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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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Simulation of processes predicted by theory of frozen plasticity
Nekola, Ondřej ; Flegr, Jaroslav (advisor) ; Ponížil, Petr (referee)
The question of the tempo of evolution is amongst the oldest conundrums in evolutionary biology and has not been satisfactorily answered yet. One of the attempts to do so is the frozen plasticity theory, which postulates that a sexually reproducing species is only capable of evolution within short periods of time after its genetic polymorphism decreases e.g. as a consequence of peripatric speciation. In the longer periods of evolutionary stasis, its evolution is limited by frequency- dependent selection and pleiotropy. In this work, I have produced an open source software simulating the respon- ses of populations of sexually reproducing individuals to varying environmental conditions. Using this software, I simulated evolution of populations with different probabilities of arising of alelles affecting more phenotypic traits and frequency- dependent selected alleles that have opposing phenotypic effects when present at the locus in one copy, respectively two copies. I observed trends predicted by the theory of frozen plasticity: slower adap- tation to instant environmental changes, lower achieved fitness and more frequent extinctions of populations with higher portions of investigated types of alleles, but only with low effect sizes and without statistical significance. For future research, it would be desirable...
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Evolution of sociality and parental care in bees of the genus Ceratina
Mikát, Michael ; Straka, Jakub (advisor) ; Schwarz, Michael (referee) ; Bogusch, Petr (referee)
Small carpenter bees (genus Ceratina) are an excellent model taxon for the study of evolution of parental care and origin of eusociality. Prolonged offspring care is typical for this bee genus. Females usually guard their offspring until adulthood and later feed their adult offspring pollen and nectar. Moreover, most of studied species are facultatively eusocial, a trait probably inherited from the common ancestor of the genus. Although Ceratina bees have generally very interesting behavior, detailed studies were performed in only a few species, usually from North America, Japan and Australia. Only anecdotal observations of natural history existed for a few European species, and detailed research has not been performed before my thesis. The goal of my thesis is to explore the natural history of European species of Ceratina and to identify possible costs and benefits of this species' behavioral traits. I focused on following these behavioral traits: social nesting, guarding of offspring until adulthood, and feeding of mature offspring. Through my master project, I discovered biparental care in species C. nigrolabiata, therefore the most important goal of my Ph.D. project is the evaluation of costs and benefits of this behavior. Guarding of offspring by mother significantly influences their survival,...
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Body surfaces of reptiles as projection screens of evolution
Abramjan, Andran ; Frynta, Daniel (advisor) ; Rehák, Ivan (referee) ; Šulc, Michal (referee)
The PhD thesis deals mainly with the coloration (and also scalation) of selected reptile species and explores evolutionary or ecological contexts indicated by these traits. The main topics can be roughly divided into two groups: 'antipredation signals' and 'effects of parthenogenesis'. The dominant method used in most studies is visual modelling. The work consists of the following case studies. 1) Blue-tongue skinks use their conspicuous blue tongues to threaten potential predators. We found that the tongue has a relatively high UV reflectance, a typical feature of intraspecific communication in lizards. Using visual models, we investigated how the blue tongue is perceived by the conspecifics and predators (birds of prey). In both visual models, the UV-blue tongue appears more conspicuous against the natural background than a pink tongue. In addition, in the conspecifics model, its hue partially overlaps with hues of UV-blue spots, which are sexually selected traits in various species of lizards. Thus, the UV-blue tongue seems to contribute to the effectiveness of the deimatic display and its possible role in intraspecific communication cannot be ruled out either. 2) We detected UV reflectance in non-pigmented areas of the skin in the Leopard gecko (Eublepharis macularius). These form white patches...
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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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Karyotype evolution of selected families of entelegyne spiders
Kotz, Matěj ; Král, Jiří (advisor) ; Nguyen, Petr (referee)
The Araneoidea superfamily is a diverse clade of spiders with a great species diversity. The whole superfamily displays considerable conservativeness of observed karyotypes. Most likely ancestral karyotype in males is 24 acrocentric chromosomes with X1X2 sex determination system. The goal of this study is to explore the karyotype diversity of two araneoid families - Araneidae and Mimetidae. The majority of studied species exhibit the ancestral karyotype. In some species of the aformentioned families was observed sudden increase in chromosome numbers, up to 2n♂ = 52 in Araneidae and up to 2n♂ = 57 in Mimetidae. The latter number is the highest chromosome count observed in Entelegynae so far. Increase in 2n goes hand in hand with increase in sex chromosome numbers, leading up to X1X2X3X40 system in Araneidae and up to X1X2X3X4X5X6X70 in Mimetidae. I suggest polyploidy as a possible mechanism of the increase. To test this hypothesis, I measured the size of the genome using flow cytometry and used fluorescence in situ hybridization for the detection of 18S rRNA and 5S rRNA genes. For one species, probe for U2 snRNA gene was also optimized as part of this thesis. In many species studied, these techniques were used for the first time ever. In the case of the family Mimetidae, the largest genomes in...
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Echinoids, their evolution and response to the Cretaceous paleoenvironmental events
Hedánková, Karolína ; Košťák, Martin (advisor) ; Nohejlová, Martina (referee)
The bachelor thesis briefly summarizes knowledges about the evolution of sea urchins (Echinoidea; Echinodermata) with a focus on the successful order Spatangoida and their diversification in the dynamic Mesozoic environment. Attention is paid in particular to significant palaeoceanic changes, such as anoxic events (OAE = Oceanic Anoxic Event) and extinctions. Responses to OAE1-OAE3, as well as the last mass extinction (within the "Big Five") at the Cretaceous-Paleogene (K-Pg) boundary, are briefly discussed. Sea urchins, as an important part of benthic communities, prove to be a suitable model group not only for understanding the dynamics of evolution, but also successful strategies for surviving crisis events and new adaptations. Key words: Mesozoic, echinoids, evolution, events
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The evolution of SARS-CoV-2 virus during the pandemic of COVID-19
Karban, Šimon ; Tachezy, Ruth (advisor) ; Pačes, Jan (referee)
Coronaviruses are animal and human viruses which, in the case of humans, cause respiratory diseases. The genome of coronaviruses is non-segmented and encodes several structural and several non-structural proteins. As their genome consists of single-stranded RNA in a positive sense, they encode RNA-dependent RNA polymerase. The origin of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is uncertain and may never be known. However, this thesis covers up-to-date knowledge and the arguments for the main theories on the emergence of this virus. The pandemic of disease COVID-19 caused by the SARS-CoV-2 had an enormous impact on the health and lives of people worldwide. The length and severity of the pandemic were caused by the characteristic of the virus, transmissibility and asymptomatic type of infection with severe symptoms in elderly and chronically ill individuals and the fast evolution of the virus after its appearance in humans. This thesis will describe important characteristics of the most important variants of the virus and changes which gave them a selection advantage. In the end, trends in the evolution of SARS-CoV-2 will be discussed. Keywords: SARS-CoV-2, Coronaviridae, variants, phylogeny, origin, evolution
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Diversity of iris coloration during evolution of geckos (Gekkota)
Ozerskyi, Serhii ; Brejcha, Jindřich (advisor) ; Šmíd, Jiří (referee)
Iris is an anatomical structure that performs the function of a diaphragm in the visual system of the eye. It usually occupies most of the visible part of the eye. In addition to the main function - not to let light pass by the pupil, iris can play many different roles due to the great variability of its coloration. Iris can be part of a camouflage or aposematic color, play a different role in intra- or interspecific communication. In some species, its color changes depending on age, season, biological cycles, or even quickly become marked in response to stimuli. Geckos (Gekkota) are distinguished by a particularly large variety of iris color. And in many of them, the iris pattern resembles branching veins. What significance and evolution history this pattern has is of interest. I used various models of evolutionary reconstruction in the R program to study the evolution of veined pattern of coloration of the iris, as well as phylogenetic comparative methods and binary character evolution model to identify its connections with the fusion of life and the contrast in brightness between the eye and the eye ring. It was revealed that the veined pattern is an ancestral condition for geckos and is present in most modern species. Most precisely, the evolution of the vein pattern is described by all rates different...
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