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Searching repetitive DNA in nucleotide sequences
Moskovská, Kateřina ; Provazník, Ivo (referee) ; Kubicová, Vladimíra (advisor)
This bachelor thesis deals with problem of repetitive DNA and algorithms for searching tandem repeats. Tandem repeats are important for biological industry. They are used as gene marker for creating genetic maps, profiles of DNA for paternity testing and in forensic sphere. Tandem repeats wreak several sever humen illness and it is another reason for their searching. Therefore are algorithms for searching of tandem repeats objects of many studies. We can divided algorithms to two main groups – algorithms based on string matching and algorithms based on digital signal processing. Task of this bachelor thesis is choose one member of each group and propose their implementation and than implement them in program Matlab. Result of this thesis should be comparison both programs. This comparison pass off on the basis of chosen criterion and several sequences. Both program transform these sequences and than can be programs compare.
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Conservation genetics of the grey wolf in Central Europe
Valentová, Kamila Anna ; Hulva, Pavel (advisor) ; Galov, Ana (referee)
Conservation genetics of the grey wolf in Czech Republic and adjacent regions is studied in the present thesis. Analyses of twenty-one microsatellite loci, one sex-determining amelogenin gene and mitochodrial control region were used to verify species determination, identify individuals and estimate relationships between them, analyse population structure and estimate demographic trends based on samples collected between 2014 and 2021. Genetic detection of red fox and dog samples incorrectly assigned to wolves illustrates the hurdles of field monitoring of grey wolf. Direct evidence for the occurrence of F1 hybrids was not found. Wolves from Bohemia showed lower values of allelic richness in comparison to the ones from Western Carpathians, probably as a consequence of recent expansion. Geographic distances between detection sites of identical individuals were relatively small or moderate in this study, suggesting regular movements of animals within their home ranges. Only two long-distance dispersal events exceeding 300 km were detected. Results of parental analysis provided evidence of pack distribution within the studied area. Most relationships were detected between wolves in the northern region of Czech Republic where the first recolonizing wolf pack in 2014 was registered. Within the studied...
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Evolution of intraspecific diversity of invasive pathogen of alder Phytophthora ×alni
Pecka, Štěpán ; Koukol, Ondřej (advisor) ; Sedlářová, Michaela (referee)
Phytophthora alni s. l. (Peronosporomycetes: Stramenopila) is an invasive pathogen causing phytophthora root and collar rot in alders. It has been known from Europe since the '90s and from the Czech Republic since 2001. Three species were found are known within species complex P. alni s. l. Two of these species hybridized in Europe and created third triploid species called Phytophthora ×alni (Phytophthora alni subsp. alni). Dozens of genotypes have been identified with the help of microsatellites in previous studies, nevertheless only one genotype (Pxa-1) was dominating and most of other genotypes were closely related to it. The trend of increasing or decreasing incidence of this genotype differed among these studies. This thesis compares changes in the P. ×alni population in Vltava basin over the last 14 years during which a significant decrease in number of available hosts of this pathogen took place. Multilocus genotypes were determined using a set of 10 microsatellite markers. Among the 94 P. ×alni isolates reliably genotyped, 23 were of different genotypes. None of these genotypes, however, were found on the same localities repeatedly (except the dominant genotype). Incidence of the dominant genotype increased over time (from 63 % to 86 %). Most of the other genotypes were only slightly...
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Evolution of karyotype, sex chromosomes and gene clusters in selected taxa of araneomorph spiders
Voráčková, Diana ; Forman, Martin (advisor) ; Sadílek, David (referee)
Spiders (Araneae) are a diverse group with various sex chromosome systems. The most common is X1X20 sex determination, X1X2 denotes two non-homologous X chromosomes and 0 the absence of Y. The presence of Y chromosome is rare among spiders and has been described mainly in Synspermiata, X1X2Y is probably ancestral constitution for this clade. The family Sicariidae was chosen to elucidate the evolution of sex chromosomes in Synspermiata. Karyotypes of 10 species whose 2n ranged from 19 to 23 were investigated in this study. The most common finding was X1X2Y in all studied Loxosceles species. The derived XY system was discovered in Sicarius. Furthermore, the distributional pattern of molecular cytogenetic markers (genes for 18S rRNA, 5S rRNA, histone H3 and U2 snRNA) was analysed using fluorescence in situ hybridization (FISH). These markers were found exclusively on autosomes, on one or two pairs. FISH with whole-genome probes of both sexes was performed to reveal distribution of Y specific sequences. Various patterns of Y differentiation were found in certain species. Y chromosome was small in all Sicariidae. A larger Y with a pronounced accumulation of Y-specific sequences has been detected in previous works - in the X1X2Y system of a synspermiate Pholcus phalongoides (Pholcidae). Pilot...
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Population genetics of grey wolf in Western Carpathians
Veselovská, Lenka ; Hulva, Pavel (advisor) ; Suchomel, Josef (referee)
The grey wolf is a top predator that plays a keystone role in maintaining the ecological balance of forested habitats. This master thesis focuses on the population structure and demography of the grey wolves in Slovakia, using data collected over two winter seasons between 2017 and 2019. Special attention is directed to the Western Carpathians. In Slovakia, the range of the wolf may cover up to 60% of the whole area. The population size and structure of grey wolves are influenced by both natural factors, such as mountain ranges isolation and dispersal, and anthropogenic influences, such as population fragmentation caused by linear infrastructure and increased mortality from traffic collisions. Additionally, the annual culling quotas for grey wolves have had an impact on their populations until recently. Mainly a non-invasive genetics approach utilizing selected 10 nuclear microsatellite markers, a marker for sex detection and mitochondrial sequences was used. Firstly, the species determination was verified and data quality filtering was carried out under statistical control. The sex ratio of the examined sample was 1:1,3. Mitochondrial data were assigned to haplotypes to help infer population origin. Bayesian clustering analysis of microsatellite data using the STRUCTURE program was used to...
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Spatial molecular ecology of the brown bear in Western Carpathians
Šrutová, Jana ; Hulva, Pavel (advisor) ; Hájková, Petra (referee)
In the current human-dominated landscape, wildlife populations are more often exposed to the island effect, loss of genetic variation and the associated risk of extinction vortex. Landscape genetics studies microevolutionary processes in populations and their relationships to landscape features. Integration of the results of genetic analyses and the results of habitat modeling of the species under study helps to identify transition zones between suitable habitats or anthropogenic barriers to gene flow in the landscape. Analysis of the spatial population structure of wildlife populations is an important tool for the conservation and management of populations. Between 2019-2021, 2172 mostly non-invasive brown bear (Ursus arctos) samples were collected in Slovakia, mostly collected in the Western Carpathian region. Using a microsatellite panel containing 10 polymorphic loci and the SRY gene for sex determination, a total of 1036 genotypes were identified, including 632 unique genotypes. The population seems to be relatively diversified and the observed heterozygosity is comparable to other demographically stable bear populations in Europe. Using STRUCTURE, a Bayesian clustering analysis was performed, which divided the population into three or four subpopulations according to the selected method. The...
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Genetic analysis of dicyemid infrapopulations suggests sexual reproduction and host colonization by multiple individuals is common
FLEGROVÁ, Tereza
This study explores the infrapopulation structure of Dicyema moschatum in its host Eledone moschata with the use of microsatellite markers. In order to assess the infrapopulation diversity, set of eight microsatellite markers was selected and respective oligonucleotides were designed for this population genetics study. Fragmentation method was used to analyze various microsatellite markers and the results were analyzed in bioinformatic programs that focus on standard population genetic metrics. Obtained results proved to provide new information about D. moschatum mating system and infection strategy.
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Molecular demography of brown bear in the Western Carpathians
Tkáčová, Nikola ; Hulva, Pavel (advisor) ; Tkadlec, Emil (referee)
Reliable estimates of population size are an essential tool for effective species conservation and management. The aim of this master thesis was to estimate the census population size and describe genetic variability and structure of the brown bear (Ursus arctos) using non-invasive genetics in Slovakia, which includes the majority of the West Carpathian population. A total of 2,172 samples were obtained during 2019-2021. The majority of the samples were non-invasive, mainly stool samples, which were complemented with tissue samples from roadkills or legally culled animals. Subsequently, DNA was purified and 12 microsatellite loci and the SRY sex marker were amplified. 1036 genotypes were successfully determined, of which 632 were unique. The Slovak population of bears posses a relatively high genetic diversity and similar values of heterozygosity as populations in areas with good state of conservation and relatively intact landscape. Based on Bayesian clustering analysis, population was divided into four clusters, with a certain level of gene flow. Only one cluster was detected in the eastern part of Slovakia (Eastern Carpathians). In the central part of Slovakia (Western Carpathians) all clusters were represented. Observed male to female ratio was 1.006. In males, a higher recapture rate was...
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Telestes perspective on the karstic poljes of eastern Herzegovina
Doulíková, Tereza ; Vukićová, Jasna (advisor) ; Choleva, Lukáš (referee)
The Dinaric karst region in the Balkans is one of the hot spots of biodiversity with a high number of endemic freshwater fish. The major cause of the high degree of endemism are numerous paleoclimatic and geological events that have affected the formation of the entire area. Flows of karst poljes represent a specific ecosystem to which some fishes have adapted. The poljes have been periodically flooded and these floods may activate different underground channels, which lead to interconnection of poljes. These fish species spend a part of the year in surface water and a part in groundwater and they may use the underground flows between poljes for migration. The aim of this thesis is to evaluate the genetic variability of two endemic fish species of the genus Telestes living in karst poljes in the region of eastern Herzegovina, and to detect a possible current gene flow between populations of these species due to the connection of underground flows. For this purpose, the DNA from 102 individuals from five different localities was isolated. The mitochondrial marker cytochrom b and 16 microsatellite loci were used for the analyses. The results point to very low variability between species and populations. Based on mitochondrial marker analysis, no link between populations of the species was detected,...
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Genetická struktura mediteránních populací kaloně Rousettus aegyptiacus
Marešová, Tereza ; Hulva, Pavel (advisor) ; Bryja, Josef (referee)
5 Abstract The genus Rousettus represents the only fruit bat genus distributed both in Asia and Africa reaching northern distributional limits of the Pteropodidae family. This unusual distribution pattern is related to the ability of echolocation, subsequent cave dwelling and probably other thermoregulatory and behavioural adaptations to relatively cold and dry climate. Methods for identification of genetically discrete populations were used in the presented study to acquire better comprehension of historical ways of colonization along with current dispersal and migratory patterns of the Egyptian fruit bat (Rousettus aegyptiacus) in the Mediterranean basin and adjacent range patches. Modern approaches to population and landscape genetics were applied on a dataset comprising 553 individuals from 72 localities using 20 nuclear microsatellites. Our results revealed a significant genetic distance of East African individuals and certain substructure in the northern part of the range. Cypriot population is clearly separated, and - for higher K - the isolation of colonies from Egyptian oases is highly supported. Genetic proximity of south Arabian and Sinai populations contradict current taxonomy of the species. Our findings highlight the role of seas and deserts as barriers restricting gene flow and the evolution...
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