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Speciation genomics in nightingales
Mořkovský, Libor ; Reifová, Radka (advisor) ; Macholán, Miloš (referee) ; Piálek, Lubomír (referee)
Speciationisusuallyaslowprocessoccurringoverthousandstomillionsofyears.Thismakes speciation research difficult because no direct observation or manipulation is possible. At best, we can gain some insight by inferring the population history and structure in very fine detail by investigating genetic markers in multiple individuals of the nascent species. Today, speciationresearchisinanunprecedentedpositionthankstotheadventofhigh-throughput sequencingmethods,whichmakeiteasier and cheaper than ever before to evaluate multiple markers in many individuals. Speciation is not a straightforward process that happens in the same way every time, but rather a phenomenon occurring when genetic and ecological circumstancesactinginsymphonyultimatelyleadtoreproductiveisolationoftwosubpopula- tions. This is why it is important to study multiple model systems to understand the general principles behind speciation. We worked with two species of nightingales (Luscinia luscinia andL.megarhynchos)thatdivergedapproximately1.8Mya,likelyduetoglacialfluctuations in Europe. Our main goal was to use these new high-throughput sequencing methods to (1) detect interspecific hybrids between the species, (2) estimate levels of interspecific gene flow,(3)findareasofthenightingalegenomethatunderliereproductiveisolationand,finally, (4)...
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Evolutionary importance of mixed singing in two species of nightingales
Kohoutová, Hana ; Reifová, Radka (advisor) ; Sedláček, Ondřej (referee)
Singing is important for communication in birds. Some species of birds copy singing from other species. This heterospecific copying of singing is common especially in closely related bird species, and is usually called mixed singing in such cases. Mixed singing is often asymmetric, when only one species of the pair copies a song of the congener. The meaning of mixed singing is not well explained yet. The most common mechanism is probably an error during the learning phase of singing, but in some cases mixed singing can be adaptive. In my master's thesis I deal with the evolutionary meaning of mixed singing in two closely related passerine species - Common nightingale (Luscinia megarhynchos) and Thrush nightingale (Luscinia luscinia). These species co-occur in secondary contact zone in central and eastern part of Europe. Only Thrush nightingale which is larger and probably a more dominant species, exhibits mixed singing. In playback experiments in Common nightingale I studied a possible adaptive meaning of mixed singing in relation to interspecific communication. I tested the differences in behavioural and vocal response of Common nightingales to three types of stimuli: pure singing of Common nightingale, pure singing of Thrush nightingale and mixed singing of Thrush nightingale. The tested males...
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Evolution by gene duplication with regard to subfunctionalization.
Romášek, Marek ; Krylov, Vladimír (advisor) ; Reifová, Radka (referee)
Evolution by gene duplication has been a prominent topic of biology for various decades. Novel methods and approaches recently brought about a considerable progress in our understanding of this phenomenon. The aim of this thesis is to review the modern conceptions of preservation of duplicate genes in genomes of organisms and the processes involved. Another goal is to assess the significance of the concept of subfunctionalization, resolving of ancestral functions among the duplicates, leading to their preservation.
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Current approaches to whole genome sequencing and de novo genome assembly
Halenková, Zuzana ; Reifová, Radka (advisor) ; Röslein, Jan (referee)
The cost of sequencing has fallen almost ten thousand times over the past ten years due to the development of second and third generation sequencers. Sequencing and assembling the whole genome sequence of an organism is thus becoming a more affordable tool which can be utilized in many fields of science. On the way to the complete DNA sequence of an organism, multiple important decisions have to be made. These are crucial for the successful assembly of high- quality whole genome sequence and regard sample preparation, choice of sequencing technique and choice of an appropriate approach to whole genome assembly. This bachelor thesis describes various methods which can be utilized in individual steps of the process and aspects to consider while making the decisions. Keywords: next generation sequencing, third generation sequencing, whole genome sequencing, de novo assembly, genome assembly algorithms
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Detection of structural variants in genomes of two nightingale species
Halenková, Zuzana ; Reifová, Radka (advisor) ; Jansa, Petr (referee)
Structural variants are mutations in DNA sequence affecting the location, orientation, or the number of copies of regions longer than 50 bp. Although this type of variation has the potential to cause large phenotypic changes, structural variants remain largely understudied compared to other classes of variation (such as single nucleotide polymorphisms) due to the difficulties associated with their detection. Nevertheless, it was suggested that structural variants could play a profound role in the evolution of species. Inversions particularly are considered to be a potent mechanism for both adaptation and speciation due to their ability to suppress recombination. This thesis provides the first insight into the structural variation between two closely related naturally hybridizing species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia). Structural variants were detected using long-read sequence data and high-quality de novo whole genome assemblies from one individual per species. High-confidence sets of structural variants were built by the intersection of results from several structural variant calling methods separately for each reference genome and included 18 839 variants for the common nightingale reference and 19 864 variants for the thrush...
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Inffering the demographic history of populations from genomic data
Simandlová, Sára ; Reifová, Radka (advisor) ; Černá Bolfíková, Barbora (referee)
Currently, it is not difficult to obtain genomic data even from non-model organisms. These data can give us information about the demographic history of populations. Many statistical inference procedures have been developed to infer the demographic history of populations from genomic data, and I describe them in this thesis. In the introduction, I introduce the reader to important concepts in the analysis of the demographic history of populations. I then describe the different types of genomic data that can be used to infer the demographic history of populations. I then present the flow of an experiment in inferring the demographic history of populations, where I elaborate on the steps and present the approaches and methods that are used today. I provide a basic overview of the theory and logic behind each approach. I also introduce the reader the most commonly used software packages for inferring demographic histories of populations and provide a comparison between them.
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Sperm morphology and motility in estrildid finches of the genus Lonchura
Šárová, Markéta ; Reifová, Radka (advisor) ; Frolíková, Michaela (referee)
Sexual selection plays an important role in the evolution of animals. Today we already know that it takes place not only before copulation (precopulatory sexual selection), but also after copulation. This type of sexual selection is called postcopulatory sexual selection, and occurs mainly in promiscuous species, where females mate with multiple males. In this case, sperm competition occurs in the female reproductive tract. To increase the likelihood of their reproductive success, males began to develop surprisingly diverse sperm adaptations at the morphological, physiological, or behavioural levels. These adaptations often affect sperm velocity (motility), which is a key factor for successful egg fertilization. However, the result of reproductive success can also be influenced by females, who may prefer sperm with a certain phenotype in the process of cryptic female choice, and thus, for example, obtain better genes for offspring. In some species, females even can have the ability to sort and store sperm in specialized organs in which the sperms are nourished for some time, and then used to fertilize the egg. Even in this case, the storage of sperm is often affected by sperm morphology. Due to these mechanisms of postcopulatory sexual selection, sperm are under strong selection pressure, which can...
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Inferring the demographic history of populations from genomic data
Simandlová, Sára ; Reifová, Radka (advisor) ; Černá Bolfíková, Barbora (referee)
Currently, it is not difficult to obtain genomic data even from non-model organisms. These data can give us information about the demographic history of populations. Many statistical inference methods have been developed to infer the demographic history of populations from genomic data, which I describe in this bachelor thesis. At first, I introduce the reader to important concepts in analyzing the demographic history of populations. I then describe the different types of genomic data that can be used to infer the demographic history of populations. Next, I discuss statistical methods, which include methods based on site frequency spectrum data, methods using approximate Bayesian computation, methods for determining identity, and sequential Markov coalescent methods. I provide a basic overview of the theory and logic of each approach. I then present procedures for selecting inference methods. Keywords: population genetics, demographic inference, statistical inference, whole genome data
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Meiotic effect of MutS homolog 6 (Msh6) mutation in two mouse subspecies
Fusek, Karel ; Forejt, Jiří (advisor) ; Reifová, Radka (referee)
To study hybrid sterility our laboratory uses mouse strains PWD/Ph (PWD), derived from Mus musculus musculus wild mice and the common laboratory strain C57BL/6J (B6) mostly of Mus musculus domesticus origin as a model. Crossing between PWD female and B6 male results in sterile male progeny. F1 hybrid males carry defects in the repair mechanisms of asymmetric double-strand DNA breaks (DSBs). Functional interplay of SPO11 and PRDM9 proteins in the meiotic prophase I is necessary for repairs. Its defect leads to incorrect synapse formation between homologous chromosomes, leading to halt in spermatogenesis and thus male sterility. The formation of DSBs and their subsequent repair is essential for first meiotic division. The working hypothesis stems from the findings in yeast model, where supposed antirecombinatorial mechanism of mismatch repair genes Msh6 and Msh2 prevents DSBs repairs during meiosis. Despite the functional mechanism of these two genes is not explicitly known, existence of similar repair system in mice is presumed. Variety of methods was implemented in this thesis. The effects of Msh6 deletion on meiotic prophase I and sperm maturation were performed by designing guide RNAs for CRISPR/Cas9 for creation of three knock-outs in B6 mice. The PCR was used to amplify regions adjacent to the...
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