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Interspecific hybridization in Acrocephalus warblers.
Majerová, Veronika ; Reifová, Radka (advisor) ; Kotlík, Petr (referee)
Acrocephalus warblers have gone through the adaptive radiation during last severalmillion years, which gave rise to thirty one species occupying mainly Eurasia,Africa and Australia. The majority of species are morphologically very similar,however, they differ in ecological requirements, migration strategy, and song.Interspecific hybridization seems to be quite common among Acrocephaluswarblers, not only between sister species, but also between more distantly relatedtaxa. The main goal of this study was to determine whether this hybridization leadsto gene flow between species and which factors affect the rate of interspecific geneflow. For this purpose we conducted population-genetic analysis in three Europeanspecies of the Acrocephalus warblers of the subgenus Notiocichla: reed warbler (A.scirpaceus), marsh warbler (A. palustris), and blyth's reed warbler (A. dumetorum).Our results based on the analysis of sequence data from eight nuclear loci indicate,that gene flow between the studied species occurs, but only in one direction. Thegene flow is higher between genetically more related species than betweenecologically more similar species. We also estimated that the reed warbler and themarsh warbler diverged approximately 1,1 million years ago. The blyth's warblerand ancestor of the reed and marsh warbler...
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Systematics, Phylogeny and Biogeography of the gecko genus Hemidactylus (Reptilia, Gekkonidae) in Arabia and the Near East.
Šmíd, Jiří ; Moravec, Jiří (advisor) ; Kotlík, Petr (referee) ; Rehák, Ivan (referee)
(in English) Until relatively recently, the gecko genus Hemidactylus was considered to contain only several hard-to-distinguish species in the eastern Mediterranean and the Arabian Peninsula. This was mostly given by the apparent morphological uniformity of the geckos in combination with their often synanthropic lifestyle, which facilitated the dispersal of some of the species over large ranges. However, our understanding of the diversity of the genus was about to change with the onset of molecular phylogenetic methods that became extensively available and routinely applied to tackle the questions of systematics and phylogeny of all kinds of organisms. This thesis focuses on resolving the phylogeny, systematics, and biogeography of the Arabian Hemidactylus. Using an unprecedented sampling of over 500 samples of more than 40 Hemidactylus species from the eastern Mediterranean, Arabian Peninsula, Socotra, North and East Africa and Iran and sequencing up to six genes (two mitochondrial - 12S rRNA, cyt b; four nuclear - cmos, mc1r, rag1, rag2) I reconstructed the time-calibrated phylogeny of the arid clade of Hemidactylus, inferred its complex biogeographical history in the region, and detected seven potentially new species. The results of the biogeographic analyses indicate that the current...
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Adaptive population shifts in response to climate change
Horníková, Michaela ; Kotlík, Petr (advisor) ; Munclinger, Pavel (referee) ; Bryja, Josef (referee)
Adaptive population shifts in response to climate change Ing. Michaela Horníková, Doctoral thesis Abstract Understanding of species' reactions to past climate and environmental changes is a hot topic in many fields of biology as it is relevant also for addressing species' future under the contemporary climate change. Using an emerging model species, the bank vole, I combine genomic phylogeographic data with information on known intraspecific functional variability and environmental niche modelling and aim to elucidate the particular role of intraspecific variation and ultimately selection in shaping the species' response to the climatic and environmental changes after the end of the last glaciation. Based on the mtDNA markers, bank voles exhibit a complex phylogeographic pattern suggesting population replacement events during the postglacial recolonization of Europe and thus possible involvement of selection in the process. An extensive dataset of more than 6000 SNPs was used to search for signs of population replacement in the bank vole genomic DNA and to investigate the species' postglacial recolonization history throughout its European distribution range. The genomic data revealed even more complex population history than previously detected with mtDNA markers, including not only admixture but also...
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Mitogenomic phylogeography and adaptive evolution of the bank vole Clethrionomys glareolus
Filipi, Karolína ; Kotlík, Petr (advisor) ; Munclinger, Pavel (referee)
This thesis is a part of the project aimed at sequencing the genome and transcriptome of the bank vole (Clethrionomys glareolus). The role of natural selection in the evolution of mitochondrial DNA (mtDNA) has been subject to much discussion; while some studies did not provide evidence that selection affected the phylogeography of the studied species, other considered adaptive evolution important. The bank vole is the key model we use to study the adaptation to climate change. As with other species, the phylogeography of the bank vole has been based on the variation of a small part of mtDNA. The goal of the thesis was to sequence the entire mitochondrial genome for representatives of all main mtDNA lineages of the bank vole using the Sanger and Illumina technologies, and to assess the role of selection and adaptation in the evolution and phylogeography of this species. The adaptive evolution in mtDNA probably was not the main driving force during the postlacial colonization of Europe. However, signatures of adaptive evolution have been found - an amino acid change with possible functional consequences in one gene and an excess of radical changes in physical- chemical properties of amino acids in populations at the latitudinal (northern and southern) extremes of the bank vole distribution. Key...
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Systematics, Phylogeny and Biogeography of the gecko genus Hemidactylus (Reptilia, Gekkonidae) in Arabia and the Near East.
Šmíd, Jiří ; Moravec, Jiří (advisor) ; Kotlík, Petr (referee) ; Rehák, Ivan (referee)
(in English) Until relatively recently, the gecko genus Hemidactylus was considered to contain only several hard-to-distinguish species in the eastern Mediterranean and the Arabian Peninsula. This was mostly given by the apparent morphological uniformity of the geckos in combination with their often synanthropic lifestyle, which facilitated the dispersal of some of the species over large ranges. However, our understanding of the diversity of the genus was about to change with the onset of molecular phylogenetic methods that became extensively available and routinely applied to tackle the questions of systematics and phylogeny of all kinds of organisms. This thesis focuses on resolving the phylogeny, systematics, and biogeography of the Arabian Hemidactylus. Using an unprecedented sampling of over 500 samples of more than 40 Hemidactylus species from the eastern Mediterranean, Arabian Peninsula, Socotra, North and East Africa and Iran and sequencing up to six genes (two mitochondrial - 12S rRNA, cyt b; four nuclear - cmos, mc1r, rag1, rag2) I reconstructed the time-calibrated phylogeny of the arid clade of Hemidactylus, inferred its complex biogeographical history in the region, and detected seven potentially new species. The results of the biogeographic analyses indicate that the current...
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Neutral genetic variability and structure in chamois populations in Slovakia
Hájková, Andrea ; Zima, Jan (advisor) ; Kotlík, Petr (referee)
The Tatra chamois (Rupicapra rupicapra tatrica), an endemic mountain ungulate, occurs in the High Tatra Mts. (northern Slovakia and southern Poland). In the second part of the 20th century several chamois introductions occurred in Slovakia: Tatra chamois (from the High Tatra Mts.) were introduced into the Low Tatra Mts., while Alpine chamois (R. r. rupicapra) into the Veľká Fatra and Slovenský raj Mts. The High Tatra Mts. population underwent several population declines (bottlenecks) and all other Slovak populations were founded from only a few individuals (founder effect). Moreover, because the Low Tatra, Veľká Fatra and Slovenský raj are neighbouring mountain ranges, there is a potential risk of migration and hybridisation between the subspecies. Using 18 microsatellite loci, we studied neutral genetic variability, structure and potential hybridisation in chamois populations in Slovakia. The study is based on 193 samples: 95 tissue and 5 blood samples, and 88 faecal and 5 hair samples. Low genetic variability was found in all populations, the lowest one in High Tatra Mts. population. High values of fixation index, the number of private alleles, and factorial correspondence analysis indicated strong differentiation between the studied populations. Bayesian clustering divided Slovak chamois...
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Interspecific hybridization in Acrocephalus warblers.
Majerová, Veronika ; Reifová, Radka (advisor) ; Kotlík, Petr (referee)
Acrocephalus warblers have gone through the adaptive radiation during last severalmillion years, which gave rise to thirty one species occupying mainly Eurasia,Africa and Australia. The majority of species are morphologically very similar,however, they differ in ecological requirements, migration strategy, and song.Interspecific hybridization seems to be quite common among Acrocephaluswarblers, not only between sister species, but also between more distantly relatedtaxa. The main goal of this study was to determine whether this hybridization leadsto gene flow between species and which factors affect the rate of interspecific geneflow. For this purpose we conducted population-genetic analysis in three Europeanspecies of the Acrocephalus warblers of the subgenus Notiocichla: reed warbler (A.scirpaceus), marsh warbler (A. palustris), and blyth's reed warbler (A. dumetorum).Our results based on the analysis of sequence data from eight nuclear loci indicate,that gene flow between the studied species occurs, but only in one direction. Thegene flow is higher between genetically more related species than betweenecologically more similar species. We also estimated that the reed warbler and themarsh warbler diverged approximately 1,1 million years ago. The blyth's warblerand ancestor of the reed and marsh warbler...
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Genetic variability in the European ground squirrel (Spermophilus citellus) in Czech Republic
Starcová, Magda ; Vohralík, Vladimír (advisor) ; Kotlík, Petr (referee)
The European ground squirrel (Spermophilus citellus) (hereinafter EGS) is under the Law on Nature Protection and is included as a critically endangered into the Red List of Endangered Species. In the Czech Republic, which represents the northwestern border of the species range, EGS currently occurs on 34 localities, which are relatively small and isolated from each other. The spread of this species to central Europe was connected with neolithic deforestation. Disjunctive type of distribution of EGS was caused by strong decline of its abundance during the second half of the 20th century due to changes in field management, fragmentation of landscape and other factors. It can be expected that this process left traces on the genetic structure of EGS populations. The major objective of this study was a detailed analysis of genetic variability of EGS populations in the Czech Republic and searching for corelations with available data about its biology and demography. It was used 13 microsatellite loci and in total were processed 408 samples from 27 localities in CZ and 3 samples from one Hungarian locality as an outgroup. With aid of various methods, details of substructure and diferentiation of individual populations, genetic variability, degree of inbreeding and geographic distribution of genetic variability...
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Molecular phylogeography of the tench Tinca tinca (Linnaeus, 1758)
Lajbner, Zdeněk ; Kotlík, Petr (advisor) ; Flajšhans, Martin (referee) ; Macholán, Miloš (referee)
The tench Tinca tinca (Linnaeus, 1758) is a valued table fish native to Europe and Asia, but which is now widely distributed in many temperate freshwater regions of the world as the result of human-mediated translocations. Spatial genetic analysis applied to sequence data from four unlinked loci (introns of three nuclear genes and mitochondrial DNA) defined two groups of populations that were little structured geographically but were significantly differentiated from each other, and it identified locations of major genetic breaks, which were concordant across genes and were driven by distributions of two major phylogroups. This pattern most reasonably reflects isolation in two principal glacial refugia and subsequent range expansions, with the Eastern and Western phylogroups remaining largely allopatric throughout the tench range. However, this phylogeographic variation was also present in European cultured breeds and some populations at the western edge of the native range contained the Eastern phylogroup. Thus, natural processes have played an important role in structuring tench populations, but human-aided dispersal have also contributed significantly, with the admixed genetic composition of cultured breeds most likely contributing to the introgression. I have then designed novel PCR-RFLP assays...
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Preventive and remedial conservation methodology for the collection specimens falling within palaeontology and mineralogy endangered by sulphide degradation products
Sklenář, Jan ; Ekrt, Boris ; Sejkora, Jiří ; Kolesar, Peter ; Gazdová, Zuzana ; Malíková, Radana ; Nohejlová, Martina ; Kotlík, Petr ; Novák, Michal ; Ďurovič, Michal ; Říhová Ambrožová, Jana
The methodology is a complex system of procedures involving experimentally verified as well as modified already known methods, completely novel procedures, and their combinations. Many technologies as well as materials are employed for the first time in this field. Modifications of the existing methods bring either effectivity improvements, invasivity reduction or both. This methodology is the very first to cover all phases of the collection material treatment from acquisition to final storage. The methodology structuring follows logical succession of procedures. The theoretical chapter summarizes grounds of the degradation process, materials endangered with sulphide degradation and products of it. Area maps of types of sulphides labelled by process of origin, and a map of high-risk Czech localities are also involved. This introductory chapter is followed by part devoted to methods of field work and early care, suitable preventative collection care, and procedures of the remedial care. A special remedial care chapter for paper-documentation is also involved. This chapter is followed by instrumental methods useful for detection of degradation products and their influence on specimen condition. A separate part focuses on suitable ways of documentation. The safety-hazards chapter closes the methodology. The methodology is equipped with a list of references and flow diagrams helping the user to find the suitable procedure fast and easily. The methodology project was supported by the Ministry of Culture of the Czech Republic under NAKI DF12P01OVV031.
Fulltext: nusl-203643_3 -  PDF
Slides: nusl-203643_1 - PDF; nusl-203643_2 - PDF; nusl-203643_4 - PDF; nusl-203643_5 - PDF; nusl-203643_6 - PDF
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