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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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Biology and ecological dynamics of Baltic Fucus belts
Kivader, Martin ; Neustupa, Jiří (advisor) ; Němcová, Yvonne (referee)
The belt-forming algae of the genus Fucus are key species of the otherwise species-poor Baltic Sea. The distribution of the Fucus species is limited by the reduced salinity of brackish water to which the Baltic populations have adapted. The genus Fucus is known for high phenotypic plasticity and the absence of reproductive barriers, complicating the study of its recent radiation. The recent speciacion of the Baltic endemic F. radicans from locally adapted F. vesiculosus populations probably happened twice independenly 2 500-400 years ago. Baltic Sea is the largest brackish ecosystem characterised by a pronounced salinity gradient ranging from 1.2 to 30.2 ‰. It is influenced by the discharge of over 200 rivers and water exchange with the ocean is limited by the shallow Danish Straits. Since 1970s, Fucus decline and local extinction due to eutrophication of the Baltic Sea have been reported. Baltic water has high residence time which leads to accumulation of nutrients. In 1974, Helsinki Commission was established and the Helsinki Convention on the protection of the Baltic Sea Area was signed in response to its worsening state. Fucus belts, however, continue to decline and their ability for recovery is limited. Increased sedimentation due to eutrophication has in many locations resulted in the loss of...
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Streptophytic Algae with a Focus on the Class Zygnematophyceae
Špička, Jan ; Soldán, Zdeněk (advisor) ; Ráček, Jan (referee)
This bachelor's thesis deals with streptophyte algae, with special attention given to the class Zygnematophyceae. The thesis is written as a literature review, aiming to summarize existing knowledge about streptophyte algae, particularly focusing on the class Zygnematophyceae. Additionally, the thesis elucidates the phylogenetic relationships within this group, which historically have been challenging. The thesis primarily focuses on the description, ecology, and taxonomy of streptophyte lineages, emphasizing their significance in the study of terrestrialization, or the colonization of land. A significant part of this thesis is therefore to highlight the ecological and evolutionary role of streptophyte algae, especially in the context of their adaptation to terrestrial environments. An additional aim of the thesis is to address the issues associated with the group of algae, given their inconsistent definition. The thesis points out that algae do not form a monophyletic group, as they encompass various taxonomic lineages. This thesis can serve as a foundation for further research in the field of algology, thereby contributing to a better understanding and orientation in the process of terrestrialization. It also indicates the need for more phylogenetic studies to enhance understanding of the...
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Host Specialization and Evolution of Cuckoo Behavior in Bees
Policarová, Jana ; Straka, Jakub (advisor) ; Orr, Michael Christopher (referee) ; Litman, Jessica (referee)
Cuckoo bees are nest parasites of solitary and sometimes also social bee species. They do not build their own nests. Nor do they provision their larvae. Instead, they seek out a suitable host nest to lay their eggs in, and their larvae then feed on the host's provisions. In this doctoral thesis, I examined the host specialization of cuckoo bee species. I focused on the evolution of host specialization of cuckoo bees and factors which may limit their host choice - specifically whether and how are cuckoo bees affected by host food specialization. Answering these questions required phylogenetic reconstruction of several cuckoo bee lineages. We produced the first phylogenetic reconstruction of the tribe Sphecodini (Halictidae) and revised the taxonomy of the lineages Neolarrini, Biastini and Townsendiellini (Apidae), merging them into a single tribe Neolarrini. Lastly, we reconstructed the phylogeny of the mainly Palaearctic species of the genus Nomada, on the basis of which we divided the Nomada species into 13 subgenera. The mapping of ancestral character states showed that cuckoo bees of the genus Sphecodes change hosts quite frequently during evolution and are able to switch to phylogenetically distant hosts from different families. It also appears that there is no evolutionary trend towards...
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Detection of Correlated Mutations
Ižák, Tomáš ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
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.
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Speciation rate
Leščinskij, Artem ; Storch, David (advisor) ; Macháč, Antonín (referee)
Speciation rate is a frequency at which an original species splits into two species per unit of time. Since this rate cannot be directly determined, it must be inferred from the fossil record or a reconstructed phylogeny using appropriate diversification model or nodes and branches of a phylogenetic tree. The homogeneous birth-death process is the basic method upon which other models, such as time-dependent or density-dependent models, are based. Non-model methods such as DR statistics, node-density metrics or inverstion length of terminal branches, are methods depend on reconstructed phylogenetic trees. More complex methods include MEDUSA, BAMM, CLaDS, MTBD, or trait-dependant models. Protracted-speciation models are biologically more plausible and describe speciation as a gradual process. These methods can detect more complex diversification regimes. Tip rate determines expected species-specific rate of speciation and is less dependent on the rates of extinction and diversification; rather, it corresponds to the rate of speciation. Model identifiability is a fundamental problem limiting the estimation of the speciation rate, but this limitation can be partially overcome by new techniques such as pulled rates. Keywords: speciation rate, phylogeny, diversification, evolution, model
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Genetická diverzita zástupců čeledi sezamovitých Pedaliaceae R.Br.
Šlampa, Vojtěch
The family Pedaliaceae belonging to the order Lamiales, described in 1810 by Robert Brown, is an important part of the tropical flora, which can be found mainly in Africa, Sou-theast Asia, and Australia. The family itself has 50 species and has not yet been studied very closely, except for the genus Sesamum and its representative Sesamum Indicum L., which is among the most important crops for food purposes. In this work, five representatives of the Pedaliaceae family were analyzed using the DNA barcoding method, using nuclear and chlo-roplast DNA regions, which served as a marker for their subsequent phylogenetic analysis and taxonomic classification. DNA isolation from plant samples, PCR, and DNA sequencing was performed to obtain plant DNA and the necessary results.
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Implementing modern species delimitation techniques into fungal taxonomy: Aspergillus charting the course
Sklenář, František ; Hubka, Vít (advisor) ; Haelewaters, Danny (referee) ; Janko, Karel (referee)
This thesis focuses on the implementation of modern methods and approaches for species delimitation in the genus Aspergillus, an economically important fungal genus and model organism. So far, taxonomic studies in Aspergillus regularly included multiple DNA loci (typically four), and the phylogenetic analysis itself mostly consisted of calculating a phylogenetic tree based on individual loci and the concatenated dataset, or less commonly on genealogical concordance principles. Additionally, the datasets usually contained only a limited number of strains per species. The inclusion of more sophisticated phylogenetic species delimitation methods (mostly based on Multispecies coalescent model) in Aspergillus taxonomy adds a whole new layer to the analysis that ensures much higher objectivity of taxonomic decisions. Each of the eight presented papers contains a taxonomic treatment of a particular part of the genus with phylogenetic analyses based on datasets containing DNA sequences from three to six loci or whole genome data (series Nigri). The available molecular data are analyzed by a gradually refined set of phylogenetic species delimitation methods reflecting progress made between years 2017 and 2022. The individual papers also examine some specific characteristics that suitably complement the...
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Fylogenetická analýza peniální morfologie u novoguinejských hlodavců
KOVAŘÍK, Vojtěch
This study deals with the description of the penile and bacular morphology of New Guinean rodents. I documented and scored many qualitative and quantitative characters using the stereoscopic microscope and non-destructive microcomputer tomography machine (CT). The obtained data matrix was analyzed phylogenetically, which enabled me to reconstruct ancestral conditions for Rattini, and various subgroups of hydromyine rodents. I also identified a complex evolution of penile and bacular features, and also some perspectives for future investigations.
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