This thesis describes new evolutionary artificial intelligence methods suitable for solving complex tasks. These include planning, optimization, decision, prediction and other problems. All of these are tasks which an intelligent human being can quickly learn to solve, yet they cannot be solved by machines in reasonable time. For this type of problems usually no analytical method or algorithm exists. These challenges represent the domain for artificial intelligence. This work concentrates on evolutionary methods of artificial intelligence based on genetic algorithms. Specifically grammatical evolution and differnetial evolution are described. The first part of this thesis describes the principles of genetic algorithms especially those used in grammatical evolution. Later the grammatical evolution method is described. Grammatical evolution is a genetic algorithm extended with a context-free grammar processor. This enables it to generate structured strings in an arbitrary language defined by a regular or context-free grammar. Second part of this work focuses on description of a generic computational system, which enables user-friendly control of grammatical evolution. The architecture of the system is thoroughly described. It composes of a computation service, database server and completely separated user interface. Also the problems solved using this system are described. These include symbolic regression, classification and generation of combinatorial logic circuits. All of these tasks were solved using the described implementation.

7 Abstract With the first appearance of life on Earth, organisms had to adapt to an ever-changing surrounding environment in order to survive. Since the emergence of metazoan multi- cellularity, subsets of cells could adapt to perform specific biological tasks beneficial to the whole organism, necessitating not only spatiotemporal regulation of gene expression during development, but also integration of tissue specific needs with overall organis- mal status. Within the set of evolutionary conserved regulatory systems, the family of nuclear receptor (NR) transcription factors stands out due to its high degree of evolu- tionary conservation, plasticity and uniqueness to the metazoan kingdom, regulating gene expression in response to, or in the absence of a ligand by genomic and non- genomic actions. With an increasing number of different compounds being recognized as ligands to NRs, it is now thought that ancient NRs were probably characterized by low ligand binding specificity, eventually serving as environmental sensors, integrating nutrient availability and gene expression at the base of metazoan evolution. Characteri- zation of the NR network in one of the simplest metazoan organisms, Trichoplax ad- haerens, revealed not only a functional network and sub-specialization of NR dependent gene regulation, but...

This thesis contributes to the knowledge of the species diversity of the Crenicichla lacustris sp. group in the La Plata River basin with description of three new species. Speciation mechanisms within two different species flocks from the middle Paraná/Iguazu and Uruguay Rivers were studied with a phylogenomic approach applying a novel genotyping method based on a Double-Digest Restriction site Adjacent DNA (ddRAD) sequencing. Our results support a repeated origin of morphological species being evolved several times sympatrically and independently in different drainages. A considerable role of hybridization/introgression as an evolutionary force was also proposed. The thesis further uncovers biogeographic aspects of the southern part of Brazilian shield and adjacent coastal rivers.

Phylogeny, phylogeography and evolution of UV reflecting patterns were studied in 12 species of the genus Gonepteryx. Sequences of one mitochondrial (COI) and one nuclear gene (Wingless) were used for phylogenetic analyses and reconstruction of the biogeographical events. The results were later compared with the extent of UV reflecting pattern to construct the ancestral situation and evolution of the UV pattern within the genus.

The taxonomic concept of the algal genus Mallomonas (Synurales, Synurophyceae) was based on an extraordinary morphological diversity of their siliceous scales. The main aims of this study were elucidation of phylogenetic relationships among its representatives and reconstruction of shape evolution of particular siliceous structures of their scales. Molecular data for six species were acquired for the first time, enabling a successful assessment of their phylogenetic relationships with the other representatives of the genus. On the basis of molecular data, the genus Mallomonas can be divided in two evolutionary lineages and this division is also reflected morphologically (with only a few exceptions) through presence or absence of a V-rib structure. Fine ornamentation of siliceous scales is species-specific and interestingly, the overall differences in morphology of siliceous scales are mostly reflecting phylogenetic relationships among representatives of the genus. In this context, morphological species concept of Mallomonas seems to be justified. Morphologically-based sections of the genus are often paraphyletic, because small sections (frequently containing only single species) tend to be nested within particular larger sections. The main reason for this discrepancy is accelerated morphological...

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An intraspecific coat colour polymorphism exists in the genus Acomys. Some populations are dark and others are light-colored. Dark populations live in lava deserts, savannas and in the commensal habitat of Egypt. The subject of this thesis is to compare selected populations of Acomys in behavioral test of forced exploration. They are dark commensal, light secondary non-commensal, light non- commensal, and one dark non-commensal populations. The aim of this research is to find out whether the dark commensal populations of Acomys cahirinus differ in behavior from other populations and whether dark populations differ in behavior from light populations. According to the results, the observed behavioral parameters do not show significant differences between populations. The dark commensal populations of A. cahirinus did not differ significantly from other populations in exploratory behavior. But the dark populations preferred a dark background. No apparent differences in behavior between differently colored populations were found. However, the variability in tested behavior between populations was found. Key words: exploratory behavior, melanin, commensalism, comparative approach, open field test, Acomys

This thesis is about similarities and differences between natural and artificial life. It examines how a combination of insight from the disciplines of computer science and philosophy can be used to address this issue. By applying the principles of evolution to artificial life, the paper shows the perspectives of this life form and its implications for mankind. Human history contains many attempts at constructing artificial creatures; however, this dream only became reality with the advent of digital computers. Although artificial life is built on different principles than natural life, is better to view both as complementary rather than as opposites. It is possible to speculate on symbiosis between artificial and natural elements and on the formation of hybrid life forms that combine features from both worlds. Artificial life is not dependent on biological cycles and its evolution can proceed much faster. It has the potential to overcome the necessity of death, which is characteristic of all biological entities. If we compare the intelligence of machines to that of natural organisms, it is possible to identify the differences between them. Machine intelligence has the potential to create artificial collective intelligence through computer networks that exceed the level of separate entities. Simple forms of artificial life, identifiable at present, will evolve in coming decades and raise a number of unsolved questions (i.e. ethical concerns). These issues are and will remain current.

The thesis deals with the design and implementation of algorithms for import maps into the simulator TRASI. These algorithms are capable of import map from map portal OpenStreetMaps to the simulation environment. The work deals with adjusting the internal structure of the imported intersections, so that their structure was correct according to the rules of traffic. The work deals with the design and implementation of differential evolution for the design of the structure of intersections.

South American genus Lasiocephalus colonized high altitudes of the tropical Andes, the so called páramo, from lower elevations of the Andean forest. Páramo is a specific high-altitude environment characterised by pronounced diurnal changes in temperature, growing season over the entire year, low average temperatures, generally high humidity, and intense solar radiation. These specific environmental conditions are reflected by anatomical characters of the species. Given the known phylogeny of the group it was possible to observe anatomical adaptations along steep gradient of environmental conditions from forest to páramo. The hypothesis about adaptive changes that occurred during the colonization of the páramo habitats was confirmed. Observed characteristics were, for example, leaf area and thickness, epidermal cells cuticle and cell wall thickness, epidermal cells lumen height, ratio of palisade and spongy parenchyma, stomatal area, stomata length and width, stomata pore length and sieve elements average area. Results suggest that the anatomy of the plants reflect the environmental conditions of the habitats rather than the species phylogeny.