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Phylogeography and genetic diversity of the populations of Gobius niger (Gobiiformes: Gobiidae)
Hradečný, Jakub ; Vukićová, Jasna (advisor) ; Perdices, Anabel (referee)
Gobies (Gobiiformes: Gobiidae) are the most speciose fish family and the most abundant fish group of the European seas. Yet, the population genetic diversity has been studied in only a few European goby species. Although the ocean is seemingly a continuous habitat, there are barriers to gene flow in marine environment in form of e.g. straits or marine currents. The black goby (Gobius niger) is a demersal marine fish with planktonic larvae, inhabiting the coastal waters of Europe, north Africa and the Mediterranean and Black Sea coast of the Middle East. The current work examined individuals from 28 localities across the distribution range of the species in order to study the population genetic diversity. The analyses of two mitochondrial markers (cytochrome b and D loop) revealed a complex structuring of the population and a pronounced intraspecific diversity (maximum uncorrected p-distance 6.1 %). The population is divided into four very diverse haplotype groups, with unexpected geographic pattern. While the population inhabiting the Atlantic Ocean and the North Sea is generally genetically homogeneous, with all examined individuals bearing haplotypes belonging to a single haplotype group, the Mediterranean population is very complex, displaying a presence of four haplotype groups, some of which...
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Detection of positive selection on the molecular level
Cakl, Lukáš ; Reifová, Radka (advisor) ; Munclinger, Pavel (referee)
The rise in computational power and available genomic data has made it possible to examine the traces of selection on nucleic acid sequences. To gain the most relevant results, we need to know how are said traces created, what are their properties, how to detect them and which methods to use in a given set of circumstances. This bachelor thesis is dedicated not only to the methods we use to detect positive selection and their underlying principles, but also to the theoretical models, which allowed their conception, neutral theories, against which we test our traces and the traces themselves. Due to the dynamic nature of the genome, alongside the data we have available, the properties of the selection traces are the most important factor for picking one of the methods we have available. Especially since, speaking in the terms of an evolutionary scale, certain traces are created swiftly and disappear soon afterwards, while the formation of others requires large periods of time. Keywords: darwinian selection, positive selection, statistical methods, selection detection, dna, molecular data
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Importance of morphological, ultrastructural, and molecular analyses for the higher taxonomy of ciliates
Šimáčková, Aneta ; Čepička, Ivan (advisor) ; Hampl, Vladimír (referee)
Ciliophora are one of the largest groups of protists. They have three typical features - (1). the presence of many cilia, covering the cell, (2). nuclear dualism, and (3). conjugation. The systematics of the phylum Ciliophora has changed greatly during the last decades. This was caused by the development of new methods used for studying the ciliates. The first systems were based on the morphology of structures in the oral region. Based on these structures, Levine et al. published a system of ciliates in 1980, which they divided into three classes. However, it was found later that this system was not natural because oral structures do not reflect the phylogeny, and the structure of somatic structures was shown to be a more useful feature. Small and Lynn created a system based on the structure of somatic kinetids, where they divided the ciliates into three subphyla and eight classes. However, subsequent molecular analyses did not support this system. They divided the ciliates into two subphyla (Postciliodesmatophora and Intramacronucleata), and the number of classes was elevated to eleven. Today, additional six new classes of ciliates are recognised. They were created mainly on the based of phylogenomic and phylogenetic analyses. The classes of the subphylum Intramacronucleata are grouped into three...
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Hyaloscyphaceae - current view on phylogeny and diverzity
Bundová, Kateřina ; Koukol, Ondřej (advisor) ; Šandová, Markéta (referee)
The family Hyaloscyphaceae (Helotiales) includes microscopic species of fungi characterized by sessile apothecium with excipular hairs; these hairs are very important in taxonomy of the group. Most species of the family are saprobes and these saprobic species grow on herbaceous or woody litter, most often they grow on fallen needles, cones and stems of coniferous wood. Distribution of the family is cosmopolitan and has center of occurence in temperate and boreal forests, however members of the family also occur in tropic and subtropic forests. This family is probably a polyphyletic group of several lineages and needs to be analyzed further. The aim of this bachelor's thesis is to organize and compare the views on phylogeny of Hyaloscyphaceae, from the first morphological studies until the current molecular studies, and then to summarize all the genera of fungi which belong to this family. And to describe ecological and species diversity.
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