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Pozitive and negative selection of mitochondrial genome
Svoboda, Matěj ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with positive and negative selection detection in mitochondrial genome of invertebrates and vertebrates. The component of this paper is to interpret the theory of evolution and evolution models. The main objective of this bachelor thesis is to formulate the algorithm package for a positive and negative selection detection in a program environment, RStudio. Consequently, outcomes of algorithm are compared to values acquired by tool PAML.
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Detection of positive selection on the molecular level
Cakl, Lukáš ; Reifová, Radka (advisor) ; Munclinger, Pavel (referee)
The rise in computational power and available genomic data has made it possible to examine the traces of selection on nucleic acid sequences. To gain the most relevant results, we need to know how are said traces created, what are their properties, how to detect them and which methods to use in a given set of circumstances. This bachelor thesis is dedicated not only to the methods we use to detect positive selection and their underlying principles, but also to the theoretical models, which allowed their conception, neutral theories, against which we test our traces and the traces themselves. Due to the dynamic nature of the genome, alongside the data we have available, the properties of the selection traces are the most important factor for picking one of the methods we have available. Especially since, speaking in the terms of an evolutionary scale, certain traces are created swiftly and disappear soon afterwards, while the formation of others requires large periods of time. Keywords: darwinian selection, positive selection, statistical methods, selection detection, dna, molecular data
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Pozitive and negative selection of mitochondrial genome
Svoboda, Matěj ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with positive and negative selection detection in mitochondrial genome of invertebrates and vertebrates. The component of this paper is to interpret the theory of evolution and evolution models. The main objective of this bachelor thesis is to formulate the algorithm package for a positive and negative selection detection in a program environment, RStudio. Consequently, outcomes of algorithm are compared to values acquired by tool PAML.
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Consequences of an infectious disease on genetic information in DNA sequences in bats
Nováková, Markéta ; Martínková, Natália (advisor) ; Lučan, Radek (referee)
Whitenose syndrome is an emerging fungal disease of bats causing massive dieoffs in North American populations. The fungus causes lesions on bat skin, mainly on noses, ears and wing membranes. The infection by the fungus is accompanied by serious disruption of metabolism and hibernation physiology that is lethal to bats in North America. European bats seem to survive the disease in greater numbers. Since the fungus is probably of European origin, this study assumes that bats in Europe have developed inheritable defence mechanisms to the disease. The infection by the fungus serves as a strong selective pressure. We tested sequences of 7 genes for signs of positive selection using maximum likelihood approach. We detected past positive selection in the gene for transglutaminase 1.
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