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Implemenation of the RAD sequencing methods to the population genetic studies of hedgehogs from the genus Erinaceus
Loudová, Miroslava ; Černá Bolfíková, Barbora (advisor) ; Choleva, Lukáš (referee)
Hedgehogs from the genus Erinaceus are an important model organism for studying the postglacial recolonisation of Europe and the processes that take place in the secondary contact zones of their areas of distribution. In this study, five individuals of white-breasted hedgehog (Erinaceus roumanicus), four individuals of western hedgehog (Erinaceus europaeus) and one estimated hybrid were analysed. Geographical distribution of individuals used in the study covers the region of the Central Europe, however in the further research expansion of analsysed individuals will be needed and the whole Palearct should be sampled. The main goal was to implement novel methods in research of hedgehogs, which will enable to map the population-genomic structure of the genus Erinaceus in western Palearct. The method RADSeq (Restriction site associated DNA sequencing) enables to obtain polymorphic markers, e.g., SNPs which we used (Single Nucleotide Polymorphisms) across the genome. In this work it was analyzed 16382 SNPs. Using the binary data which indicates the presence and absence of SNPs for each species, hypotheses raised under classical analyzes of genetic markers from previous studies have not been fully confirmed. In further research it will be necessary to verify possible occurrence of biases connected with...
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Genomic approach in speciation studies
Habalová, Kateřina ; Hulva, Pavel (advisor) ; Mikulíček, Peter (referee)
Speciation, adaptation and hybridization are three concepts, each one referring to different process but having a common evolutionary context. Maternal line splits into two sister lines or only one line cleaves from maternal one during speciation. However it leads to formation of new species. Adaptation and hybridization can lead to formation of new species as well. New species arise by adapting to new conditions during adaptation. Within hybridization it is a desecendant of two different lines mating amongst themselves. Most of this thesis is being addressed to these issues, the lesser part is addressed to specific examples. The chapter about next-generation sequencing methods is also included, as these methods have been used more frequently recently. Key words: speciation, adaptation, hybridization, genomics, next-generation sequencing
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Evolution and genomics of symbionts in Hippoboscidae
ŠOCHOVÁ, Eva
Obligately blood-sucking parasites harbour symbiotic bacteria providing them B-vitamins and cofactors missing from their blood diet. Within Hippoboscoidea group (parasites of birds and mammals), tsetse flies as medically important vectors have been studied extensively while bat flies and louse flies tend to be neglected. This thesis is composed of two complementary manuscripts focused on phylogeny and origin of bacterial symbionts in Hippoboscidae family (manuscript 1) and their genome evolution (manuscript 2). First, phylogenetic approach was employed to determine lineages of obligate and facultative symbionts present in this group. Second, genomic and phylogenomic analyses were carried out to better understand evolution of obligate endosymbionts from the Arsenophonus genus in this group. Results of the two studies indicate that relationships between Hippoboscoidea and their symbionts are extremely dynamic with frequent replacements of obligate symbionts. This hypothesis is supported by both phylogenetic and genomic evidence, in particular, Arsenophonus endosymbionts of Hippoboscidae represent several distinct lineages (of likely different ages) with noticeable differences in genome features and metabolic capabilities. The data presented in this thesis thus greatly extend our knowledge about evolution and genomics of symbiotic bacteria in Hippoboscidae and bloodsucking hosts in general.
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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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