable of warehouse model creation, generation of synthetic customer orders, optimization of product allocation using state of the art techniques, extensive warehouse simulation, and a pathfinder capable of finding the shortest path for orders going through the system. The work presents the comparison between different approaches based on many parameters to reach the most efficient allocation of products to warehouse slots. The author conducted tests on an experimental warehouse featuring almost twice the throughput -- 57%. The benefit of this work is a possibility to create model of an already built warehouse and its simulation and optimization, driving impact on the throughput of the warehouse, saving the user's resources, or helping him in planning and bottle-neck identification. Furthermore, this thesis introduces a new approach to warehouse optimization and new optimization criteria.

Natural selection and other components of evolutionary theory are known to be particularly challenging concepts for students to understand. To help illustrate these concepts, we developed a simulation model of microevolutionary processes. The model features all the components of Hardy-Weinberg theory, with population size, selection, gene flow, nonrandom mating, and mutation all being demonstrated in the simulations. By using this freely available computer model, students can develop and test hypotheses with replicated virtual experiments. Because the model is an agent-based simulation, there is biologically realistic variability in the results. Students using the model see results both numerically and graphically and these are reinforced by an animation of the virtual fish in the simulated experiment.

The question of the tempo of evolution is amongst the oldest conundrums in evolutionary biology and has not been satisfactorily answered yet. One of the attempts to do so is the frozen plasticity theory, which postulates that a sexually reproducing species is only capable of evolution within short periods of time after its genetic polymorphism decreases e.g. as a consequence of peripatric speciation. In the longer periods of evolutionary stasis, its evolution is limited by frequency- dependent selection and pleiotropy. In this work, I have produced an open source software simulating the respon- ses of populations of sexually reproducing individuals to varying environmental conditions. Using this software, I simulated evolution of populations with different probabilities of arising of alelles affecting more phenotypic traits and frequency- dependent selected alleles that have opposing phenotypic effects when present at the locus in one copy, respectively two copies. I observed trends predicted by the theory of frozen plasticity: slower adap- tation to instant environmental changes, lower achieved fitness and more frequent extinctions of populations with higher portions of investigated types of alleles, but only with low effect sizes and without statistical significance. For future research, it would be desirable...