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Genetic diversity within pennate diatoms: implications for taxonomy and ecology.
Urbánková, Pavla ; Kulichová, Jana (advisor) ; Trobajo, Rosa (referee) ; Poulíčková, Aloisie (referee)
In past decades, molecular methods helped to discover extensive diversity hidden in mor- phologically delimited diatom species. Diatom taxonomy awaits revision and molecular meth- ods will play an important role in this pursuit. DNA-barcoding is a relatively cheap and rapid way to incorporate molecular data in the diatomological research.The crucial step, which deter- mines its efficiency, is marker selection. Therefore, we examined the performance of candidate barcode markers in the model genus Frustulia. Molecular data from the study helped to sup- port delimitation of two new species, Frustulia curvata and Frustulia paulii. Similar to previous research, the best-performing markers were part of the large ribosomal subunit and part of the RUBISCO gene. We encountered a case where these two markers disagreed. Similar gene tree discordances might compromise molecular species delimitation, which is based on single molecular loci. The use of both markers in a dual-locus barcode can mitigate the risk and draw attention to problematic cases that merit further study. However, the superior mean of spe- cies delimitation, which we used to set species limits in the complex Eunotia bilunaris-flexuosa, provides algorithms that use multiple loci and accommodate our understanding of molecular evolution. Several...
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Molecular variability and distribution of the Frustulia rhomboides species complex (Bacillariophyceae)
Urbánková, Pavla ; Kulichová, Jana (advisor) ; Bešta, Tomáš (referee)
Recent use of molecular methods to revisit taxonomically problematic diatom species revealed severe limitations of morphological species concept. Characterization of diatom species which was based solely on the morphology of their frustules often generated too broad species boundaries which inevitably lead to wrong conclusions about their ecology and distribution. Widespread opinion that many diatom species are cosmopolitan generalists resulted in a theory that dispersal of diatoms is not limited by geographical distance. However, a number of recent studies showed that dispersal of diatoms is governed by the same rules which matter for macroorganisms. Proposed master thesis addresses the topic of diversity and dispersal in diatom species complex Frustulia rhomboides sensu lato in Europe and New Zealand. Results suggest that: (1) although revealed molecular variability in this complex shows clear ecological and biogeographical signal, it is not correlated in morphology. This is another support to general need for adoption of different species concept in diatoms. (2) A considerably uneven ratio in species diversity of genus Frustulia found in ecological similar habitats in Europe and New Zealand supports the idea that diatom dispersal is limited and stressed the need for studies dealing with biogeography.
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Sexual incompatibility of protist cryptic species
Jelínková, Lucie ; Škaloud, Pavel (advisor) ; Urbánková, Pavla (referee)
The systematic and the evolutionary biology attempt to define a species category or a species taxon from the beginning of their existence. Specific taxons are considered species on the base of different criteria, so on the base of different species concepts. Most of these concepts emerged previous century. The biological species concept has been assumed to be most important species concept for dozens of times. It was based on a presence of the reproduction isolation of two species. However, its applicability was questioned by the existence of many asexual lineages and also the lineages with a large degree of hybridization between an approved species. This thesis is trying to give a description of the biological species concept and its changes during the time. And it is also trying to answer the question of its simultaneous usability for protist.
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Genetic diversity within pennate diatoms: implications for taxonomy and ecology.
Urbánková, Pavla ; Kulichová, Jana (advisor) ; Trobajo, Rosa (referee) ; Poulíčková, Aloisie (referee)
In past decades, molecular methods helped to discover extensive diversity hidden in mor- phologically delimited diatom species. Diatom taxonomy awaits revision and molecular meth- ods will play an important role in this pursuit. DNA-barcoding is a relatively cheap and rapid way to incorporate molecular data in the diatomological research.The crucial step, which deter- mines its efficiency, is marker selection. Therefore, we examined the performance of candidate barcode markers in the model genus Frustulia. Molecular data from the study helped to sup- port delimitation of two new species, Frustulia curvata and Frustulia paulii. Similar to previous research, the best-performing markers were part of the large ribosomal subunit and part of the RUBISCO gene. We encountered a case where these two markers disagreed. Similar gene tree discordances might compromise molecular species delimitation, which is based on single molecular loci. The use of both markers in a dual-locus barcode can mitigate the risk and draw attention to problematic cases that merit further study. However, the superior mean of spe- cies delimitation, which we used to set species limits in the complex Eunotia bilunaris-flexuosa, provides algorithms that use multiple loci and accommodate our understanding of molecular evolution. Several...
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Dispersal mechanisms of protists
Křivská, Lucie ; Škaloud, Pavel (advisor) ; Urbánková, Pavla (referee)
Protists are ubiquitous organisms, they are main particles in foodchains, but they also cause many economical problems in areas of healthcare, agriculture and in food industry. Their biogeography is discussed in many academical debates and even that our methods are relatively advanced, there is still not only one accepted theory but two of them. However it is true that the moderate endemicity model is probably the correct one. This text sums up our existing knowledge in the field of protist distribution and their dispersal over whole planet, in terrestrial and aquatic environments. Mechanisms of dispersal are very coplicated and complex problematics. The resting stages are also important for successful dispersal, not only as a reaction to unfavourable conditions. Dispersal is affected by climatic conditions in investigated area and thus it is not easy to predict the patterns of dispersal. Human influence is getting more important on biogeography of microorganisms, including the history. This topic is becoming more popular these days as it becomes obvious it is importnat to know the patterns of dispersal. There are also adaptations and tolerances discussed. Keywords: environmental factors, dispersal, distribution, endemic species
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Applications of diatom and chrysophyte silica structures in nanotechnologies
Burýšková, Barbora ; Němcová, Yvonne (advisor) ; Urbánková, Pavla (referee)
Diatoms and chrysophytes are single-celled organisms who have mastered the ability of controlling the biomineralization process. By incorporating silicon into their cell walls diatoms are able to create elaborate 3D silica structures with hierarchically ordered patterns and pores at the nano- to millimetre scale. In nature, diatoms inhabit almost all aqutic and aeroterrestrial environments. They play an important role in the global biogeochemichal silicon cycle and contribute significantly to oceanic primary production. The morphology of diatom cell walls (frustules) is species specific and the frustules exhibit unique photonic, optical and mechanical properties. There are more than 12 000 diatom species on earth, which represents the vast diversity of silica frustule shapes, applicable in nanotechnologies. However, only a few species have been used in experimental praxis so far. The cells of silicifying chrysophytes are covered with scales composed of the same material as the diatom frustules. The potentional use of chrysophyte silica scales in nanotechnologies is in the early stages of investigation. The aim of this bachelor's thesis is to recapitulate the findings on diatom and chrysophyte silica structures use in emerging nanotechnology applications, and to summarize published information on...
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Diversity of the genus Frustulia in northern Europe
Scharfen, Vojtěch ; Urbánková, Pavla (advisor) ; Veselá, Jana (referee)
Genus Frustulia was chosen for this work due to the continuity of the previous research of our phycological group. Using molecular techniques, it was found that a number of morphologically defined species of diatoms is cryptic species complex, which may have limited dispersal. The aim of this study was to: 1) evaluate the diversity of the genus Frustulia in northern Europe by molecular methods and classify found species in the phylogenetic context of related species; 2) find out if it possible to identify the isolated species in natural samples by using morphological characters. There have been analyzed 234 strains by molecular methods. Isolated ones were in four clades. 86 % of the strains belonged to a generic complex F. crassinervia-saxonica. Two strains were identified as species F. gaertnerae and F. septentrionalis. The last line was not described yet so it was labeled as F. sp. This line is closely related to the species F. maoriana, which is considered to be endemic in New Zealand. Phylogeny of the genus was created based on a dataset of four molecular markers. Published morphometric data were then compared with 264 cells photos taken by scanning electron microscope. There was done surveillance comparison of the results of the analysis of quantitative and qualitative characters with...
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Sexual incompatibility of protist cryptic species
Jelínková, Lucie ; Škaloud, Pavel (advisor) ; Urbánková, Pavla (referee)
The systematic and the evolutionary biology attempt to define a species category or a species taxon from the beginning of their existence. Specific taxons are considered species on the base of different criteria, so on the base of different species concepts. Most of these concepts emerged previous century. The biological species concept has been assumed to be most important species concept for dozens of times. It was based on a presence of the reproduction isolation of two species. However, its applicability was questioned by the existence of many asexual lineages and also the lineages with a large degree of hybridization between an approved species. This thesis is trying to give a description of the biological species concept and its changes during the time. And it is also trying to answer the question of its simultaneous usability for protist.
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