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Genomic approaches for studying speciation
Vozárová, Zuzana ; Reifová, Radka (advisor) ; Hulva, Pavel (referee)
Technological advances in DNA sequencing along with the emergence of new informatics approaches have created new possibilities in many biological fields. In this bachelor thesis, I will focus on the informatics approaches used in speciation genomics, that is research field focused on the problematics of the origin of new species. I will introduce some statistical methods used by these approaches for parameter estimation. The four particular methods I will write about are Maximum likelihood estimation, Bayesian model, Markov chain Monte Carlo and Iterative approach. I will describe several methods used for the detection of interspecific hybrids and recent as well as historical interspecific gene flow. These methods include NewHybrids, the hybrid index, genomic and spatial clines and coalescent-based methods. The thesis demonstrates the usefulness of the connection of applied mathematics and genomics for addressing general biological issues, and speciation particularly.
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Analysis of structure and origin of multiple sex chromosomes in \kur{Leptidea} wood white butterflies
POSPÍŠILOVÁ, Kristýna
Previous studies have shown a dynamic karyotype evolution and the presence of complex sex chromosome systems with 3-4 W chromosomes and 3-6 Z chromosomes in Leptidea wood white butterflies. To dissect the evolutionary history of multiple Z chromosomes of Leptidea species, we used identified and selected bacterial artificial chromosome (BAC) clones containing orthologous genes of Bombyx mori chromosome Z and 17, isolated them from the available BAC library and used them as probes for physical mapping by BAC-FISH, first in L. juvernica, then in the closely related L. sinapis. In both Leptidea species, the majority of BAC clones corresponding to the linkage group Z of the B. mori reference genome hybridized to one chromosome of the complicated sex chromosome multivalent. Thus, we named it as Z1 chromosome. Location of all Z-derived BAC clones was identical in both species suggesting a conserved synteny and gene order between L. juvernica and L. sinapis Z1 chromosome. Moreover, our findings indicate that the Z1 chromosome is probably the ancestral Z chromosome in the genus Leptidea. Results of BAC-FISH mapping with clones corresponding to the linkage group 17 of the B. mori reference genome revealed the fusion/translocation event between an ancestral Z chromosome and the chromosome corresponding to B. mori chromosome 17 and supported a previous hypothesis about the role of chromosomal rearrangements in the formation of multiple sex chromosomes in Leptidea butterflies.
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Karyotype evolution of the family Araneidae
Pajpach, Filip ; Král, Jiří (advisor) ; Sember, Alexandr (referee)
Orb-weavers (Araneidae) are a diversified spider family comprising more than 3,100 species in more than 170 genera. Together with 13 other families, they con- stitute to superfamily Araneoidea. The presented thesis focuses on karyotype evo- lution of Araneidae, including its comparison with a related family Tetragnathidae. The results obtained from 19 araneid and four tetragnathid species confirm previ- ously postulated hypothesis that the ancestral karyotype of Araneoidea (including Araneidae) consists of 24 acrocentric chromosomes in males, including two acro- centric X chromosomes of system X1X20. However, there is a tendency of 2n decrease in some araneids due to centric fusions. In these cases, centric fusions affected most autosomes (and sometimes gonosomes as well); number of chromosome pairs de- creased from 11 to six. Three independent reduction events were detected in this thesis. Furthermore, pattern of nucleolar organizer regions (NORs) was studied in this thesis using fluorescent in situ hybridization, since data on evolution of this marker are scarce in spiders. Striking variability in NORs number was discovered, ranging from one to 13 loci. Remarkably, multiple centric fusions were always ac- companied by considerable increase of NORs number. In araneids and tetragnathids possessing...
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Analysis of dosage effect of speciation gene Prdm9 on fertility of mouse hybrids
Flachs, Petr ; Trachtulec, Zdeněk (advisor) ; Stopka, Pavel (referee) ; Král, Jiří (referee)
(eng) The phenomenon of hybrid sterility represents one of the evolutionary mechanisms that enables speciation. Only a few speciation genes have been uncovered. The only one found in mammals is Prdm9 (PR-domain 9). Data in the literature on the involvement of Prdm9 in decreased fertility of various semifertile hybrid males of house mouse subspecies were scarce before the results of this thesis were completed, despite that such males are much more frequent in nature than the fully sterile ones. Utilizing a panel of genetic tools and a battery of phenotyping tests, this thesis shows a central role of Prdm9 in fecundity of hybrids, including many fertility disorders and age dependency. Both increasing and reducing the Prdm9 gene dosage significantly elevated fertility parameters. Surprisingly, even the allele that in one copy causes full hybrid sterility increased F1 hybrid fertility when present in multiple copies. The PRDM9 protein also plays a role in identifying the sites of meiotic recombination. This study also points out the principles of allelic competition in determination of the sites of preferred recombination (hotspots), which suggests a possible link between both previously described Prdm9 roles. This thesis summarizes a set of three logically interconnected publications with the ambition...
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Transformation of trace element speciation in disturbed soil profile
Kochergina, Yulia
Distributions of toxic trace elements were studied in soils before and after disturbation of their profiles.Two areas with different vegetation cover were selected: beech (Fagus sylvatica) and spruce (Picea abies) forests at the Načetín site in the Ore Mts. In the past, this area belonged to places with extreme levels of acidic atmospheric deposition. The studied areas are not placed too far from each other and have thus approximately the same climatic conditions, geological background and pollution input. On the other hand, physicochemical properties of soils (pH, CEC, BS, Ctot, Stot) and concentrations of major and trace elements are different. At selected sites in spruce and beech stand, two soil probes to a depth of 40-50 cm were dug in 2010 and samples of individual soil horizont were collected for chemical analyses (approximately 0.5 kg). Four samples from L, H, A and B horizons were taken in the spruce forest area and five samples from L, H, A, B and C horizons were taken in the beech forest. In 2011, the sites were re-sampled and samples were taken from horizons that were disturbed in 2010, paralleled by samples of undisturbed soil horizons from the same probe sites. Trace element concentrations were determined by ICP-MS, the speciation of individual elements in the soils was determined by...
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Population genetics and speciation in Stylops (Strepsiptera)
Kodejš, Karel ; Straka, Jakub (advisor) ; Černá, Kateřina (referee)
This thesis is focused to population genetics of selected species of genus Stylops in Europe. Within this genus, five species was analysed by usage of two approaches - microsatellite analysis in Stylops ater and analysis of mitochondrial DNA in all five species. Mitochondrial gene for cytochome c oxidase (1st subunit) was used. For microsatellite analysis was performed bayesian clustering analysis and ABC approach (Aproximate Bayesian Computation). Mitochondrial markers were processed by making haplotype networks and demography analysis by computing Bayesian skyline plots. For Stylops ater, surprisingly low lewel of population subdivision was detected, yet with clearly differentiated population clusters from Scandinavia and baltic coast of Europe, which may imply period of isolation of these populations or relativelly recent population expansion and genetic differentiation due to lower population sizes. Next, hypotesis of possible temporal segregation of subpopulations of Stylops nevinsoni based on different aktivity period of their host species groups, was supported. In other three species, population subdivision was observed to be related either due to host specialisation (Stylops mellitae) or geographic consequences (S.nassonowi, S.spreta). Interesting finding is also detection of population...
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Haldne's rule and mechanisms of hybrid female sterility in birds
Baránková, Lucie ; Reifová, Radka (advisor) ; Jansa, Petr (referee)
Hybrid sterility is one of the mechanisms of intrinsic postzygotic reproduction barriers between species and plays a key role in the process of speciation, which is emergence of new species. In accordance with Haldane's rule, hybrid sterility affects preferably the heterogametic sex, which means that in organisms with XY chromosomes, such as mammals or drosophila, male sterility will be affected by sterility of hybrid offspring, while organisms with ZW chromosomes such as birds or butterflies, will be a sterile hybrid female. Symptoms and mechanisms of hybrid sterility are well studied in organisms with heterogametic males, whereas far fewer studies have been performed on organisms with heterogamous females. In my bachelor thesis I will introduce the basic theories explaining the two general rules of speculation, the Haldane rule and the associated great influence of chromosome X or Z on the occurrence of hybrid sterility. Furthermore, in my work I will deal with the manifestations of hybrid sterility of females in birds and in the selected species will introduce the mechanisms that cause this sterility. Key words: Haldane's rule, hybrid sterility, speciation, birds, postzygotic izolation
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The role of high-altitude habitats for speciation of central European endemics from the genus Campanula
Folbrová, Magdaléna ; Šemberová, Kristýna (advisor) ; Reif, Jiří (referee)
Mountain environment plays an important role in plant's life. Extreme conditions lead to continuous speciation accompanied by a complex processes e.g. geographical isolation (variation) or polyploidization. These processes can be studied by using a suitable model plant, represented in this thesis by selected mountain endemic bellflowers species belonging to Campanula rotundifolia agg. These species appear to be morphologically very similar but they are supposed to be of different origin. Mountain ecosystem is considered to be one of the most diverse and the most valuable environment for nature conservation. It hosts many endangered plants as well as plants protected by law. From the model group, these plants are represented by Campanula bohemica Hruby, Campanula gelida Kovanda and Campanula rotundifolia subsp. sudetica (Hruby) Soó. This thesis aims to sum up the up the current knowledge about a high altitude environment and endemism and to give a description of speciation mechanisms leading to the variability of mountain Campanula species. Further descriptions of their endangerment level, conservation and origin are also given. The subsequent MSc Thesis, introduced in the last part of this thesis, aims to reveal the origin of Czech and Slovakian mountain Campanula endemics. It is mainly focused on...
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Genomic approach in speciation studies
Habalová, Kateřina ; Hulva, Pavel (advisor) ; Mikulíček, Peter (referee)
Speciation, adaptation and hybridization are three concepts, each one referring to different process but having a common evolutionary context. Maternal line splits into two sister lines or only one line cleaves from maternal one during speciation. However it leads to formation of new species. Adaptation and hybridization can lead to formation of new species as well. New species arise by adapting to new conditions during adaptation. Within hybridization it is a desecendant of two different lines mating amongst themselves. Most of this thesis is being addressed to these issues, the lesser part is addressed to specific examples. The chapter about next-generation sequencing methods is also included, as these methods have been used more frequently recently. Key words: speciation, adaptation, hybridization, genomics, next-generation sequencing
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Variability in health state of mice in Mus musculus musculus and Mus musculus domesticus hybrid zone
Bílková, Barbora ; Vinkler, Michal (advisor) ; Vetešníková Šimková, Andrea (referee)
House mouse hybrid zone is a complex of subspecies Mus musculus musculus, Mus musculus domesticus and their hybrids. This hybrid zone is considered as a tension zone, maintained by balance between dispersion of individuals towards the zone center and negative selection against the hybrids. Decreased anti-parasite resistance could be one of selective factors which maintain the hybrid zone. In this thesis, I use hematological methods and skin-swelling test to compare variability in mouse health state within the house mouse hybrid zone. The skin-swelling test is a method measuring pro-inflammatory immune responsiveness. Since the commonly adopted method to perform this test does not allow clear interpretation of the test results, in this thesis I also aim to optimise the test protoco . I found that utilization of concanavalin A (ConA) is more suitable in mice than application of the commonly used phytohemaglutinin (PHA). Assessment of health state of mice by both hematological methods and skin-swelling test consistently indicates increased ability of anti-parasitic resistance in the subspecies M. m. musculus compared to subspecies M. m. domesticus. Hematological examination further shows better health state of hybrid individuals compared to parental subspecies. Our results support hybrid resistance hypothesis....
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