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Mitogenomic phylogeography and adaptive evolution of the bank vole Clethrionomys glareolus
Filipi, Karolína ; Kotlík, Petr (advisor) ; Munclinger, Pavel (referee)
This thesis is a part of the project aimed at sequencing the genome and transcriptome of the bank vole (Clethrionomys glareolus). The role of natural selection in the evolution of mitochondrial DNA (mtDNA) has been subject to much discussion; while some studies did not provide evidence that selection affected the phylogeography of the studied species, other considered adaptive evolution important. The bank vole is the key model we use to study the adaptation to climate change. As with other species, the phylogeography of the bank vole has been based on the variation of a small part of mtDNA. The goal of the thesis was to sequence the entire mitochondrial genome for representatives of all main mtDNA lineages of the bank vole using the Sanger and Illumina technologies, and to assess the role of selection and adaptation in the evolution and phylogeography of this species. The adaptive evolution in mtDNA probably was not the main driving force during the postlacial colonization of Europe. However, signatures of adaptive evolution have been found - an amino acid change with possible functional consequences in one gene and an excess of radical changes in physical- chemical properties of amino acids in populations at the latitudinal (northern and southern) extremes of the bank vole distribution. Key...
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Development of Grey Partridge (Perdix perdix) microsatellite markers
Vaněčková, Dominika ; Munclinger, Pavel (advisor) ; Burri, Marta (referee)
The aim of this work was the construction of set of microsatellites for the Grey Partridge (Perdix perdix). I succeeded in isolation of seven new specific microsatellites. Another microsatellite markers were passed from close relative galliform species (Galliformes). On the whole I gained 18 microsatellite loci which were used for study of population charakteristics of three partridge populations from Stodůlky, Písecko and Milešín. The analysis showed conspicuous structuredness of these populations and surprisingly low values (less then 100) of their effective population sizes. Seven of the microsatellites were chosen for analysis of paternity. Indeed I found the evidence of extrapair paternity in this putatively monogamous bird. Finally I conclude, on the basis of sequenation of mitochondrial control region that our populations belong to the western linage of mitochondrial DNA.
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Hybrid origin of beavers in Central Europe
Albrechtová, Alena ; Munclinger, Pavel (advisor) ; Bryja, Josef (referee)
The aim of the master diploma work is to investigate origin of Czech populations and genetic variability of almost all Eurasian populations of the European beaver (Castor fiber). For our purposes we collected specimens from Czech populations, reintroduced population in Kirov district in Russia and all European and Asian refugia. At the end of the 19th century the species was on the verge of extinction due to overhunting, surviving only in eight isolated refugial areas. The population size at the end of the 19th century was estimated as 1 200 animals. The number of individuals has increased thanks to the legal protection and reintroductions. The current population size is estimated at 640 000. It is obvious that the populations of beaver have recently undergone severe bottleneck. Beaver was completely extirpated in the Czech Republic in the 18th century. Since the 80th of the 20th century beavers re-established in the Czech Republic due to migration from neighbouring countries and reintroduction programmes, however we knew only little about the origin of beavers in the Czech Republic. I showed that our beavers are derived from individuals in France, Germany, Norway and east Europe. Mitochondrial DNA of Castor canadensis has not been found in Czech beavers. I studied microsatellite loci (first use for...
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Determination of mtDNA sequence variation in czech population for the usage in forensic genetics.
Řadová, Marie ; Coufalová, Pavla (advisor) ; Vaněk, Daniel (referee)
In forensic research and practice is used an analysis of nuclear DNA commonly. However, in some cases we can use only mitochondrial DNA. The mtDNA is maternally inherited and it is located in the each cell approximately in 500 copies. Barring mutation in special noncoding segments, the mtDNA sequence of siblings and all maternal relatives is identical. This unique haplotyp can be helpful in forensic cases, such as analyzing the remains of a missing person, where known maternal relatives can provide reference samples for direct comparison to the questioned mtDNA type. MtDNA is also very resistant to the external influences, so in the cases where the amount of extracted DNA is very small or degraded it is more likely that a DNA typing result can be obtained by typing mtDNA than by typing polymorphic markers found in nuclear DNA. If we want to have a certain probability to exclude or confirm the match of two samples, classify suspect or missing person into a population, we need some enough wide comparison by the population databases. Then we can study the frequencies of different haplotypes in particular population. The aim of this thesis is summery of history of DNA analysis, mtDNA sequencing and comparison of data available in published databases in the world and mainly in the Czech Republic. There is also...
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The mitochondrial genome in the ontogenesis
Töröková, Petra ; Brdička, Radim (advisor) ; Černý, Viktor (referee)
The main goal of this study is the comparison of sequences of the HVRII region of the mitochondrial genome in the cord blood sample and the saliva sample of the same individual, taken at average ten years from his/her birth. It is known that during ontogenesis the human genome changes. All the more the mitochondrial genome which shows a higher mutation rate, and moreover it is not taken care of it by repair mechanisms. In older individuals, there was found a distinctive amount of mitochondrial variations cumulated in different tissues in the process of the ontogenesis. This study is focused on the detection of these changes already in younger individuals. The tissue-specific variability which is created during ontogenesis might have an adverse influence on all sorts of the mtDNA based studies. The samples were taken in two regions (Teplice / Prachatice) that differ in the pollution of environment. With regard to that, the samples with discovered changes were compared from the standpoint of the region, which they had come from, with the aim to prove the influence of environment on the mutagenesis of the mitochondrial DNA. Samples were also compared from the point of view of sex. Furthermore the variability of the collection of Czech population was evaluated and the estimation of the genetic...
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User interface for data extraction from GenBank data format
Jurečková, Kateřina ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis contains a literature review on the topic of the GenBank database, its most used flat file format gbk and its comparison with other formats of sequential data. Furthermore this thesis describes the structure of mitochondrial DNA of animals and plants and plastid DNA of plants. In the practical part of this thesis is evaluation of successful automatic data extraction from GenBank flat file format from whole mitochondrial sequences by genbankread function in Matlab. And it describes also a new application for GenBank data extraction. In the end this application is used in analyses of mitochondrial genomes.
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Effect of different numerical representations of DNA on molecular taxonomy
Blaschová, Eliška ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
This paper introduces the classical and molecular taxonomy used for classification of organisms. It represents the direction of DNA barcoding as a possibility to identify unknown organism. Acquired mitochondrial DNA sequences in DNA barcoding can by transform by suitable method to numerical representation that will properly inform about the organisms relationship to other taxa. In this work, we consider three methods of numerical representation: the 1st and 4th quadrant EIIP values and 3D numerical representation reduction. The practical part is programmed identification analysis, which assigns the test organisms reference organism. Testing is performed at 4 reference files and analyzed 5 files. The work summarized the success assigning the correct reference for the selected method of numerical representation.
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Mitochondrial DNA for molecular taxonomy
Kalianková, Kateřina ; Babula, Petr (referee) ; Maděránková, Denisa (advisor)
This work deals with mitochondrial DNA and molecular taxonomy. Structure and composition of animal cell, deoxyribonucleic acids and mitochondrial ribonucleic acids are described in the introduction. Another part contains information of DNA barcoding and numerical representation of genomic sequences. Programs are described in the practical part.
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Similarity/dissimilarity analysis of genomic data on the basis of graphical representation
Těthal, Jiří ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
The work deals with the identification of species of animal through the density of nucleotids of mitochondrial gene CO1. In the first part the theory summarized information about DNA barcoding and the mitochondria, cellular organel that with this method is closely related. The second part deals with virtually comparing different sequences using the density of nucleotides. For this it was created program, which uses two functions, the first of the specified nucleotide sequence calculates the density and one can compare the density by distance methods.
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Comparison of mitochondrial DNA for species identification
Labounek, René ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
The work deals with the method of recognizing species on the analysis of mitochondrial DNA segment. This analysis and classification using segment gene called CO1 in literatures such as barcode of life. In the beginning of work is analyzed the mitochondrial theory of heredity and conditions of formation of barcode. Practical use is based on this theory in creating database of barcodes generated to different animal species. Data used for creating the library are drawn from public databases NCBI and BOLD Systems. The next part of this work concerns about methods of comparison of the individual barcodes to the others and especially to the barcode of human. Three main computing methods were used tore these analyses: Needleman-Wunsch algorithm, Smith- Waterman algorithm and comparison of similarities using distance matrix. This work also concerns about transformation of DNA molecule sequences from symbols to numeric formats, which is required for the distance matrix comparison method. Algorithms for searching for a barcode of a species and vice versa were created to ease the work with data.
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