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Barcoding společenstva makrozoobentosu Křesánovského potoka
PEJCHAROVÁ, Eliška
Molecular genetic methods, including barcoding, have been increasingly utilized in recent years for the analysis of communities of macrozoobenthos and many other organisms. Morphological identification of precise species of mayflies, caddisflies, or stoneflies in their larval stage is demanding and requires a significant amount of time and expertise. Barcoding analysis can help to classify disputed species more accurately. The aim of this thesis is to use the barcoding method to determine selected representatives of macrozoobenthos and verify the morphological determination of macrozoobenthos representatives. The studied locality is Křesánovský Stream in southern Bohemia. DNA was extracted from the collected samples and using mitochondrial gene CO1 and primer pairs LCO1490, HCO2198, jgLOC1490, and jgHCO2198, sequences were created and tested in the BLAST program. The most similar sequences from publicly available databases were obtained, compared to sequences from this thesis and the exact species were subsequently determined. A total of 57 samples were studied, from which 29 species were morphologically identified (six species of mayflies, eight species of caddisflies, seven species of stoneflies, three representatives of beetles, four species of dipterans, and one specimen of Gammarus fossarum), and 30 species were identified through barcoding (11 species of mayflies, eight species of caddisflies, five species of stoneflies, two species of dipterans, three species of beetles, and one species of fleas). Morphological determination was successful in 63% of cases. The success rate was 74% for mayflies, 67% for caddisflies, 33% for stoneflies, and 25% for dipterans. The specimen of Gammarus fossarum was morphologically identified correctly. Barcoding appears to be a suitable method for studying macrozoobenthos and an excellent complement to morphological analysis of samples. However, it has its limitations, and it is not appropriate to consider it as the sole method for determining macrozoobenthos samples.
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Barcoding of Czech butterflies
ŠKOPEK, Patrik
The aim of this thesis was to extract DNA of Czech butterflies and sequence their mitochondrial gene cytochrome c oxidase subunit I (i.e., the barcode), in order to uncover their genetic and intraspecific relationships and geographical differences. Moreover, I compared the sequences with data from other European countries. I extracted DNA from butterfly legs, amplified the target DNA fragment with PCR (polymerase chain reaction), and check the PCR product quality on an agarose gel. PCR products were sequenced. In total, I collated 500 sequences from 87 species (61.7% of the Czech fauna). Phylogenetic trees were built by maximum likelihood and Bayesian inference methods. To reveal the potential cryptic diversity and lineages, I used GMYC analysis. The results of GMYC were distributed into four groups: 71 species (81.6%) contained a single entity, two species pairs (4.6%) were merged into two entities, 10 species (11.5%) were split into more entities (potential cryptic diversity) and two species (2.3%) were both split and merged with a different species. To Czech samples of 33 Lycaenid species, I added database samples from Romania and Germany. Their relationships were compared based on a phylogenetic tree. In the case of 10 species (30.3%), data from one country was missing. In 19 species (57.7%), the Czech samples were related to both Romanian and German samples. One species (3%) was related to Romanian samples and one species to German samples. Two Czech species (6%) formed a separate branch in the tree. This work served as a preliminary study into the Czech butterfly mitochondrial diversity and barcoding efficacy, but more data is needed to complete the study.
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Analýza chromosomu W u skvrnopásníka lískového, \kur{Lomaspilis marginata}
DEMKOVÁ, Miriam
The aim of this master thesis was to analyse variability of sex chromosomes in Lomaspilis marginata (Geometridae). Several families of this species were tested for the presence of sex chromatin and also for their variability in the W chromosome composition using comparative genomic hybridization. My results of this study indicated existence of at least three different types of the W chromosome in the investigated species.
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Identifikace forenzně významných druhů hmyzu s výskytem v chladných měsících
Skoupá, Kristýna
The identification of insect inhabiting dead bodies is particularly relevant in the area of forensic science, especially for post-mortem interval determination, as evidence of post-mortem manipulation of the body, evidence of the presence of toxic substances, etc. This work deals with the determination of forensically important insects occurring in cold months and extreme conditions based on molecular-genetic analyzes. For this purpose, were established 3 experimental fields in Brno-venkov and Blansko district and at the bottom of the Macocha Abyss with a specific cave microclimate. DNA isolation was performed, amplified the cytochromoxidase I gene and sequenced this part of mitochondrial DNA of insect specimens. Then the sequence was compared to the BLAST and BOLD databases, the BOLD showing a higher percentage of matching. This way, were identified 24 insect species from a total of 13 different families. The most of the trapped insects formed Calliphora vicina and Calliphora vomitoria, typical representatives of winter necrophagous fauna.
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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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Fylogeneze, diverzita, distribuce a hostitelská specifita parazitů Haemoproteus spp. (Apicomplexa: Haemosporida: Haemoproteidae) u suchozemských želv Palearktu.
MARŠÍKOVÁ, Aneta
This study provides unique data on distribution, prevalence, host specificity, phylogeny, and intraspecific variability of two Haemoproteus species of Palearctic tortoises. Analyses based on cytochrome b sequences confirm the existence of two monophyletic lineages/species of Haemoproteus infecting Testudo tortoises. Microscopically, the species corresponding to H. anatolicum was revealed in blood smears of T. graeca, and H. caucasica was detected in two tortoise species, T. graeca and T. horsfieldii.
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Application of DNA barcoding on genus \kur{Folsomia} (Collembola) and mitochondrial geonome of \kur{F. candida}
SLÁMOVÁ, Martina
Mitochondrial molecular marker COI was tested for use in species identification of selected species of genus Folsomia (Collembola). Marker was succesfuly amplified and sequenced. Dendrogram constructed by Neighbor-Joining method with Kimura-2-Parameter model grouped all individuals into presumed species clusters and high intraspecific variability of F. quadrioculata suggests the existence of cryptic species. Furthermore, 65 % of mitochondrial geonome of F. candida was obtained with 16 tRNA genes, 9 proteincoding genes and 2 rRNA genes identified. So far the genome characteristics correspond to the one described in G. hodgsoni.
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