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Methods to detect selection in DNA sequences
Procházka, Ondřej ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The topic of semestral thesis is methods to detect selection in DNA sequences. In the begining of the thesis we will describe molecular evolution. It will be written what made the evolution and how the evolution is shown. Moreover there are gen mutations and mechanisms of diffuse and fixation. It will be defined what pozitive, negative and neutral selection is. The thesis is focused on evolution distance of synonymous and nonsynonymous substitution. There will be described three methods – Nei-Gojobori, Li-Wu-Luo and Comeron. All these methods will be described with mathematic formulas. There will be statistic test to decide what kind of selection ti is – there will be used z-test. In the practical part, there will be information about developed software what counts selection pressure from sequences from databazes in format GenBank and it shows parts where selection is. The software will be used for two data sets with two different genetic codes. The result will be discussed. We will discuss results of all three methods of selection pressure and influence of input parametrs.
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Evolutionary implications of innate immunity receptors polymorphism
Bainová, Zuzana ; Vinkler, Michal (advisor) ; Zajícová, Alena (referee)
Interactions between hosts and their parasites are considered to be one of the major forces driving animal evolution. It can be assumed that the evolutionary changes will occur especially in host molecules directly involved in these interactions. The first line of host defense is formed by innate immunity receptors among which also pattern recognition receptors (PRRs) belong. PRRs detect the presence of parasites at the beginning of their invasion by binding characteristic structures of their bodies (so called pathogen-associated molecular patterns, PAMPs, e. g. lipopolysaccharide, flagellin or peptidoglycans) or abnormal self molecules (damage-associated molecular patterns, DAMPs, e.g heat shock proteins). Although this mechanism of immune system activation is based on the recognition of ligands that are relatively evolutionarily conservative in pathogens, growing body of evidence suggests that PRRs are highly polymorphic on both interspecific and intraspecific level. High frequencies of minority alleles can be observed in most populations studied. It has been proven that particular alleles of many PRRs may associate with increased or decreased resistance to various infectious or autoimmunity diseases. Relationship between polymorphic receptor and a disease could be the main force, which shapes the...
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Botany in Czech lands at the turn of the 20th century: theoretical aspects of the work of Josef Velenovský
Kaiprová, Sofie ; Čermáková, Lucie (advisor) ; Janko, Jan (referee)
The work is a literary research on the theoretical and evolutionary concepts in botany in the Czech environment at the turn of the 19th and 20th century with a focus on the work of Josef Velenovský (1858-1949). The work maps the historical context of Velenovský's work, deals with the transformations of Velenovský's vision of evolution and the most interesting aspects of his theoretical thinking about biology. At the beginning he fully acknowledges Darwin's theory, in the late age he holds a completely contradictory theory. Key words: history of botany, Josef Velenovský, evolutionary theory, natural selection, altruism
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Reception od Darwin in biology
Richter, Jiří ; Markoš, Anton (advisor) ; Flegr, Jaroslav (referee)
Reception of Darwin in biology conveys a story of evolutionary biology with emphasis on the divergent reception of Charles Darwin's theories by biologists in the past 150 years. Given the influence of Darwin's thought, a unique tradition has emerged in the scientific field. Every fifty years starting from the publishing of The Origin of Species, scientists gather to celebrate Charles Darwin as a thinker and a person. An immense amount of literature on Darwin and evolutionary biology has been produced by authors and publishers worldwide, thus the recurring commemorative events provide a fine start to the historical survey of Darwinism and are used as such in Reception of Darwin in biology.
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Evolutionary implications of innate immunity receptors polymorphism
Bainová, Zuzana ; Vinkler, Michal (advisor) ; Zajícová, Alena (referee)
Interactions between hosts and their parasites are considered to be one of the major forces driving animal evolution. It can be assumed that the evolutionary changes will occur especially in host molecules directly involved in these interactions. The first line of host defense is formed by innate immunity receptors among which also pattern recognition receptors (PRRs) belong. PRRs detect the presence of parasites at the beginning of their invasion by binding characteristic structures of their bodies (so called pathogen-associated molecular patterns, PAMPs, e. g. lipopolysaccharide, flagellin or peptidoglycans) or abnormal self molecules (damage-associated molecular patterns, DAMPs, e.g heat shock proteins). Although this mechanism of immune system activation is based on the recognition of ligands that are relatively evolutionarily conservative in pathogens, growing body of evidence suggests that PRRs are highly polymorphic on both interspecific and intraspecific level. High frequencies of minority alleles can be observed in most populations studied. It has been proven that particular alleles of many PRRs may associate with increased or decreased resistance to various infectious or autoimmunity diseases. Relationship between polymorphic receptor and a disease could be the main force, which shapes the...
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The role of nest in reproduction of the Great Reed Warbler
Jelínek, Václav ; Procházka, Petr (advisor) ; Krist, Miloš (referee) ; Trnka, Alfréd (referee)
7 Abstract Bird nests protect eggs and nestlings, allowing the parents to leave their offspring and subsequently return to them. Their thermoregulatory properties reduce energetic costs of incubation and brooding of nestlings. For all these reasons, nests are key structures for the reproduction of a majority of avian species and as such they should be subject to natural selection. Several hypotheses describing selection pressures which affect the size of nests or some of their parts have been suggested. In my PhD thesis, I investigated some of them in the great reed warbler (Acrocephalus arundinaceus) - an open nesting passerine species with very variable nest size. For this purpose, I used a large dataset of several hundred measured great reed warbler nests, nest enlargement experiments and an experiment with artificial nests. In accordance with previous studies, we did not find that nest size affects the probability of common cuckoo (Cuculus canorus) brood parasitism, while it was influenced by other factors, such as timing of breeding, reed density around the nest and nest visibility from the nearest potential cuckoo perch site. More interestingly, we found that cuckoos adjust their nest-searching strategy in relation to availability of host nests. When host nests were scarce, cuckoos parasitized all of...
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Methods to detect selection in DNA sequences
Procházka, Ondřej ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The topic of semestral thesis is methods to detect selection in DNA sequences. In the begining of the thesis we will describe molecular evolution. It will be written what made the evolution and how the evolution is shown. Moreover there are gen mutations and mechanisms of diffuse and fixation. It will be defined what pozitive, negative and neutral selection is. The thesis is focused on evolution distance of synonymous and nonsynonymous substitution. There will be described three methods – Nei-Gojobori, Li-Wu-Luo and Comeron. All these methods will be described with mathematic formulas. There will be statistic test to decide what kind of selection ti is – there will be used z-test. In the practical part, there will be information about developed software what counts selection pressure from sequences from databazes in format GenBank and it shows parts where selection is. The software will be used for two data sets with two different genetic codes. The result will be discussed. We will discuss results of all three methods of selection pressure and influence of input parametrs.
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Art as Evolutionary Adaptations
LATUROVÁ, Martina
The content of this bachelor work is to introduce the main concepts of evolutionary aesthetics. It uses the ideas come of the Charles Darwin's adaptive theories to explain the origin of Art. It attempts to defend the belief that Art is able to provide some advantages in the fields of natural and sexual selection for survival or reproduction. This work will rely in particular on the contemporary naturalistic aesthetics theories of Denis Dutton and Geoffrey Miller.
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Is it possible to demonstrate selection in science teaching? Simulation of natural selection in a model organism.
MARVANOVÁ, Aneta
This thesis examines the effect of natural selection on the rate of development of Microvelia reticulata. Natural selection is an integral part of evolutionary biology. The main task was to determine whether the selection of the developmental rate reflected in the change of development. Selected individuals were reared in the same conditions from egg to imago in a total of three replications in a strain selected for rapid development, slow development and unmanipulated control. There was distinct increase in developmental rate between initial and first selected generation all replications of control strain, followed by slight decrease in all succeeding generations. Similar pattern was present in the strains selected for slow development. A comparably distinct increase in developmental rate appeared also in the strains selected for the fast development, but it was not followed by succeeding slowdown, or the slowdown of the developmental rate was not as remarkable as in other strains. According to not too convincing results and remarkable time and space demands of this research, it is unreal to run similar long-term experiment in school conditions. Research was supported by project of the Grant Agency of the Czech Republic no. P505/10/0096.
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