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Phylogeny of selected species groups of the genus Torymus (Hymenoptera: Torymidae)
Křížková, Barbora ; Janšta, Petr (advisor) ; Skuhrovec, Jiří (referee)
Chalcid wasps (Chalciodiodea) is superfamily within parasitic group of the order Hymenoptera. These insects attack other arthropods. My thesis is focused on phylogeny of selected species groups of the genus Torymus Dalman 1820, whose range of hosts includes mainly gall-forming insect as gall wasps (Hymenoptera: Cynipidae) and gall midges (Diptera: Cecidomyiidae). Using genes 28D2 rDNA, COI and CytB, I constructed phylogenetic trees, which helped with discussing current view on classification of the genus and with inferring new findings about co-evolution with host organisms. Previously established morphological - ecological species groups were not supported by my analyses in many cases. Morphological traits seem to be convergent for many species. They often do not support observed monophyla as apomorphies. On the other hand, ecology and natural habitat of species was common for many branches in my cladograms. It was found out, that recent hosts are not probably original hosts of the group. Adaptive radiation in different habitats is likely to be the phenomenon that stands behind present-day host range of Torymus species. This process could have occurred after swapping to gall midges and gall wasps. Key words: Chalcidoidea, Torymus, phylogeny, parasitoid, host specifity, co-evolution
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Evolution of Morality, Morality of Evolution
Šafránek, Jakub ; Komárek, Stanislav (advisor) ; Stella, Marco (referee)
The goal of this work is to present attitudes of two contemporary authors who are in the center of the evolutionary-origin-of morality debate, that is theories of Richard Dawkins and Frans de Waal. The critical reflection of their works on this topic will center around the building blocks of morality and the supposed "moral sense", which according to the dutch primatologist humans to some extent share with some of their living evolutinary relatives. In case of Richard Dawkins we are about to review his meme theory and parasytical character of some elements of culture. Morevoer there will be presented accounts of the dual inheritance theorists, which in authors opinion can reunite both presented authors and thier attitudes, i.e. put the parasytic/independent character of memes in accordance with the building blocks of morality approach. This approach in turn can explain many phenomena of human contemporary morals and their limits. Keywords: Morality, evolution, dual inheritance theory, coevolution, memes
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Multilokusová charakteristika symbiontů entomopatogenních hlístovek rodu \kur{Steinernema}
FAKTOROVÁ, Lucie
During the evolution some groups of organisms have become coevolutionary associated with other groups, as is the case of host symbiont systems. To explore coevolutionary history of hosts and their associated symbionts, phylogenetic reconstruction of symbionts and phylogenetic reconstruction of hosts are usually compared. Coevolution is described by coevolutionary events (cospeciation, host switch, duplication, failure to diverge events and linage sorting events). The aim of this work was to test the suitability of MLST method for the complex of entomopathogenic nematodes from the genus Steinernema (with detailed analysis of Steinernema feltiae) and their symbiotic bacteria Xenorhabdus bovienii and subsequently use cophylogenetic comparative analysis to determine their level of cospeciation.
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Coevolution in Evolutionary Circuit Design
Veřmiřovský, Jakub ; Hrbáček, Radek (referee) ; Drahošová, Michaela (advisor)
This thesis deals with evolutionary design of the digital circuits performed by a cartesian genetic programing and optimization by a coevolution. Algorithm coevolves fitness predictors that are optimized for a population of candidate digital circuits. The thesis presents theoretical basis, especially genetic programming, coevolution in genetic programming, design of the digital circuits, and deals with possibilities of the utilization of the coevolution in the combinational circuit design. On the basis of this proposal, the application designing and optimizing logical circuits is implemented. Application functionality is verified in the five test tasks. The comparison between Cartesian genetic programming with and without coevolution is considered. Then logical circuits evolved using cartesian genetic programming with and without coevolution is compared with conventional design methods. Evolution using coevolution has reduced the number of evaluation of circuits during evolution in comparison with standard cartesian genetic programming without coevolution and in some cases is found solution with better parameters (i.e. less logical gates or less delay).
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Symbolic Regression and Coevolution
Drahošová, Michaela ; Žaloudek, Luděk (referee) ; Sekanina, Lukáš (advisor)
Symbolic regression is the problem of identifying the mathematic description of a hidden system from experimental data. Symbolic regression is closely related to general machine learning. This work deals with symbolic regression and its solution based on the principle of genetic programming and coevolution. Genetic programming is the evolution based machine learning method, which automaticaly generates whole programs in the given programming language. Coevolution of fitness predictors is the optimalization method of the fitness modelling that reduces the fitness evaluation cost and frequency, while maintainig evolutionary progress. This work deals with concept and implementation of the solution of symbolic regression using coevolution of fitness predictors, and its comparison to a solution without coevolution. Experiments were performed using cartesian genetic programming.
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Detection of Correlated Mutations
Ižák, Tomáš ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
Tato práce zkoumá existující možnosti a metody detekce korelovaných mutací v proteinech. Práce začíná teoretickým úvodem do zkoumané problematiky. Využití informací o korelovaných mutacích je především při predikci terciální struktury proteinu či hledání oblastí s významnou funkcí. Dále následuje přehled v současnosti používaných metod detekce a jejich výhody a nevýhody. V této práci jsou zkoumány zejména metody založené na statistice (například Pearsonově korelačním koeficientu nebo Pearsonově chi^2 testu), informační teorii (Mutual information - MI) a pravděpodobnosti (ELSC nebo Spidermonkey). Dále jsou popsány nejdůležitější nástroje s informací o tom, které metody používají a jakým způsobem. Také je diskutována možnost návrhu optimálního algoritmu. Jako optimální z hlediska úspěšnosti detekce je doporučeno využít více zmíněných metod. Také je doporučeno při detekci využít fyzikálně-chemických vlastností aminokyselin. V praktické části byla vyvinuta metoda využívající fyzikálně-chemických vlastností aminokyselin a fylogenetických stromů. Výsledky detekce byly porovnány s nástroji CAPS, CRASP a CMAT.
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Coevolutionary Algorithm in FPGA
Hrbáček, Radek ; Vašíček, Zdeněk (referee) ; Drahošová, Michaela (advisor)
This thesis deals with the design of a hardware acceleration unit for digital image filter design using coevolutionary algorithms. The first part introduces reconfigurable logic device technology that the acceleration unit is based on. The theoretical part also briefly characterizes evolutionary and coevolutionary algorithms, their principles and applications. Traditional image filter designs are compared with the biologically inspired design methods. The hardware unit presented in this thesis exploits dual MicroBlaze system extended by custom peripherals to accelerate cartesian genetic programming. The coevolutionary image filter design is accelerated up to 58 times. The hardware platform functionality in the task of impulse noise filter design and edge detector design has been empirically analyzed.
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Coevolution of Cartesian Genetic Algorithms and Neural Networks
Kolář, Adam ; Král, Jiří (referee) ; Zbořil, František (advisor)
The aim of the thesis is to verify synergy of genetic programming and neural networks. Solution is provided by set of experiments with implemented library built upon benchmark tasks. I've done experiments with directly and also indirectly encoded neural netwrok. I focused on finding robust solutions and the best calculation of configurations, overfitting detection and advanced stimulations of solution with fitness function. Generally better solutions were found using lower values of parameters n_c and n_r. These solutions tended less to be overfitted. I was able to evolve neurocontroller eliminating oscilations in pole balancing problem. In cancer detection problem, precision of provided solution was over 98%, which overcame compared techniques. I succeeded also in designing of maze model, where agent was able to perform multistep tasks.
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The symbiotic bacteria of lice of genus \kur{Polyplax}: general phylogenetic and genomic characterisation
ŘÍHOVÁ, Jana
Blood-sucking lice of the genus Polyplax harbour two bacterial endosymbionts, one from family Legionellales and the other from family Neisseriales. Fylogenetic and genomic analyses reveal typical features of endosymbiotic bacteria and coevolution history with the host. In the genome of the endosymbiont from family Legionellales I found operon, which encodes biosynthesis of biotin, essential vitamin, especially for blood-sucking insects living on low-nutrient diet. This operon was probably horizontally transfer from Wolbachia, nutrient endosymbiont of bedbug Cimex lectularius.
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