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Taxonomy, phylogeny and phylogeografy of selected groups of aquatic beetles (Coleoptera: Hydrophilidae, Hydraenidae) of the Caribbean region
Deler-Hernández, Albert ; Fikáček, Martin (advisor) ; Ribera, Ignacio (referee) ; Archangelsky, Miguel (referee)
This thesis is focused in the representatives of beetle families Hydrophilidae and Hydraenidae of West Indies and adjacent regions. It consists of two parts, the phylogenetic part and the systematic part. The phylogenetic part focuses on the hydrophilid genera Phaenonotum and Crenitulus of Greater Antilles: beetles were sampled in all four main islands (Cuba, Hispaniola, Puerto Rico and Jamaica) and analyzed using the combination of molecular and morphological data. The genus Phaenonotum contains four single-island endemics, of which those from Cuba, Jamaica and Hispaniola are wingless and form a clade that diversified ca. 46 million years ago (Ma) and likely colonized the Caribbean via the GAARlandia land bridge. In contrast, the Puerto Rican endemic and the two remaining non-endemic species colonized the Greater Antilles by over- water dispersal during the Oligocene-Miocene. The analysis of the genus Crenitulus revealed that Greater Antillean species belong to two separate clades: the Crenitulus yunque clade endemic for Cuba and Hispaniola, and the Crenitulus suturalis clade containing specimens from Greater Antilles and from northern America. A detailed revision of the Crenitulus yunque clade using morphology and molecular-based species delimitation recognized 11 species locally endemic for...
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Evolutionary forces of Central European taxa of the genus Dactylorhiza
Bílá, Klára ; Urfus, Tomáš (advisor) ; Figura, Tomáš (referee)
Genus Dactylorhiza, comprising green terrestrial orchids, belongs to of the most taxonomically complex groups of Europeran flora. Basic species often hybridise between each other and there is a lot of taxonomically challenging hybrids and hybridogenous lineages. Essential parental species of majority of hybrids and hybridogenous lineages are D. incarnata, D. maculata and D. fuchsii. Sister genus of Dactylorhiza is Gymnadenia which shares some similar features with Dactylorhiza species. Dactylorhiza viridis, formerly classified into the genus Coeloglossum, is the earliest diverged species. Diversity centre probably takes place in the Mediterranean Basin from where Dactylorhiza species migrated back to the Central Europe in postglacial. Major force of the genus evolution is polyploidisation which together with hybridisation leads to establishment of allopolyploid lineages. Unique feature of many orchids (including genus Dactylorhiza) is partial endoreduplication, which somatic endopolyploidisation of certain part of genome takes place. Pollination type is also important for Dactylorhiza microevolution. Deceptive flowers of Dactylorhiza genus are mainly pollinated by naive bumlebees but even beetles or ants can be pollinators. Majority of Dactylorhiza species are threatened by habitat loss during last decades....
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Phylogenetic analysis and molecular detection of coronaviruses
MARHOUNOVÁ, Lucie
The aim of this bachelor thesis was to get acquainted with the creation of phylogenetic trees, which describe the relationships between coronaviruses and compare and assess the suitability of used and designed primers for the detection of a new type of coronavirus SARS-CoV-2. According to phylogenetic trees, it is possible to determine the evolutionary relationship of the studied organisms, which during evolution are subject to changes in their sequences, so-called mutations. These changes determine their development. The theoretical part of the bachelor thesis was focused on general acquaintance with viruses and subsequently coronaviruses and a new type of coronavirus SARS-CoV-2. SARS-CoV-2 has posed and continues to pose a major threat to the world. Furthermore, the issue of phylogenetics and finally the PCR detection method were discussed. In the practical part, phylogenetic trees were created using the computer program MEGA-X using the Neighbor-Joining method, which examined the phylogenetic relationships between coronaviruses focused mainly on SARS-CoV-2. The nearest coronaviruses of this new type of SARS-CoV-2 coronavirus were further compared using special BLAST software, which reported the percent agreement of the studied sequences. During these analyzes, SARS-CoV-2 was found to be most like the bat coronavirus RaTG13. Primers that are commonly used to detect SARS-CoV-2 are not disclosed, therefore primers from the CoVrimer web application have been used, where primers that have been used for scientific research are available. These were compared with the primers designed by the author. The design was performed as part of a bachelor's thesis using a special application Pirmer-BLAST. The primers obtained from the CoVrimer application were not designed to comprehensively distinguish all SARS-CoV-2 variants studied.
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Fylogeneze a taxonomie vybraných druhů sinic čeledi Merismopediaceae s využitím metody single cell sequencing
POKORNÝ, Jan
Thanks to new molecular methods, which have been used for revision of many traditional cyanobacterial taxa, their real systematic positions have become clearer. Merismopediaceae is a relatively understudied group of Cyanobacteria, therefore many subordinate taxa have not been sufficiently molecularly reviewed. In this thesis standard molecular methods of the polyphasic approach were used on environmental isolates as well as cultured strains of Merismopediaceae taxa. Subsequent phylogeny analysis based on 16S rRNA gene shows the polyplyly of genera Merismopedia and Eucapsis. The thesis also includes the very first molecular evidence of the taxonomic position of the genus Microcrocis.
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World travellers: phylogeny and biogeography of the butterfly genus Leptotes (Lepidoptera: Lycaenidae)
PAPP MAREŠOVÁ, Jana
In this thesis, we investigated phylogenetic and biogeographical relationships of neglected butterflies of the subtribe Leptotina (Lepidoptera: Lycaenidae), widely distributed in tropical and subtropical areas around the world. We used both mitochondrial and nuclear markers and different molecular analyses to resolve relationships within the subtribe. We also focused on diversification times and biogeographical patterns of Old World taxa and detailed phylogeography of the most widespread species, Leptotes pirithous.
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Fylogeografie komplexu \kur{Phasianus colchicus}
KOFRÁNEK, Zdeněk
Rod Phasianus se v současné době dělí do 2 druhů a 33 poddruhů, které obývají široký areál, táhnoucí se od Japonských Ostrovů až k pohoří Kavkaz. Tato studie měl pracovala s fenotypovými charakteristikami rodu Phasinus za účelem jeho Evoluce. Získané výsledky byly srovnány s dostupnými molekulárními studiemi, zaměřenými na tu samou skupinu .Ve výsledku se ukázalo ,že fenotypové charakteristiky tohoto rodu nám nabízí dostatečné množství fylogeneticky informativních znaků, které dobře korelují s jeho fylogenetickými vztahy
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