This thesis is focused on the assessment of the phylogenetic position of the Myxozoa within the Metazoa, study of the evolutionary relationships within myxosporeans and investigation into the cryptic species assemblages of several myxosporeans based on the ribosomal and protein-coding data. The major part of this work was to confirm the evolutionary trends within myxosporeans based on a single gene by other molecular markers in order to find out if the reconstructed relationships correspond to the real organismal phylogeny. This has been a crucial step for future actions in solving the discrepancies between the myxosporean phylogeny and taxonomy.

5 ABSTRACT This doctoral thesis is focused on flat-footed fly families Opetiidae, Platypezidae and genus Microsania (Insecta: Diptera). The thesis consists of general introduction to the systematics, taxonomy, diversity, zoogeography, phylogeny, and biology of the flat-footed flies. Systematics and taxonomy are summarized based on historical as well as recent literature. Each important taxon is shortly introduced and information about its taxonomy, morphology, diversity, distribution, and biology is provided. The next two chapters deal with fossil species and research on species diversity. The following part is a summary and plan for future research. Final chapter consists of 9 published peer-reviewed articles (5 in impacted international journals and 4 in journals without impact factor). The first article is a molecular phylogeny study of relationships between genera of flat- footed flies. The results show Platypezidae consisting of two well-supported clades, the first with the subfamilies Melanderomyiinae + Callomyiinae and the second formed by subfamily Platypezinae. Genus Microsania was resolved as a separate lineage distant from Platypezidae which clustered with Opetiidae as its sister group, both together forming a sister group to Platypezidae. The genus Agathomyia proved to be paraphyletic....

Paroedura genus includes 17 described species endemic to Madagascar and the Comoros Islands, where they went through a significant adaptive radiation. The genus Paroedura is monophyletic and well supported hypothesis on phylogenetic relationships among its species was published. Species vary considerably in body size and morphology and in preferences for habitat, some species live in sympatry. The genus Paroedura belongs to cytogenetically poorly studied family Gekkonidae which exhibits high variability in modes of sex determination and in comparison with basal gecko lineages, also considerable variability in the chromosome number and morphology. Karyotypes of only two species of the genus (P. picta, P. sp.) have been published. The aim of my thesis was to describe karyotypes of both sexes in all available species of the genus using conventional and molecular cytogenetic methods, to perform the phylogenetic analysis of karyotype evolution and chromosomal rearrangements in the genus, to assess the role of these rearrangements in the speciation of the genus and to detect sex chromosomes. I acquired karyotypes of both sexes in nine species representing the most of major phylogenetic lineages of the genus. According to the results, species can be divided into three groups according to diploid...

We can find a lot of microorganisms living in snow including psychrophilic snow algae from the order Chlamydomonadales (Chlorophyta). They are adapted to the extreme conditions in this habitat and can cause the phenomenon of coloured snow. The species Chlamydomonas nivalis (Bauer) Wille is the most commonly associated with red snow in alpine and polar regions during summer season worldwide. In the field material, we can find red spherical cells without flagella and any morphological characteristics suitable for species determination. Until now, this species has not been isolated into laboratory culture and its life cycle is unclear. Furthermore it has been shown that red coloured snow can be caused by more species which used to be determined as Chlamydomonas nivalis. The aim of this study was to collect samples of red snow from different parts of Europe, to describe the morphological variability of Chlamydomonas nivalis-like snow algae in relation to region of origin, to try to isolate laboratory strain of this species and to describe its position and distribution by phylogenetic analysis of laboratory strains and field samples. Red snow samples were collected from 30 European localities in Slovenian Alps, Romania, Dolomites, Ötztal, Wallis and Sarntal Alps, High Tauern, Ortler massif, in Norway,...

The research presented in my PhD thesis consists of phylogenetic, biogeographic, taxonomic and ecological research of Southern Hemisphere water scavenger beetles (Coleoptera: Hydrophilidae) with a special emphasis on New Zealand. The introductory chapter provides a brief outline on the break-up of Gondwana and geological processes that shaped New Zealand and its fauna. Furthermore, the diversity of New Zealand Hydrophilidae and worldwide diversity of the hydrophilid subfamily Cylominae and its taxonomic history are illustrated. The scientific part of the thesis contains 4 published papers and 2 manuscripts. The first study recalibrates the Coleoptera time tree, providing new age estimates for the Hydrophiloidea, among others. The new age estimate is implemented in the second study, a phylogenetic study that reconstructs the biogeography of the 'Gondwanan' Cylominae beetles. The Cylominae, whose name was reinstated through nomenclatural priority over Rygmodinae in a separate paper, are found to consist of two tribes, Andotypini and Cylomini. The disjunct distribution of Cylominae is shown to be partly the result of vicariance and partly of long-distance oversea dispersal. The most remarkable long-distance dispersal is that of the only African representative of the subfamily which reached Africa from...

Eleven species are distinguished in the genus Oxythyrea Mulsant, 1842 (Coleoptera: Scarabaeidae) nowadays. They are not divided into subspecies. Diversity of the genus is concentrated in the Mediterranean and Oxythyrea funesta (Poda, 1761) inhabit a wide area in the western Palearctic Region. It was observed in last decades, that O. funesta retreated from central Europe to south and then recolonized it back including new areas in northern regions. Master thesis is focused on resolving population structure of O. funesta and partial phylogeny of the genus Oxythyrea using molecular genetic methods. 145 individuals of O. funesta and 15 individuals of five other species of the genus Oxythyrea appear in analysis. We acquired sequences of mitochondrial genes cytochrome oxidase I (807 bp), cytochrome b (381 bp) and nuclear gene internal transcribed spacer 1 (946 bp) from these specimens. The results of phylogenetic analysis confirmed so far the only one existing interpretation of relationships within the genus Oxythyrea based on morphological data. We also confirmed complicated relationships between O. funesta and O. pantherina, which also appear in the historical development of their taxonomy. We detected different genetic lineage in Sicily, southern Italy and Tunisia using phylogenetic trees and haplotype...

Blood-sucking louse Polyplax serrata harbor two phylogenetically distinct symbiotic bacteria from the orders Legionellales (Gammaproteobacteria) and Neisseriales (Betaproteobacteria). Based on rigorous phylogenetic analyses, the first bacteria was confirmed as member of genus Legionella, and the name Candidatus Legionella polyplacis, sp. n. was proposed. Vertical transgeneration transmission was proved by visualisation of the symbiont in host tissues. Improved genome of latter symbiont is considerably larger and possesses more metabolic functions. In the genome, I found horizontally transferred operon, which encode synthesis of enzymes involved in urea cleavage.

This master thesis focuses on the phylogeny of hybridogenous and polyploid genus Curcuma from family Zingiberaceae using Next-Generation Sequencing data from hundreds to thousands nuclear loci. This approach seems to be better than widely used cpDNA and ITS sequencing especially in the case of hybridogenous and polyploid groups. Data for phylogeny reconstruction were generated using Hybridization-based sequencing (Hyb-Seq) method which combines target enrichment and genome skimming strategies. Data analysis was performed primarily using pipeline HybPhyloMaker especially created for Hyb-Seq data analysis. Twenty-seven species from the genus Curcuma and three outgroup species were sequenced in this work. Phylogenetic trees based on all 1 154 and 811 selected nuclear low- copy genes show high support values of all nodes which is in contrast to plastome and rDNA phylogeny with lower support values in some nodes and incongruences in topology compared to low-copy genes phylogeny. Phylogenetic networks inferred from low-copy genes, lineage movement analysis and monophyly tests agree with published hypotheses of interlineage hybrid origin of three species - C. vamana, C. myanmarensis and C. roscoeana. These analyzes show likely hybrid origin of C. candida too with parents from the group Curcuma I and basal...

The thesis deals with phylogeny, taxonomy and nomenclature of selected groups of the lichen genus Caloplaca. Particularly, the C. cerina group was closely investigated using molecular methods (ITS sequences), morphology and chemistry, based on material from Europe, and to some extent also from North America and western Asia. This approach resulted in the description of three new species (C. sterilis, C. subalpina, C. thracopontica), and detected an unexpected richness of lineages. Nomenclature, taxonomy, morphology and ecology of C. aurantia and C. flavescens from the C. aurantia group were studied in detail, including selection of the neotype of the former species. Their distribution was reviewed for the territory of the Czech Republic. Poorly known taxon C. aurantiomurorum from Algeria was lectotypified and synonymized with C. aurantia. Apart from the two groups, C. phlogina and C. scythica, differing partly in thallus colour and distinctly in distribution, were examined using both molecular (ITS sequences) and phenotypic data and found to be conspecific.

Tato práce zkoumá existující možnosti a metody detekce korelovaných mutací v proteinech. Práce začíná teoretickým úvodem do zkoumané problematiky. Využití informací o korelovaných mutacích je především při predikci terciální struktury proteinu či hledání oblastí s významnou funkcí. Dále následuje přehled v současnosti používaných metod detekce a jejich výhody a nevýhody. V této práci jsou zkoumány zejména metody založené na statistice (například Pearsonově korelačním koeficientu nebo Pearsonově chi^2 testu), informační teorii (Mutual information - MI) a pravděpodobnosti (ELSC nebo Spidermonkey). Dále jsou popsány nejdůležitější nástroje s informací o tom, které metody používají a jakým způsobem. Také je diskutována možnost návrhu optimálního algoritmu. Jako optimální z hlediska úspěšnosti detekce je doporučeno využít více zmíněných metod. Také je doporučeno při detekci využít fyzikálně-chemických vlastností aminokyselin. V praktické části byla vyvinuta metoda využívající fyzikálně-chemických vlastností aminokyselin a fylogenetických stromů. Výsledky detekce byly porovnány s nástroji CAPS, CRASP a CMAT.