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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...
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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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Species concept in the genus Trentepohlia (Ulvophyceae, Chlorophyta): a combination of molecular and morphological approaches
Šafránková, Michala ; Škaloud, Pavel (advisor) ; Hodač, Ladislav (referee)
In this Master's thesis I engage in the problematics of the species concept of green subaerial alga Trentepohlia (Ulvophyceae, Chlorophyta). This genus has been studied intensively since the 18th century. For more than 200 years, Trentepohlia species have been delimited using various morphological criteria. However, recent molecular studies showed inadequacies in this approach Therefore, my goal was a precise morphological study of the European Trentepohlia species and the re-evaluation of their phylogenetic position using rbcL gene sequencing. During the period 2013-2015, I carried out a detailed study of the oldest references of Trentepohlia species and compiled a delimitation key of the European species. Based on this research I concluded that it would be desirable to synonymize T. odorata with T. jolithus, as well as T. uncinata with T. arborum. I also sampled Trentepohlia species within Europe and carefully studied and described their morphology. Fresh Trentepohlia thalli were molecularly characterized by cloning, which revealed a common mixture of Trentepohlia species in what on a first sight appears to be a homogenous crust. Phylogenetic analyses based on the rbcL confirmed the ongoing inconsistencies among morphologically and molecularly delimited species and also the existence of cryptic...
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Species concept in the genus Trentepohlia (Ulvophyceae, Chlorophyta): a combination of molecular and morphological approaches
Šafránková, Michala ; Škaloud, Pavel (advisor) ; Hodač, Ladislav (referee)
In this Master's thesis I engage in the problematics of the species concept of green subaerial alga Trentepohlia (Ulvophyceae, Chlorophyta). This genus has been studied intensively since the 18th century. For more than 200 years, Trentepohlia species have been delimited using various morphological criteria. However, recent molecular studies showed inadequacies in this approach Therefore, my goal was a precise morphological study of the European Trentepohlia species and the re-evaluation of their phylogenetic position using rbcL gene sequencing. During the period 2013-2015, I carried out a detailed study of the oldest references of Trentepohlia species and compiled a delimitation key of the European species. Based on this research I concluded that it would be desirable to synonymize T. odorata with T. jolithus, as well as T. uncinata with T. arborum. I also sampled Trentepohlia species within Europe and carefully studied and described their morphology. Fresh Trentepohlia thalli were molecularly characterized by cloning, which revealed a common mixture of Trentepohlia species in what on a first sight appears to be a homogenous crust. Phylogenetic analyses based on the rbcL confirmed the ongoing inconsistencies among morphologically and molecularly delimited species and also the existence of cryptic...
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Molecular diversity and species concept of subaerial green alga Trentepohlia (Ulvophyceae, Chlorophyta)
Šafránková, Michala ; Škaloud, Pavel (advisor) ; Štifterová, Anna (referee)
This Bachelor thesis discusses green subaerial algae of the genus Trentepohlia (Ulvophyceae, Chlorophyta). Firstly, I focus on general description of the family Trentepohliaceae and the genus Trentepohlia, especially on morphology, ultrastructure and reproduction. Secondly, I summarize the knowledge of the literature available about the species of the genus Trentepohlia living in the Czech Republic. I also concern with the symbiotic relationship of these algae with other organisms and with some curiosities of their growth leading to ecological and other important consequences. Finally, in this thesis I introduce the issues of the species delimitation using traditional morphological methods in contrast to molecular approaches. There are several facts resulting from this thesis. The genus Trentepohlia is a green alga of the Chlorophyta lineage curious in some aspects, mostly due to presence of some structures among the cells (such as plasmodesmatas, MLS, carotenoids, etc.). There is also a problem of determination of individual species. For almost two hundred years, this problem has been solved by use of morphological features. However, molecular methods are often in contrast to these traditional methods. Therefore, reorganization on a genus level is essential, based on the discovery of...
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Molecular methods used for taxonomy and epidemiology of dermatophytes
Čmoková, Adéla ; Hubka, Vít (advisor) ; Hamal, Petr (referee)
In my bachelor thesis I have dealt with the role and aplication of the molecular methods in the taxonomy and epidemiology of the dermatophytes and the question of the species concepts in dermatophytes. In the first part, I focused on the evaluation of the advantages and disadvantages of the recent species concepts and their problematic application in dermatophytes. The second part is focused on the molecular methods that used genetic markers for phylogenetic analysis and species delineation within dermatophytes, e.g. the PCR-RFLP method, PCR-fingerprinting and DNA sequencing. I have evaluated the dicrimination power of the particular DNA sequence loci to distinguish closely related species. In the last part, I have summarized the molecular methods that have been used in the typization at the intraspecific level, e.g. microsatelite analysis, PCR-fingerprinting, multilocus sequence typing.
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Concept of species in bears (Ursidae): practical, historical, and theoretical viewpoint
Wagner, Jan ; Fejfar, Oldřich (advisor) ; Sabol, Martin (referee) ; Musil, Rudolf (referee)
The present thesis surveys topic of taxonomic diversity and phylogeny of bears (Mammalia, Ursidae) and aspects of its contextual setting under effects of changing conceptual and methodological viewpoints. This problem is studied from several perspectives. The historical perspective is represented by a critical overview of the history of specific and infraspecific classification of bears with special respect to mutual influences of this classification and theoretical concepts of species accepted in particular periods. The perspective of material approach is exemplified by a material-based study of taxonomical and phyletic status of selected Pliocene to Middle Pleistocene ursine taxa. Along with deconstruction of some traditional hypotheses this produced a model explaining species diversification in ursine bears and its discussion in terms of factual relevance of included background concepts. In the pre-evolutionary period the bear species were usually understood broadly, as incipient immanent entities, yet exhibiting obvious certain infraspecific variability. This was established using definitions of varieties (mostly not identifiable with present subspecies or infraspecific taxa) considered as unstable modes of particular species. Although, in the post-Darwinian period, the concept and taxonomic...
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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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Molecular phylogeny and taxonomic revision of chaetophoralean algae (Chlorophyta)
CAISOVÁ, Lenka
Since the human inclination to estimate and trace natural diversity, usable species definitions as well as taxonomical systems are required. As a consequence, the first proposed classification schemes assigned the filamentous and parenchymatous taxa to the green algal order Chaetophorales sensu Wille. The introduction of ultrastructural and molecular methods provided novel insight into algal evolution and generated taxonomic revisions based on phylogenetic inference. However, until now, the number of molecular phylogenetic studies focusing on the Chaetophorales s.s. is surprisingly low. To enhance knowledge about phylogenetic relationships among taxa within the order, the nuclear?encoded SSU rDNA sequences from 30 strains covering all three chaetophoralean families have been investigated. All revealed monophyletic groupings were further screened for molecular non-homoplasious synapomorphies within the Viridiplantae. To address the question of the correspondence between morphological characters traditionally used for taxonomical delimitation of the Chaetophorales and the tree topology favored by molecular data, the list of morphological/ ultrastructural/ecological characters was elaborated and further analyzed. In addition, to obtain a close-up view into the evolution of Compensatory Base Changes (CBCs) of the second internal transcribed spacer (ITS2) which is currently often used to delimit putative biological species, 86 newly obtained/published sequences of ITS2 for five families of the order Ulvales were analyzed. Furthermore, a detailed comparative study of all ITS2 substitutions has been done. Subsequently all revealed CBCs and hemi- CBCs have been mapped upon the ITS2 phylogenetic tree topology. Finally, CBCs/hCBCs taxonomic inference in the Ulvales has been discussed.
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