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Mutation and substitution rates in sexual and asexual forms: a clue to the persistence of sex in a model group of Cobitis?
Röslein, Jan ; Janko, Karel (advisor) ; Rothová, Olga (referee)
Univerzita Karlova v Praze Přírodovědecká fakulta Studijní program: Molekulární biologie, genetika a virologie Bc. Jan Röslein Mutační a substituční tempo u sexuálních a klonáních forem: možný klíč k vysvětlení persistence sexu u modelové skupiny sekavců Mutation AND substitution rates in sexual and asexual forms: a clue to the persistence of sex in a model group of Cobitis? Typ závěrečné práce Diplomová Vedoucí závěrečné práce: Mgr. Karel Janko, Ph.D. Praha, 2015 Velký dík náleží mému školiteli Mgr. Karlu Jankovi, Ph.D. za velmi nápomocné, direktivní vedení práce. Též bych rád poděkoval panu Mgr. Janu Pačesovi, Ph.D. za více než vzdělávací rozměr v oblasti bioinformatické analýzy a Mgr. Ladislavu Pekárikovi, Ph.D., Mgr. Janu Kočímu za pomoc při analýze vybraných kapitol. Také bych rád poděkoval rodině za podporu. Všem participantům na této diplomové práci se hluboce omlouvám za způsobenou psychickou újmu. Prohlášení: Prohlašuji, že jsem závěrečnou práci zpracoval/a samostatně a že jsem uvedl/a všechny použité informační zdroje a literaturu. Tato práce ani její podstatná část nebyla předložena k získání jiného nebo stejného akademického titulu. V Praze dne 12. 8. 2015 Podpis: Abstrakt Klíčová slova: Abstract Key words: Obsah 1...
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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...
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Mutation and substitution rates in sexual and asexual forms: a clue to the persistence of sex in a model group of Cobitis?
Röslein, Jan ; Janko, Karel (advisor) ; Rothová, Olga (referee) ; Reifová, Radka (referee)
TITLE: Mutation and substitution rates in sexual and asexual forms: a clue to the persistence of sex in a model group of Cobitis? AUTOR: Jan Röslein DEPARTMENT: Ústav živočišné fyziologie a genetiky AVČR, v.v.i. SUPERVISOR: Mgr. Karel Janko, Ph.D. ABSTRACT: Subject of this thesis is to test several hypotheses about the evolution of asexual reproduction in model group of fish family Cobitis and its mutual competition among sexual and asexual forms, which touches one of the oldest unresolved issues of biology. Specifically, the work deals with the accumulation of non-synonymous mutations, which accelerated accumulation in the genome of clonal lineages theoretically leads to increased extinction compared with sexually reproducing populations (so-called. The theory of Muller's ratchet and Kondrashov's hatchet). This thesis is based on a normalized cDNA sequencing data from oocytes and liver tissue, which has served as a base matrix (generated based on non-normalized cDNA data) for transcriptome sequencing (RNAseq). Consequently, the RNAseq data have served as validation for acquired polymorphisms, detection of differential expression of allele- specific expression (ASE) hybrid biotypes. This diploma thesis balances among the edges of vast spectrum of hypotheses regarding the evolution of the genus hybrid...
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The role of northern refugia in Europe phylogeograpy
Benešová, Markéta ; Hulva, Pavel (advisor) ; Janko, Karel (referee)
Changeover between glacials and interglacial period singificantly affects species distribution for hundreds thousands years. Along with the traditional conception species distribution was restricted to refugia in southern Europe during glacials, Mediterrain, from where they recolonized northern parts of ranges after deglaciation. However, according to new findings many species could have had refugia to the north from this classical refugia, in central Europe. Northern refugia were often located in proximity of mountain systems or in rock massifs. Some species are, however, so adaptable that their dispersal was continuous even during ice ages to the north from southern refugia and they were able to live in cold regions. Even cold-adapted species contract to refugia, but instead of glacials their distribution is restricted during interglacial periods. Their ranges either contract to the north of Europe or undergo altitudinal shifts. Species can have refugia also in accordance with the gradient of oceanic-continental climate. In above mentioned types of refugia, complicated demographic processed connected with decreasing population size could take place, often resulting in speciation process.
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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...
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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...
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Parthenogenetic lizards of the genus Darevskia as an evolutionary model
Abramjan, Andran ; Frynta, Daniel (advisor) ; Janko, Karel (referee)
Several parthenogenetic lineages occur within the lizards of the genus Darevskia (Sauria: Lacertidae) which are endemic to southern Transcaucasus. High level of heterozygosity, cause by thein hybrid origin, is one of the crucial aspects of thein evolutionary potential, as well as the asexual reproduction. Heterosis on one side is in the opposition to the outbreeding depression and genetic uniformity of the clones on the other side. Aim of this work is to evaluace if these aspects influence viability of parthenogenetic species and differ them from the sexual ones. We chose the amount of asymmetries as a measure of developmental instability, which we studied on three meristic characters. We also evaluated the pattern of asymmetries in lateral blue spots, which are of signaling importace in lacertid lizards. Our results suggest that there isn't significant difference between parthenogenetic and sexual species in developmental stability, but the sexual ones are more sensitive to population changes. Absence of males may have perhaps the greatest influence on coloration, resulting in loss of symmetry in the blue spots.
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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...
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Phylogeography of Pipistrellus pipistrellus species complex
Chudárková, Adéla ; Hulva, Pavel (advisor) ; Janko, Karel (referee)
(in English) Pipistrellus pipistrellus species complex contains two sympatric species inhabiting Europe and part of West and Central Asia (Pipistrellus pipistrellus s. str, Pipistrellus pygmaeus s. str) and several other lines, isolated in the Mediterranean (North Africa, islands and peninsulas of the Mediterranean Sea). This taxon is a part of the extensive radiation within the genus Pipistrellus, which in today's concept includes about 30 species. Mosaic line of P. pipistrellus complex, located at different stages of diversification and secondary contacts in the Mediterranean biodiversity hotspot, is a suitable model for research on speciation. In this thesis we focused on analyses of distribution, phylogeography, population structure and demography based on mitochondrial data from 323 individuals, representing almost the entire range. Control region of mitochondrial DNA was chosen as a genetic marker. Variability in the 378 pb long fragment acknowledged the existence of several genetically distinct lines whose species status is discussed. Observed fylogeografic pattern confirms the existence of groups of radiation centers in the Mediterranean region. An allopatric speciation was there, two of the lines (P. pipistrellus s. str and P. pygmaeus s. str.) later expanded into Europe and their ranges...
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Lost sex: multilocus DNA evolution the hybrid fish complex C.taenia (Teleostei)
Choleva, Lukáš ; Janko, Karel (advisor) ; Mikulíček, Peter (referee) ; Hulva, Pavel (referee)
12 General summary "It is unwise to intrude the suggestion of parthenogenesis, even of a modified sort, into vertebrate literatures. The phenomenon is so at variance with what is known and beleived about vertebrates development that I am sure no vertebrate morphologists would admit for a moment that the natural development from egg to sexual maturity of an individual vertebrate without the direct inclusion of the male element is within the realm of probability", reacted the morphologist Howell (1933. Science 77: 389-390) sarcastically on the discovery of the first recognized asexual vertebrate, a live-bearing fish Poecilia formosa (Hubbs et Hubbs 1932. Science 30: 628-630). "The examples of parthenogenesis has been reported in almost all vertebrate groups," (Lampert 2008. Sexual Development 2: 290-301). The ongoing effort to explain the widespread occurrence of sexual reproduction among animals is often called the "queen of problems in evolutionary biology", and there is still no consensus regarding the explanation. Simultaneously, asexual reproduction exists among some animals. Here, the 'asexuality' refers to any reproductive process that does not involve sex (Mendelian meiosis is mising), except self-fertilization. One individuum produces a progeny genetically identical to its parent, except those sites...
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