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Detection of positive selection on the molecular level
Cakl, Lukáš ; Reifová, Radka (advisor) ; Munclinger, Pavel (referee)
The rise in computational power and available genomic data has made it possible to examine the traces of selection on nucleic acid sequences. To gain the most relevant results, we need to know how are said traces created, what are their properties, how to detect them and which methods to use in a given set of circumstances. This bachelor thesis is dedicated not only to the methods we use to detect positive selection and their underlying principles, but also to the theoretical models, which allowed their conception, neutral theories, against which we test our traces and the traces themselves. Due to the dynamic nature of the genome, alongside the data we have available, the properties of the selection traces are the most important factor for picking one of the methods we have available. Especially since, speaking in the terms of an evolutionary scale, certain traces are created swiftly and disappear soon afterwards, while the formation of others requires large periods of time. Keywords: darwinian selection, positive selection, statistical methods, selection detection, dna, molecular data
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Haemoproteus in passerines: Prevalence and infekction dynamics
Chalupová, Barbora ; Svobodová, Milena (advisor) ; Munclinger, Pavel (referee)
The genera Haemoproteus and Plasmodium are widespread genera of blood parasites from phylum Apicomplexa. Both genera have dixenous life cycle and their definitive hosts belong to the order Diptera. Both parasites can be found in birds where asexual division takes place. The infection with genera Haemoproteus and Plasmodium is usually asymptomatic; during long lasting chronic phase relapses of the infection can occur. We gained 1 092 blood samples from 29 trapped species of passerines in Milovice forest during seasons 2017-2019. Haemosporidians were detected in 48 % of samples. The prevalence of genus Plasmodium was 16 %, the prevalence of genus Haemoproteus was 22 % and 10 % we could not specify the parasite. We have found six new lineages of genus Haemoproteus, provisionally named Haemoproteus lineages coccoc_1, coccoc_2, coccoc_3, coccoc_4, embcit, fricoe which total prevalence was 14 %. Lineage Haemoproteus sp. coccoc_1 was the most noticed one and its prevalence was 12 %. Plasmodium relictum clone Peng14-121Br2AF and isolate Cc_P1 was the second most prevalent (13 %). Infection dynamics was studied in samples gained in years 2014-2019. Forty individuals were examined between years and twenty-seven individuals were examined intraseasonally. Three individuals were trapped both intra- and...
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Meiotic homologous recombination and hybrid sterility
Gergelits, Václav ; Forejt, Jiří (advisor) ; Macholán, Miloš (referee) ; Munclinger, Pavel (referee)
(English) Meiotic homologous recombination, homologous chromosomes synapsis, and F1 hybrid sterility (enabling formation of species) are mutually interconnected phenomenons, one being the prerequisite to the latter. In the present thesis, these phenomenons were investigated on a genetic and mechanistic level using a mouse subspecies as a model. Noncrossovers (NCOs, gene conversions), 90% prevalent resolution of Prdm9- determined meiotic double-strand breaks (DSBs), were uniquely identified and characterized on a chromosome-wide level. The mean gene conversion tract length, based on 94 NCOs events, was calculated to be 32 bp. On a local level, the NCOs overlapped the known hotspots of PRDM9-controlled histone trimethylation and DSB formation, indicating their origin in the standard meiotic DSB repair pathway. On chromosome-wide level, NCO and CO distributions differed, in particular COs being relatively preferred over NCOs in subtelomeric regions. A specific subset of nonparental/asymmetric NCOs and COs was underrepresented in our datasets, proposing their problematic repair, hypothetically enabled by sister chromatids, and thus not contributing to indispensable homologous synapsis. Genome-wide crossover (CO) rates, genetically and mechanistically crucial ~10% of DSB repair, were proven to be...
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Candidate genes for behavioural adaptations in tropical and temperate birds
Křístková, Barbora ; Munclinger, Pavel (advisor) ; Macholán, Miloš (referee)
The use of candidate genes has become a widespread approach in the study of behavioral adaptations. Gene function is often maintained in very distant evolutionary lines. This approach allows us to extend knowledge about non-model species. I studied the influence of selection on candidate behavioral adaptation genes associated mainly with biorhythms. I was interested in comparing genetic variability between closely related species of songbirds from tropical and temperate zones. These environments differ mainly in the conditions stability. Tropical species live in very stable conditions with generally low seasonality, unlike temperate species. Timing of events of cirkanual cycle of temperate birds is essential because of the alternating of conditions of the environment. I therefore assumed a reduction in genetic variability in migrating temperate zone species compared to tropical species due to stabilizing selection. The study is based on analyzes of microsatellite loci in the exon region. I involved analysis of neutral microsatellites as a control for possible genetic variability reduction coming from different reasons than selection. Neutral microsatellites are expected to not be influenced by selection. In tropical species I found reduced genetic variability of neutral microsatellites. That might...
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Population genetics of bees
Beranová, Tereza ; Straka, Jakub (advisor) ; Munclinger, Pavel (referee)
Bees are one of the most important group of all insect, which plays a significant role in crop pollination. This bachelor thesis is review of articles, which speaks about genetic diversity of Apidae (Apoidea, Anthophila) and factors, which influence genetic diversity of this family. This thesis represents anthhropogenic impact, such as urbanization and fragmentation, and impact, which was not caused by human population, such as, climate change and parasite impact, on bee population. Part of this thesis is created by bee life overview and basic information about population genetics. The aim of this work is finding extent of declining pollinator problem, especially wild bees and also naming the bacic methods, which are used in this work. Key words: population, DNA analysis, threats, conservation genetics, bees, biogeography
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Genetic consequences of bottlenecks and population admixture in Eurasian beaver (Castor fiber)
Náhlovský, Jan ; Munclinger, Pavel (advisor) ; Hulva, Pavel (referee)
In the last few centuries beavers passed through dramatic declining of the population size followed by expansion supported by reintroductions. The genetical variability is much decreased due to this bottleneck. Current beavers possess 31 known recent mitochondrial haplotypes, among which some were described independently several times. The haplotypes form two clusters, which serve as a base for dividing beaver populations into the west and east ESU. While microsatellite loci show moderate variability, the diversity of Y chromosome loci is very low. There are only ten described alleles of the DRB second exon, which belong to the MHC loci. No mitochondrial haplotype or MHC allele is shared between relict populations. This is not noticeable in samples from the time before the bottleneck. Described subspecies are therefore only the artefact of the recent bottleneck. Newly established populations comprise in many cases beavers of various origin and are more or less admixed. It seems, that the admixed populations have higher viability and conversely in some relict populations it is possible to find the evidence of the inbreeding depression. Thus, for reintroductions it is advantageous to use individuals from several source relict populations or to use beavers from admixed populations. Several species passed...
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The use of conserved microsatellite locus for the study of the population structure of afromontain birds
Franková, Martina ; Munclinger, Pavel (advisor) ; Bartáková, Veronika (referee)
The Sky islands are alpine habitats that are geographically separated by the surrounding lowlands. These dynamic systems affect species distribution and population structure. They are also generators of diversity with a high degree of endemism and offer considerable potential to explore how different evolutionary processes lead to species formation. This work was focused on the analysis of the population structure of six species of songbirds living on the Sky islands of the Cameroon volcanic line. Conservative microsatellite loci were used for this analysis. I tested 17 conservative loci, each of them was amplified in at least 4 species. Reduced polymorphism is unlikely affected by genetic distance, but by phenomena such as genetic bottleneck, founder effect, or long-term inbreeding. Despite the higher incidence of null alleles and lower locus variability, I was able to use the data in population studies. Among the populations of endemic species Cyanomitra oritis and Arizelocichla tephrolaema, I detected an increase in genetic differentiation and near- zero gene flow between the sky islands. Conversely, species with wide distribution of Cinnyris reichenowi and Linurgus olivaceus showed extensive gene flow between sky islands. Partial isolation in sky islands was detected in Cryptospiza reichenovii and...
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Coevolution of avian ectoparasites in the tropics
Gajdošová, Magdalena ; Munclinger, Pavel (advisor) ; Votýpka, Jan (referee)
Host-parasite associations are born by cospeciations or by host switches. Feather lice have traditionally been used as model parasites for studying these events and underlying ecological factors. By now tens of analyses have addressed comparisons of host and parasite phylogenies to study cospeciations and host switches in lice, however, these analyses are strongly biased towards the temperate zone. Tropical environment could provide new insight into the origin of host-parasite interactions, because it is ecologically unique. This work aims to supplement the knowledge of host-parasite associations in lice using coevolution analyses of two feather lice genera and their passerine hosts in tropical rainforest in Cameroon. It shows that lice in the tropics cospeciate rarely. To assess whether host switches are non-random and occur preferentially between hosts with specific traits, this work also analyses relations between parasite genetic distances and hosts' trait similarities. No effect of host morphology and spatial distribution was found. However, genetic distances of the lice strongly correlate with genetic distances of their hosts.
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Avian malaria parasites and their vectors
Synek, Petr ; Munclinger, Pavel (advisor) ; Hypša, Václav (referee) ; Široký, Pavel. (referee)
Parasites causing avian malaria belong to the group Haemosporida, which represents a monophyletic group of dixenic protists within Apicomplexa. Their asexual reproduction takes place in a vertebrate intermediate host, and the formation of gametes and sporogony occur in blood-sucking dipteran insects, which are the definitive hosts of these parasites. Three main genera (Plasmodium, Haemoproteus and Leucocytozoon) are found mostly in their avian hosts. We focused on the Haemosporida of wild birds and their transmission by insect vectors in natural populations, which had previously been a neglected area. Our results were obtained both by traditional methods (investigation of infections by microscopy of blood smears) and mainly by molecular methods (e.g. nested PCR) centered around work with unique haplotypes of the haemosporid lineages. The aim of our work was to determine the range of possible insect vectors of avian haemosporidians in the territory of the Czech Republic, taking into account the specificity of the parasites within these vectors, and to describe the diversity of haemosporidians in the populations of their bird intermediate hosts. We chose four different species of birds from four orders (Passeriformes, Strigiformes, Accipitriformes, and Galliformes). As potential vectors of avian...
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