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Concept of species in bears (Ursidae): practical, historical, and theoretical viewpoint
Wagner, Jan ; Fejfar, Oldřich (advisor) ; Sabol, Martin (referee) ; Musil, Rudolf (referee)
The present thesis surveys topic of taxonomic diversity and phylogeny of bears (Mammalia, Ursidae) and aspects of its contextual setting under effects of changing conceptual and methodological viewpoints. This problem is studied from several perspectives. The historical perspective is represented by a critical overview of the history of specific and infraspecific classification of bears with special respect to mutual influences of this classification and theoretical concepts of species accepted in particular periods. The perspective of material approach is exemplified by a material-based study of taxonomical and phyletic status of selected Pliocene to Middle Pleistocene ursine taxa. Along with deconstruction of some traditional hypotheses this produced a model explaining species diversification in ursine bears and its discussion in terms of factual relevance of included background concepts. In the pre-evolutionary period the bear species were usually understood broadly, as incipient immanent entities, yet exhibiting obvious certain infraspecific variability. This was established using definitions of varieties (mostly not identifiable with present subspecies or infraspecific taxa) considered as unstable modes of particular species. Although, in the post-Darwinian period, the concept and taxonomic...
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The genus Neotinea Rchb.f. in Europe
Vavřina, Štěpán ; Chumová, Zuzana (advisor) ; Vosolsobě, Stanislav (referee)
The thesis deals with the genus Neotinea from the phylogenetic, molecular and ecologic points of view. Most of its species have been classified in the genus Orchis until the use of molecular methods. Within the Orchidoideae, Neotinea forms a sister clade to the genera Anacamptis, Serapias, Ophrys and Himantoglossum. Six species are accepted now. The current taxonomic circumscription calls for a revision under the influence of new knowledge. Especially in N. tridentata, which contains several well-differentiated lineages and is the ancestor of the tetraploid N. commutata. Also the relationship between N. lactea and N. conica remains unresolved. The genome size within the genus ranges from 6.48 pg in N. maculata to 31.14 pg in N. lactea. All species except N. commutata, whose tetraploid origin is debated, are diploid (2n = 42). Partial endoreplication is present in the genus. The range of endoreplicated DNA is relatively narrow regardless of differences in genome size. Species prefer open, slightly basic habitats. In mycorrhizal interactions they appear generalistic with a preference for Ceratobasidiaceae. At the level of reproductive strategies, the genus Neotinea prefers the generative mode over the vegetative one. N. maculata is autogamous, the other species are allogamous, food deceptive, with...
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Review of taxonomic history of bats of the family Molossidae of the Old World
Forró, Beáta ; Benda, Petr (advisor) ; Staňková, Markéta (referee)
0 Abstract This thesis deals with systematics and taxonomic expressions of the relationships within the Molossidae family. Further attention is devoted to the species that occur in the Old World. The work consists of four chapters: introduction, basic characteristics of the family, description of particular species and conclusions. The second chapter, focused on the characteristics of the family Molossidae, consists of a description of the family systematics, its distribution range, morphological characters and the role of molecular genetics in the taxonomy of this family. The third chapter briefly discusses the genera of the New World thereafter looks in detail at the evolution and various views on the taxonomy of the species in the Old World. The species on which the thesis focuses belong to the following genera: Platymops, Sauromys, Cheiromeles, Myopterus, Otomops, Chaerephon, Austronomus, Ozimops, Micronomus, Setirostris, Mops, Tadarida, and Mormopterus. The aim of this thesis is to summarize the opinions on the systematic arrangement as well as taxonomic representation of relationships in the Molossidae family of the Old World and to reveal areas that require further attention. It also provides a description of alternative taxonomic arrangements based on the available evidence.
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Metagenomic analysis of animal gut microbioma based on diet
Spanakis, Martin Nikolaos ; Čejková, Darina (referee) ; Bartoň, Vojtěch (advisor)
This bachelor’s thesis deals with the sequencing of the microbiome and its composi- tion. It focuses on the gut microbiome of animals, which differs among animals with different diets. The work describes theoretical knowledge about metagenomic analysis of the microbiome, such as sampling procedures, various sequencing methods and data processing. The practical part of the work includes the preparation of the dataset, which includes the collection of data and their preparation for the following metagenomic anal- ysis. The result of the work is the taxonomic classification of bacterial species in the samples and the analysis of their diversity according to the type of diet of individual animals.
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Tracing Microendolithic Ichnocenoses: A paleoecological and taphonomic approach over the Phanerozoic
Herenio Kerkhoff, Marta Leticia ; Holcová, Katarína (advisor) ; Skupien, Petr (referee) ; Soták, Ján (referee)
The microbial endoliths study from the Western Carpathians region was a semi-quantitative survey that included six sampling localities. Samples, ranging from Upper Oligocene to Miocene (Serravalian), came from three localities in Czechia (Mikulov, LOM-1 and Hevlín), two in Slovakia (DNV and LKŠ) and one place in Hungary (Tard Clays, Rozalia Quarry). The main goal of this project was to verify how different levels of hypoxia, established for studied intervals, would affect the microendolilthic assemblages present in tests of benthic foraminifera. Additionally, microbial activity and byproducts, and the overall interplay between bioerosion and bioprecipitation are also analysed. The degree of hypoxy was established using ratio of oxic/dysoxic and hypoxic foraminifera, defined as Benthic Foraminifera Oxygen Index (BFOi) Sampled index shows a predominance of dysoxic indicators, with rare oxic elements. Secondary electron elemental analysis (EDX) reveals a significant enrichment of sulphur, phosphorus and iron in biofilm samples from DNV and Hevlín, when compared to the rock matrix surrounding it. Resin casts reveal a predominance of Dysphotic to Deep Euphotic zones ichnocenosis, with a predominance of Chlorophyte, Rodophyte and heterotroph burrows. Few representatives of Cyanobacteria traces, such as...
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Contributions to the taxonomy, biogeography, ecology and pathogens of parasites (Diptera, Acari) of Old World bats
Ševčík, Martin ; Benda, Petr (advisor) ; Stanko, Michal (referee) ; Bartonička, Tomáš (referee)
The dissertation thesis presents contributions solving several faunistic, biogeographical, taxonomic, and phylogenetic problems of selected groups of bat parasites together with surveys of potential pathogens in some representatives of these parasitic groups linked to the bats of the Old World. In the first part of the thesis, the taxonomy of prostigmata mites - chiggers (Trombiculidae) - coming from Eurasia and Africa is elaborated. Results of a detailed morphological and morphometric study are the descriptions of five new taxa belonging to four genera: Chiroptella, Grandjeana, Rudnicula, and Trombicula. At the same time, the results revise the differentiation within the group Trombicula sensu stricto, summarize the findings of species of individual genera and correct the inclusions of the originally described species within individual genera, with the final output of creating identification keys to the genera. The first sketch of the results of the study of the relations between chiggers and bats is included in this section, representing the description of the specific links among individual segments of both groups. In addition, there are studies presenting new findings and morphometric examinations of velvet mite nymphs collected from bats in Indonesia, as well as morphometric data and...
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Phylogeographic and systematic studies of selected bat taxa of the western part of the Old World
Uvizl, Marek ; Benda, Petr (advisor) ; Bryja, Josef (referee) ; Csorba, Gabor (referee)
Bats attract attention due their extraordinary adaptations including their ability to actively fly and echolocate, and extended lifespan, phenotypic diversity, etc. The phylogeny was analysed using cutting-edge molecular methods. However, the molecular revision of several species and species groups is still pending, especially those with wide distribution ranges or cryptic species complexes, even in the western part of the Old World. This specification encompasses Europe, the Middle East, Central Asia, and Africa and it represents the traditional research area for Central European (Czech and Czechoslovak) bat researchers. In my PhD thesis, I aimed to revise the phylogenetic and phylogeographic relationships of six less studied species and/or species groups of bats, using a combination of molecular and morphological phylogenetic approaches. The sequences of both mitochondrial and nuclear genetic markers were generated from over 10 species. These sequences were used to construct phylogenetic trees, haplotype networks, and estimate the time of divergence of studied species. The main results of my PhD thesis were: (1) filling gaps in the knowledge of the distribution ranges of species from the M. nattereri species complex (Vespertilionidae) by including and identifying samples from the Middle East; (2)...
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Yeasts and wine
Palíková, Petra ; Vadkertiová, Renata (referee) ; Vránová, Dana (advisor)
This thesis deals with isolation and identification wine yeasts from grapes and must. For analysis was used white wine Sauvignon that was grown and producing after needs ecological agriculture. Remove samples were processed in laboratory and by the help of dilution method were obtained pure culture isolated yeasts. In the following step, by the application of commercial kit UltraCleanTM Microbial DNA Isolation Kit we were able to isolated individual DNA that it was used to the next analysis. Isolated DNA was amplification by PCR method with ITS1 and ITS4 primers. PCR products were detected on agarose gel. Amplification samples were chopped five restriction endonucleases: HaeIII, HinfI, TaqaI, AluI and MseI. Chopped DNA was detected by the same way as PCR products and it was compared with restriction patterns of collection yeasts. In the next step it was compared genetic similarity of isolated yeasts by using BioNumerics software. As a criterion it was used Pearson coefficients and UPGMA clastering analysis. The result is dedrogram of genetics similarity isolated yeasts.
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Bioinformatic Tool for Classification of Bacteria into Taxonomic Categories Based on the Sequence of 16S rRNA Gene
Valešová, Nikola ; Hon, Jiří (referee) ; Smatana, Stanislav (advisor)
Tato práce se zabývá problematikou automatizované klasifikace a rozpoznávání bakterií po získání jejich DNA procesem sekvenování. V rámci této práce je navržena a popsána nová metoda klasifikace založená na základě segmentu 16S rRNA. Představený princip je vytvořen podle stromové struktury taxonomických kategorií a používá známé algoritmy strojového učení pro klasifikaci bakterií do jedné ze tříd na nižší taxonomické úrovni. Součástí práce je dále implementace popsaného algoritmu a vyhodnocení jeho přesnosti predikce. Přesnost klasifikace různých typů klasifikátorů a jejich nastavení je prozkoumána a je určeno nastavení, které dosahuje nejlepších výsledků. Přesnost implementovaného algoritmu je také porovnána s několika existujícími metodami. Během validace dosáhla implementovaná aplikace KTC více než 45% přesnosti při predikci rodu na datových sadách BLAST 16S i BLAST V4. Na závěr je zmíněno i několik možností vylepšení a rozšíření stávající implementace algoritmu.
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Virtual Herbarium with e-Learning Features
Semmler, Jiří ; Burget, Radek (referee) ; Rychlý, Marek (advisor)
This thesis is concerned with analysis, design and implementation web information system for management of virtual digital herbarium for high or middle schools. Online available services can not provide any alternative where students can cooperate with teachers in creating own virtual digital herbarium. This service provides a platform for creating own collection of pictures of plants with stress on their categorization to the taxonomy, detailed description, checking plagiarism and communication between students and teachers.
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