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Character-based methods for DNA barcoding
Kalianková, Kateřina ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This work deals with character-based DNA barcoding. DNA barcoding and character-based DNA barcoding methods are described in the introduction. Another part contains information of method CAOS (Characteristic Attributes Organization), method BLOG (Barcoding with LOGic) and method BLAST. Programs are described in the practical part. The end contains results.
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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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Identification of Organisms Based on Analysis of Nucleotide Density Vectors
Maděránková, Denisa ; Babula, Petr (referee) ; Schwarz, Daniel (referee) ; Provazník, Ivo (advisor)
Most methods for analysis of genomic data work with symbolic sequences. Numerically represented genomic sequences can be analyzed by signal processing methods. A new method of numerical representation of DNA sequences, nucleotide density vectors, is proposed in this thesis. Usability of this method for purposes of molecular species identification is tested on DNA barcoding sequences. DNA barcoding is modern and popular methodology based on comparison of short mitochondrial DNA sequences. Beside species identification by proposed method based on nucleotide density vectors, higher taxa rank identification (e.g. families) was also tested. Furthermore, dendrograms were constructed from standardly used evolutionary distances and distances between nucleotide density vectors and the dendrograms were compared.
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Analysis of animal mitochondrial genes for DNA barcoding
Brabencová, Klára ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
The aim of this work is a literature review on the topic of the mitochondrial genome and DNA barcoding, building a dataset of mitochondrial sequences from GenBank database and creatione of a software function for extraction of individual genes that are present in the mitochondrial genome. This function was developed in Matlab. DNA barcoding is a method that uses short DNA sequence of mitochondrial genome for identification of species. There is no comprehensive work examining the appropriateness of different mitochondrial genes. This aim investigates the potential of other mitochondrial genes and evaluate their effectiveness for DNA barcoding and calculation of intra-and interspecific variability.
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Character-based methods for DNA barcoding
Kalianková, Kateřina ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This work deals with character-based DNA barcoding. DNA barcoding and character-based DNA barcoding methods are described in the introduction. Another part contains information of method CAOS (Characteristic Attributes Organization) and method BLOG (Barcoding with LOGic). Programs are described in the practical part. The end contains results.
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Fuzzy classification of DNA sequences
Těthal, Jiří ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The work deals with the fuzzy classification of DNA sequences. In the first part the theory summarized information about Fuzzy logic and methods of its use in the classification of biological sequence data. The second part is practically deal with the classification algorithm for assessing the similarity of sequences. Specifically, the dividing of coding and non-coding parts of the sequence and the use of fuzzy classification in DNA barcoding.
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Host specificity of tropical bark and ambrosia beetles (Coleoptera: Curculionidae: Scolytinae, Platypodinae)
HULCR, Jiří
Host specificity of tropical bark and ambrosia beetles was surveyed by rearing the beetles from 13 host trees in a lowland rainforest in Papua New Guinea. Ploeophagous bark beetles show narrow host specificity (usually family-level) typical for herbivorous insects, fungus-growing ambrosia beetles display almost no host fidelity. In both groups of species, the local diversity of plants is unlikely to have played a role in the clade diversification. The ambrosia symbiosis (scolytine beetles and fungi) is shown to be less specific than previously assumed, based on a discovery of new association between Scolytodes unipunctatus (genus of phloem feeders) and three unrelated groups of ambrosia fungi. The hypothesis that apparent polyphagy may conceal specialized populations within a species of a herbivore is tested for Homona mermerodes (Lepidoptera, Tortricidae). The haplotype diversity of the species show no congruence with host plants or geographic origin, confirming polyphagy of the species.
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Molecular biodiversity inventory of the ichthyofauna of the Czech Republic - presentation of the started project
Mendel, Jan ; Halačka, Karel ; Vetešník, Lukáš ; Papoušek, Ivo ; Bartoňová, Eva ; Šanda, R. ; Koníčková, Milena ; Urbánková, Soňa
The study based on international cooperation would like to contribute in a significant way to identification and description of the species diversity of the complete Czech ichthyofauna using a comprehensive approach. The inventory and subsequent cataloguing concentrate on recent native and non-native species of fishes and lampreys living in natural waters of CR. The obtained results are used for inter-continental comparison of all fish species using the "DNA barcode" within the BoLD platform. The final summary evaluation will contribute to updating of the data for monitoring within the system Natura 2000 and will provide vital information and recommendations to the ANCLP CR. The new system of species collections of type specimens designed on the basis of a comprehensive approach and creation of a detailed voucher will mean significant contribution to the Czech museums.
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