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Methods for phylogenetic supertree reconstruction
Kosíř, Kamil ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The Phylogenetic reconstruction has seen great development in the last 30 years. Computers have become more powerful and more generally accessible, and computer algorithms more sophisticated. It comes the effort of scientists to reconstruct the entire tree of life from a large amount of phylogenetic data. Just for this purpose are formed phylogenetic supertrees that allow the combination of all information gathered so far. The aim of this work is to find a method to construct supertree that will give correct results.
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Gene order conservation in bacterial genomes
Martinková, Tereza ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
Theoretical part of the thesis deals with basic concepts such as bacterial genome, comparative genomics and mainly synteny blocks. Here is explained what synteny is and what is its importance. In the theoretical part, the GenBank format is also mentioned, its content and usage. The practical part is focused on searching similarities in DNA sequences of reference bacteria with selected bacteria, their sorting by means of greedy algorithm and visualization of similarities using phylogenetic tree.
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Bootstrap methods in phylogenetics
Sedlář, Karel ; Vohánka,, Jaroslav (referee) ; Škutková, Helena (advisor)
In recent decades, phylogenetic reconstruction has noted great development. It was achieved by using newly acquired molecular characteristics and processing that it began to be taken as an objective science. Rapid development showed that it is necessary to evaluate the results because new techniques provided phylograms from unreliable data. For these purposes, statistical sampling methods have been applied to the phylogeny, of which bootstrapping began later to dominate. However, it also has limitations, which should be considered during interpreting the results it provided to us. This work demonstrates by combining the principles of bootstrapping and consensus trees we can obtain phylograms with better properties than those of conventional phylograms.
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Biological sequence classification utilizing lossless data compression algorithms
Kruml, Ondřej ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
Tato diplomová práce se zabývá možností využití bezeztrátových kompresních algoritmů ke klasifikaci biologických sekvencí. Nejdříve je představena literární rešerše o bezeztrátových kompresních algoritmech, která byla využita k výběru slovníkového algoritmu vytvořeného A. Lempelem a J. Zivem v roce 1976 (LZ77). Tento algoritmus je běžně používán k datové kompresi a v předkládané práci byl modifikován tak, aby umožnil klasifikaci biologických sekvencí. K algoritmu byly navrženy další modifikace, které rozvíjí jeho klasifikační možnosti. V průběhu práce byla sestavena sada datasetů biologických sekvencí, která umožnila podrobné testování algoritmu. Algoritmus byl porovnán s klasickými zarovnávacími metodami: Jukes-Cantor, Tamura a Kimura. Bylo ukázáno, že algoritmus dosahuje srovnatelných výsledků v oblasti klasifikace biologických sekvencí a dokonce je u 20% datasetů překonává. Lepší výsledky dosahuje zejména u sekvencí, jež jsou si vzájemně vzdálené.
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Gene order conservation in bacterial genomes
Martinková, Tereza ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
Theoretical part of the thesis deals with basic concepts such as bacterial genome, comparative genomics and mainly synteny blocks. Here is explained what synteny is and what is its importance. In the theoretical part, the GenBank format is also mentioned, its content and usage. The practical part is focused on searching similarities in DNA sequences of reference bacteria with selected bacteria, their sorting by means of greedy algorithm and visualization of similarities using phylogenetic tree.
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Evaluation of Organisms Relationship by Genomic Signal Processing
Škutková, Helena ; Tkacz, Ewaryst (referee) ; Schwarz,, Daniel (referee) ; Provazník, Ivo (advisor)
This dissertation deals with alternative techniques for analysis of genetic information of organisms. The theoretical part presents two different approaches for evaluation of relationship between organisms based on mutual similarity of genetic information contained in their DNA sequences. The first approach is currently standardized phylogenetics analysis of character based records of DNA sequences. Although this approach is computationally expensive due to the need of multiple sequence alignment, it allows evaluation of global and local similarity of DNA sequences. The second approach is represented by techniques for classification of DNA sequences in a form of numerical vectors representing characteristic features of their genetic information. These methods known as „alignment free“ allow fast evaluation of global similarity but cannot evaluate local changes. The new method presented in this dissertation combines the advantages of both approaches. It utilizes numerical representation similar to 1D digital signal, i.e. representation that contains specific trend along x-axis. The experimental part of dissertation deals with design of a set of appropriate tools for genomic signal processing to allow evaluation mutual similarity of taxonomically specific trends. On the basis of the mutual similarity of genomic signals, the classification in the form of dendrogram is applied. It corresponds to phylogenetic trees used in standard phylogenetics.
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Genetická diverzita zástupců rodu Euphorbia L.
Mityagina, Maria
We now have a rare opportunity to understand the history of species evolution and their connections to one another on the globe thanks to phylogenetics. Modern methods of taxon classification rely less on external morphology and more on molecular-biological investigations. This approach enables us to determine the geographic origins of organisms, track their expansion, and monitor changes in their genetic information. These factors are crucial for understanding the diversification of species. In this study, we applied evolutionary genetics to the family Euphorbiaceae. Then we chose three representatives of genus Euphorbia L. and with the help of PCR analysis with primers for nuclear and chloroplast DNA regions, the kinship of these species was established (Euphorbia ramipressa (K265), Euphorbia inarticulata (K266), Euphorbia tortirama (K267)).
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Phylogeographic patterns and microevolutionary mechanisms in oceanic dolphins
Křišťanová, Žaneta ; Hulva, Pavel (advisor) ; Vokurková, Jana (referee)
This bachelor thesis discusses the current findings regarding the phylogeography of the Delphinidae family. It is mainly focused on phylogenetic structure and speciation of Delphinidae, as well as on the ways of differentiation of trophic niches and the evolution of ecotypes. In the past, the Pleistocene climate oscillation had a major influence on the development of individual species and populations. Currently, it is anthropogenic activities that cause fundamental changes in habitats and thereby change the living conditions for cetaceans. In several species of Delphinidae, the emergence of ecotypes has been recorded, where different populations of the same species use different ecological niches. This thesis is mainly dedicated to the ecotypes of the bottlenose dolphin (Tursiops truncatus). Variability in coloration, body length and spine morphology was noted for individual ecotypes. The spine is an important adaptation to the environment in Delphinidae. In this research, phylogenetic relationships between family of Delphinidae, life strategies and food niche of selected species of the genera Tursiops, Stenella and Delphinus are also described.
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Hlodavci jako rezervoár hantavirů
KAMIŠ, Jan
This study reveals the presence of hantaviruses in free-living rodents and insectivores in urban areas in the Czech Republic. A large number of hantavirus reservoir hosts were tested for hantavirus RNA in different tissues, using universal and specific primers for amplification of the large and medium fragments of hantavirus genomic RNA. Phylogenetic relationships of obtained nucleotide sequences of hantaviruses were reconstructed. Four different species of hantaviruses were detected, including two species pathogenic (or potentially pathogenic) for humans, suggesting a threat for public health. Additionally, inter-family spillover infections and hantavirus species-associated tissue tropism were recorded in rodent hosts.
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