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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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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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Nectogalini shrews in Central Europe: fossil record, taxonomy, range dynamics.
Pažitková, Barbora ; Horáček, Ivan (advisor) ; Farková, Lucie (referee)
History of shrew clades composing the tribe Nectogalini (including the European genus Neomys) is only poorly comprehended, both due to fragmentarity of their fossil record and incompatibility of the discrimination criteria applied in extant taxa with actual character availability in fossil material. Thus, the presented study started with a thorough biometric reexamination of extant taxa (144 ind. of N. fodiens and N. milleri, 45 ind. ofAsiatic forms) with aid of 217 metric variables and establishing a series of discrimination criteria applicable to fragmentary fossil record. Using it, I analyzed 112 fossil items available from MN15 to Q4 sites of Czech Republic and Slovakia. A rich sample from the present glacial cycle (MIS 5b to Recent) demonstrated that both N. fodiens and N. milleri colonized the region of Central Europe either in earlier stages of Vistulian glacial, in early post-LGM glacial and throughout whole Holocene (though their distribution patterns were perhaps mostly mosaic in both species). The items from the late Biharian (Q2) and the earliest Middle Pleistocene (Q3) were found to represent a single clade characterized by relatively broad phenotype variation. This form, belonging clearly to the genus Neomys, was coidentified with Neomys newtoni Hinton, 1911. The pattern of its...
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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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Diversity and phylogeny of the lacertid lizards (Lacertidae) with emphasis on the tribe Eremiadini
Hlaváč, Denis ; Šmíd, Jiří (advisor) ; Chmelař, Jan (referee)
The family Lacertidae (lizards) belongs to the class Reptilia (reptiles) and the order Squamata (scaly reptiles). This family consists of two subfamilies, Lacertinae and Gallotinae, which are diversified into 45 genera and approximately 368 species. The subfamily Lacertinae is divided into two tribes, namely the tribus Eremiadini and Lacertini. The tribe Lacertini can be further divided into two clades: the Ethiopian and the Saharan-Eurasian clade. The subfamily Lacertinae, with approximately 354 species, is much larger than the subfamily Gallotinae, which consists of only 14 species. From the subfamily Lacertinae, the larger tribus Eremiadini is formed by 215 species classified in 22 genera. Representatives of this family can be found in Europe, Africa and Asia, but the center of origin is Europe. They belong to the dominant species of herpetofauna in Europe. The Eremiadini tribe separated from the rest of the Lacertidae family in the past and migrated to Africa, where it diversified into its present form. Currently, the diversity of the Eremiadini tribe is concentrated in Africa, but a large number of species also occur in Asia. The body is small to medium in size, which usually does not exceed 90 mm without the tail. The body shape is slender and the tail is relatively long compared to the body...
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The Rufous Sengi is not Elephantulus Multilocus reconstruction of evolutionary history of sengis from the subfamily Macroscelidinae
KRÁSOVÁ, Jarmila
We conducted multilocus phylogeny and divergence dating of sengis also known as elephant shrews from the subfamily Macroscelidinae. For the first time, we provided genetic evidence that the East African Rufous Sengi (Elephantulus rufescens) is closely related to the recently delimited genus Galegeeska known from the Horn of Africa and comprising a single species G. revolii. Our findings are in concordance with morphological traits and also biogeographical patterns known from Eastern Africa. Based on the results of divergence dating, the genus Galegeeska originated in the Pleistocene era.
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Diverzita a fylogenetické vztahy hlodavců v horských oblastech východní Afriky
KRÁSOVÁ, Jarmila
The Eastern Afromontane region of Africa is characterized by striking levels of endemism and species richness. Therefore, it was recognized as the Eastern Afromontane biodiversity hotspot (EAMBH) with numerous endemic plants and animals including mammals. Some parts of EAMBH (e.g. Ethiopian Highlands) are still under-represented in terms of biodiversity research in comparison with areas where sampling was relatively intensive in the last decades (e.g. Albertine Rift). This thesis describes genetic diversity, evolutionary history and taxonomy of several rodent species inhabiting mountain areas of Eastern Africa and Angola with a special focus on neglected areas such as Ethiopian and Angolan Highlands. Molecular-genetic analyses detected considerably higher diversity of small mammals than previously expected. Several candidates for new species were suggested and some of them also formally described based on phylogenetic and morphometric analyses. Molecular dating placed most of the diversifications into the eras of Pliocene and Pleistocene confirming the hypothesis that Plio-Pleistocene climate fluctuations together with topographically diverse landscape of Eastern Africa contributed to the high level of species diversity observed today.
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