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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...
triggers of asexual reproduction: on the crosslink between hybridization, asexuality, polyploidy and speciation on example of Cobitidae loaches
Marta, Anatolie ; Janko, Karel (advisor) ; Arai, Katsutoshi (referee) ; Trachtulec, Zdeněk (referee)
(in English) Sexual reproduction is considered a nearly universal feature of all eukaryotic organisms and has been hypothesized to be their ancestral state. Sexual reproduction is mainly represented by meiotic division, recombination, production of haploid gametes and fertilization. Although molecular and cytological mechanisms underlying meiosis are highly conservative they may be disrupted in numerous ways leading to the emergence of so-called asexual lineages. The proximate origins of asexuality may differ for particular taxa. In vertebrates, asexuality frequently is triggered by interspecific hybridization. Nowadays "classical" theories predict that asexuals should not be able to persist on a long-term evolutionary scale. However, the hybrid lineages have to overcome short-term disadvantages, such as postzygotic barriers ranging from complete hybrid sterility to altered meiosis resulting in asexual reproduction and even ploidy elevation. Despite that hybrid sterility is one of the most common outcomes of interspecific hybridization, however various lineages found their ways to alleviate these problems and produce viable clonal gametes. The knowledge about proximate mechanisms of unreduced gamete formation in asexual lineages is very limited as many studies were restricted due to methodological...
Phylogeography of Rousettus aegyptiacus in the Mediterranean region
Dundarova, Cheliana ; Hulva, Pavel (advisor) ; Janko, Karel (referee)
The genus Rousettus has distributional pattern unique among fruitbats comprising both Asia and Africa and reaching northern distributional limits of the family in Persia, Arabia and Mediterranean basin. This could be ascribed to the ability of echolocation, consequent cave dwelling, and presumably other site-specific adaptations, which enabled dispersal independent of forest block and surviving in Mediterranean type of climate. Using fastly evolving mitochondrial marker, we aimed to assess genetic variability, its geographic distribution and demography of northern populations of the Egyptian fruitbat (Rousettus aegyptiacus). Mitochondrial network indicates deep genetic divergence between disjunct Mediterranean and eastern African parts of the range. Basal position of Sinaic and Jordanian haplotypes within northern clade indicate important role of these regions in colonization of eastern Mediterranean. Generally, the northern haplogroup is moderately diversified with partial geographic localization of particular haplotypes. Significant isolation by distance pattern suggests relatively pronounced site fidelity of particular colonies, at least in terms of maternal gene flow. Landscape genetics analyses indicate discontinuities in distribution of mitochondrial genetic variability, in some cases correlating with...
The role of ecological factors in maintenance of sexuality
Toman, Jan ; Flegr, Jaroslav (advisor) ; Janko, Karel (referee)
The existence and widespread distribution of sexual reproduction despite its obvious disadvantages is an evolutionary enigma. According to the theory of frozen plasticity, the evolution of sexual and asexual species is fundamentally different. One of the implications of this theory are different ecological preferences of these species. Sexual species should prefer biotically and abiotically variable environments because of their ability to quickly and reversibly respond to unpredictable changes. On the other hand, asexual species should prosper in biotically and abiotically stable environments because of their ability to perfectly adapt even to extreme environmental factors in the long term. I decided to test these predictions in the metastudy comparing ancient asexual clades (in which we can be sure about their obligate asexuality and evolutionary longevity) with their sexual sister or closely related ecologically comparable clades. The hypothesis of the preference of asexual species to biotically and abiotically homogenous environments was supported by the results of this metastudy. On the other hand, the hypothesis of supposed ability of asexual species to perfectly adapt to a broader range of environmental conditions, tested on the comparison of temperature ranges of activity of previously...
Evolutionary history of hedgehogs from genus>Erinaceus
Černá Bolfíková, Barbora ; Hulva, Pavel (advisor) ; Janko, Karel (referee) ; Kryštufek, Boris (referee)
Hedgehogs from the genus Erinaceus are extremely interesting and suitable model organisms for studying impacts of climatic changes during Pleistocene on species and speciation processes. Erinaceus europaeus and E. roumanicus, which have diverged in southern refugia, formed a secondary contact zone in Central Europe. The widest part of this zone is situated in Czech Republic. Our work benefits from this position and processes that take place here such as reinforcement, character displacement and hybridization are discussed. Moreover, we addressed several questions about biological invasions and topics connected to peripatric processes. Using combination of nuclear and mitochondrial DNA we detected differences in population structure between the species and also between sexes. E roumanicus is mainly restricted to lowlands. Ranges of both species expand and hybridization may play role during formation of reproductive isolation. We did not observed ecological character displacement when using 3D geometric morphometry approaches. Populations in sympatry are more similar than in allopatry. Our data are enhanced by description of parasite fauna of sympatrical populations and we discuss the role which they may play in evolution of the hedgehogs. Study proceeded in New Zealand was based on comparison of...
Species limits within Aspergillus section Restricti inferred from multiple gene phylogenies and phenotype analysis
Sklenář, František ; Hubka, Vít (advisor) ; Janko, Karel (referee)
Section Restricti is one of the last sections of the genus Aspergillus that hasn't been revised in the modern taxonomic era. All species are osmophilic, have simple morphology and they are mainly important because of the food, feed and seed spoilage, some of them also have negative influence to the indoor air. The section consists of seven species according to the last taxonomic revision from 2008 based only on molecular data. It currently consists of six asexual and one homothalic species. 126 isolates from the section coming from four continents were studied in this thesis, including ex-type strains. Revision of the section was carried out combining molecular phylogenetic analysis and conventional taxonomic methods. Modern methods of species delimitation based on multispecies coalescent model were used for the phylogenetic reconstruction. From the conventional methods analysis of morphology (macro- and micromorphology including scanning electron microscopy) and physiology (ability of growing in osmotic gradient and several different temperatures) was performed. Apart from the seven known species, eight new undescribed species were discovered. Majority of the new species belongs to the Aspergillus penicillioides species complex. Key words: Aspergillus restrictus, osmophilic fungi, species...
The effect of climatic changes on genetic build-up of populations and their role in promoting adaptive radiations
Štefková Kašparová, Eva ; Janko, Karel (advisor) ; Šabacká, Marie (referee) ; Hulva, Pavel (referee)
The Southern Ocean and its enormously cold, remote and yet the wildest continent, the Antarctic, have experienced numerous rapid climatic changes. It used to be viewed as a barren wasteland with limited knowledge of species diversity or phylogeography. Recently, all aforementioned premises are being increasingly questioned, and this thesis aims to shed light on them. Firstly, multi-locus genetic markers were used to evaluate if it is the lifestyle, benthic or pelagic, including the duration of the pelagic larval period that determines the population connectivity of particular notothenioid species. It was the adult's fish lifestyle along with the oceanographic factors that are responsible for the gene flow between localities. Secondly, is lifestyle a factor determining the extent to which Pleistocene growing grounded ice sheet affected species past population dynamics? The attention was paid to Notothenioidea fish, then to Echinoidea sea urchins, and lastly to NCBI database available antarctic marine shelf and deep-sea fauna. Our findings suggest that the last glacial maximum affected more profoundly the population size of benthic shelf species. At the same time, those living in the water column or inhabiting deep slopes had more ancient population size changes. The Antarctic terrestrial evolution...
Genomic architecture and molecular mechanisms of hybrid sterility in mice.
Vališková, Barbora ; Forejt, Jiří (advisor) ; Janko, Karel (referee) ; Macholán, Miloš (referee)
Hybrid sterility is one of the reproductive isolation mechanisms restricting gene flow between the related species and leading to speciation. PR domain containing 9 (Prdm9), the only known vertebrate hybrid sterility gene, determines the sites of programmed DNA double-strand breaks (DSBs) and thus specifies hotspots of meiotic recombination but in hybrids between two mouse subspecies causes failure of meiotic chromosome synapsis and hybrid male sterility. In the present study on sterile hybrids, the five smallest autosomes were more prone to asynapsis. To manipulate with the synapsis rate, random stretches of consubspecific homology were inserted into several autosomal pairs. Twenty seven or more megabases of consubspecific sequence fully restore synapsis in a given autosome. Further, at least two symetric DN double-strand breaks per chromosome were necessary for successful synapsis. Moreover, F1 hybrids had sperm when synapsis was rescued in at least three of four segregating chromosomes. To verify the assumption of a lack of symmetric DSBs in meiotic chromosomes of sterile males the chemotherapeutic drug cisplatin was used to induce exogenous DNA DSBs. Cells treated with 5 mg/kg and 10 mg/kg of cisplatin showed increased number of DSBs monitored by immunostaining of RPA and DMC1 sites and...
Historical record of the fairyshrimp Branchinecta gaini in the James Ross archipelago, and its phylogeography
Pokorný, Matěj ; Sacherová, Veronika (advisor) ; Janko, Karel (referee)
The Fairy shrimp Branchinecta gaini Daday, 1910 is the largest freshwater invertebrate in Antarctica and the top-level consumer of local freshwater food webs. Ecological demands of B. gaini that are accompanied by 'ruderal' life strategy together with its spatial distribution that exceeds to Patagonia indicate that it had survived last glacial period in South America and expanded to Antarctica shortly after this epoch endeed. On James Ross Island that is the most extreme environment where B. gaini occurs today was this fairy shrimp considered extinct until year 2008. Its disappearance was based on paleolimnological analysis of several lake sediment cores according to which it inhabited this island between years 4200 to approximately 1500 before present when it died out because of changes in lake catchments caused by harsh neoglacial conditions. Paleolimnological analysis of Monolith Lake presented in this study has shown that this assumption was wrong and B. gaini has lived on James Ross Island throughout neoglacial period up to recent time. Phylogeographic analysis of 16S rDNA of specimens from Patagonia, South Orkneys, South Shetlands and James Ross Island revealed that its high morphological diversity is not supported by this gene and that all examined populations of B. gaini is one species with very few...

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1 Janko, Kristian