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Gene order conservation in bacterial genomes
Martinková, Tereza ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
Theoretical part of the thesis deals with basic concepts such as bacterial genome, comparative genomics and mainly synteny blocks. Here is explained what synteny is and what is its importance. In the theoretical part, the GenBank format is also mentioned, its content and usage. The practical part is focused on searching similarities in DNA sequences of reference bacteria with selected bacteria, their sorting by means of greedy algorithm and visualization of similarities using phylogenetic tree.
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Phylogeny and phylogeography of the cyprinid fish genus Pelasgus (Teleostei: Cyprinidae)
Viñuela Rodríguez, Nuria ; Vukićová, Jasna (advisor) ; Rovatsos, Michail (referee)
The genus Pelasgus (Cyprinidae) is endemic to the southern part of the Balkan Peninsula and includes seven species. In this work, a multilocus approach has been applied to study phylogenetic relationships between the species and their populations and to revise their distribution areas. 180 specimens from 47 localities from 30 river drainages were analyzed, comprehensively covering the distribution range of the genus. Moreover, samples from type localities of all species were included in the analyses. Mitochondrial (cytochrome b) and nuclear markers (the first intron of ribosomal protein S7, recombination activating gene RAG1 and rhodopsin) were used. Existence of seven well supported lineages was revealed based on cytochrome b, which is the most variable marker. These lineages correspond to P. laconicus, P. marathonicus, P. minutus, P. stymphalicus, P. thesproticus, P. prespensis and Pelasgus sp. The most variable nuclear marker was first intron of S7, which provides almost the same results as cytochrome b, revealing six well supported lineages, whereas RAG1 and rhodopsin appear to be less informative, revealing only four well supported clades. These markers did not separate several species (P. marathonicus, P. stymphalicus, P. thesproticus, and Pelasgus sp.) due to low variability of the markers...
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Germination requirements of rare and common plant species of Giant Mountains
Paulů, Andrea ; Münzbergová, Zuzana (advisor) ; Moravcová, Lenka (referee)
For a long time studies were focused on searching optimal conditions of germination of individual species. During the last few years studies have started to search for a relationship between germination and various species characteristics. Most of them, however, use only one temperature during germination tests. Very few studies use more than one temperature during the germination tests. In the last years studies started also to compare germination between rare and common species, but these studies compare just a few species. There are no studies which would compare germination on broader range of species. Aim of this study was to indentify which factors are determing germination of species and to find relationships between germination and characteristics of rare species (n=62). Another aim was to find out differences in germination of pairs (n=24) of closely related rare and common species. To test the germination I have chosen a methodology with several consecutive temperatures. Throughout the time of testing , the seeds were placed either in light or in dark. The dataset was processed by linear regression. The results show that germination requirements of species are determinet by time of flowering, weight of seeds, dispersal mode, species requirements for soil humidity and nutrients and type of...
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Review of the phylogenetic hypotheses of Cobitoidea
Dvořák, Tomáš ; Ráb, Petr (advisor) ; Musilová, Zuzana (referee)
Phylogenetics is a field of systematic biology which aims to uncover the evolutionary relations betweenll species on the principle of finding their common ancestor. Phylogeny can be applied on many diferent markers, but among the most common are genetic and morphological ones. The results of the phylogenetic analyses can be applied in many other fields of research. We can use them e.g. in answering questions concerning geological events (when using fishes as model, most often in some river flow changes). Cobitoidea is a superfamily of fishes, which belongs to cypriniformes - the biggest group of primary freshwater fishes. Cobitoidea contain 10 families - Gyrinocheilidae, Cobitidae, Balitoridae, Botiidae, Vaillantellidae, Ellopostomatidae, Barbuccidae, Serpenticobitidae, Nemacheilidae, Gastromyzontidae, and the Catostomidae might be considered as belonging into Cobitoidea as 11th family. The distribution area of Cobitoidea covers almoust whole Europe and Asia and that of Catostomidae also North America. There is no major river system in whole Eurasia that would not be inhabited by loaches. Every major river basin contains one to tens of loach species, therefore loaches can be considered one of the most characteristic element of the Eurasian freshwater fauna. In Cobitoidea, we can also find many...
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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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The use of environmental sequencing in the studies on eukaryotic diversity
Lukešová, Soňa ; Hampl, Vladimír (advisor) ; Škaloud, Pavel (referee)
The bachelor's thesis focuses on environmental sequencing method and its usage in examining the diversity of microbial eukaryotic organisms. It describes the method, its mechanism, application and the problems associated with it. The work describes the current view of the phylogeny of the major eukaryotic lineages with their closer characteristics. Particular attention is paid to newly discovered groups. The work addresses the relationships inside these groups, summarizes findings of their ecology, food resources, and morphology. A separate chapter is devoted to the occurrence of the protist groups in extreme environmental conditions. Key words: Diversity of eukaryotes, environmental DNA, sequencing, rRNA, phylogenetics.
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Fylogeneze vybraných druhů letounů Afriky na základě cytogenetického a molekulárního přístupu
Koubínová, Darina ; Zima, Jan (advisor) ; Macholán, Miloš (referee) ; Martínková, Natália (referee)
Phylogenetic relationships of a sample comprising 248 bats belonging to 19 species and four families (Hipposideridae, Rhinolophidae, Molossidae and Vespertilionidae) from Senegal (Western Africa) were investigated with the use of multi-locus sequence data and non- differentially stained chromosomes. The karyotypes of Hipposideros ruber, H. tephrus, H. jonesi and H. cyclops were described for the first time. The standard Hipposideros formula was recorded in H. tephrus, H. jonesi and H. ruber (2n = 32, FNa = 60, FN = 64). The karyotypes of H. cyclops (2n = 36, FN = 66) and H. gigas (2n = 52, FN = 64) substantially diverged from this typical chromosomal complement. Rhinolophus landeri and R. fumigatus shared the same diploid number (2n = 58), but differed in the chromosome morphology (R. fumigatus - FNa = 60, FN = 64; R. landeri - FNa = 64, FN = 68). Rhinolophus landeri was found karyotypically distinct to other African populations, thus signalling a possible presence of cryptic forms within this species. The karyotypes of Chaerephon pumilus and Mops condylurus had a 2n = 48, FN = 54 and were similar to other previously studied species of this chromosomally conservative family. Chromosomal, Bayesian, maximum likelihood and genetic distance analyses revealed an indication for the existence of cryptic...
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Ultrastructure of eustigmatophycean algae
Fišerová, Melánie ; Němcová, Yvonne (advisor) ; Hyliš, Miroslav (referee)
In 1971, the algal class Eustigmatophyceae, Stramenopiles, was detached by Hibberd and Leedale from the class Xanthophyceae, Stramenopiles, on the basis of prominent ultrastructural differences in vegetative cells and more importantly in zoospores, such as the presence of big extraplastidial stigma. The class was divided into four families, six genera and twelve species. It seems so far, that there is a deep dichotomy within the class. Eliáš et al. (unpublished) recom- mend to establish two orders based on molecular sequencing of 18S rDNA and rbcL: Eustigmatales (sen- su Eustigmatophyceae described by Hibberd) and Goniochloridales (order containing Goniochloris, Pseu- dostaurastrum and undescribed relatives). The order Eustigmatales is divided into three separate lineages, most likely families: Eustigmataceae (A1), Monodopsidaceae (A2) and a new family Pseudellipsoidiona- ceae (A3). In this study the ultrastructure of 10 eustigmatophycean strains from three separate lineages was investigated. The typical characteristics of this class as chloroplast without a girdle lamella, a reddish glo- bule and lamellate vesicles were found in all strains studied. The appearance of the lamellate vesicles was found to change during the life cycle. My research indicates that other characteristics, formerly...
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Diversity, distribution and genetic structure of the tribe Pipistrellini
Eliášová, Kristýna ; Hulva, Pavel (advisor) ; Fornůsková, Alena (referee)
This literature review discusses phylogenetic relationships within the family Vespertilionidae with a detailed focus on tribus Pipistrellini relations and then the individual genera and species within this tribe. A historical summary of efforts to resolve the phylogenetic relationships within the taxon first on the basis of morphological studies, comparison of karyotype and most recently on the basis of genetic markers. Mitochondrial genetic markers are useful in studying phylogeography, as this paper shows on the example of the Pipistrellus species complex and on species Nyctalus azoreum, Nyctalus leisleri, Nyctalus noctula and Pipistrellus abramus. Furthermore, this work describes the current distribution of individual taxa of tribe, the fossil record and migration behavior of European temperate species in the context of their population structure (also studied in some species using mtDNA and microsatellites) and Annex shows the areas extending all five genera Pipistrellini tribe. Key words: Pipistrellini, phylogenenetics, phylogeography, distribution, population structure
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Genome size evolution in the Zingiberaceae
Pospíšilová, Monika ; Fér, Tomáš (advisor) ; Kolář, Filip (referee)
The purpose of this study is to evaluate the existing knowledge on the evolution of genome size and also to focus on genome in the phylogenetic context. Among angiosperms we find a wide range of C-values (1C = 0.63 pg ? 1C = 127.4 pg), but the modal value is 0.6 pg. We still do not know much about the nature and mechanisms of plant genome size evolution, but we are learning more and more every year. There are already dozens of studies dealing with the dynamics of genome size of smaller taxonomic groups and on four of these they demonstrate possible approaches. Researching within higher taxonomic groups such as families is difficult and so more valuable. New research on the evolution of genome size in the family Zingiberaceae has started and my master thesis dealing with the Globbeae tribe should be part of it.
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