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Species delimitation in Aspergillus section Candidi
Glässnerová, Kateřina ; Hubka, Vít (advisor) ; Caboň, Miroslav (referee)
Aspergillus section Candidi encompasses white- or yellow-sporulating species mostly isolated from indoor and cave environments, soil, food, feed, clinical material and dung. Their identification is non-trivial due to largely uniform morphology. This work aims to re- evaluate the species boundaries in the section Candidi and present an overview of all existing species along with information on their ecology. For this work, a set of 113 strains of different origins was gathered. DNA sequences of the genes for β-tubulin (benA), calmodulin (CaM), and the second largest subunit of RNA polymerase (RPB2) were used for molecular analyses, and species delimitation methods based on a multispecies coalescent model were applied. Classical phylogenetic methods and the genealogical concordance species recognition approach were used for comparison. Phenotypic studies involved comparisons of macromorphology on four cultivation media, seven micromorphological characters and growth in temperatures ranging from 10 to 45 řC. For the final decision about species boundaries, an integrative approach consisting of four criteria was defined, based on which seven existing and two undescribed species were supported. The revised section Candidi comprises nine species, some of which manifest a high level of intraspecific...
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Species delimitation in lobose amoebae
Foučková, Martina ; Čepička, Ivan (advisor) ; Škaloud, Pavel (referee)
Lobose amoebae - amoebas that create lobopodia - are distributed among the supergroup Amoebozoa, Excavata, Rhizaria and the genus Anaeramoeba (Eukaryota incertae sedis). For their species delimitation (i.e., pinpointing boundaries between particular species), morphological features are used most often, such as the size and shape of the cell, appearance of the hyaloplasm, pseudopodia and subpseudopodia, granuloplasm with cytoplasmatic inclusions, number and size of nuclei, shape of the uroid and cysts if present. The morphological characteristics are easily documented using a light microscope. Ultrastructural features, such as the ultrastructure of nuclei and nucleoli, surface structures, and organelles, are used as well. Nowadays, species are also described and distinguished employing molecular methods, mostly analyses of the SSU rRNA and actin genes, COI barcoding, and ITS sequences, which allow detection of cryptic species. Before the sequencing era, RFLP, RAPD and isozymes methods were also used for delimitation of species. This thesis focuses on particular methods and features used for species delimitation of lobose amoebae on the basis of 125 selected species belonging to Amoebozoa (orders Acanthamoebida, Pellitida, Himatismenida, Dermamoebida, Thecamoebida, Vannellida, Dactylopodida,...
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