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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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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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