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Implemenation of the RAD sequencing methods to the population genetic studies of hedgehogs from the genus Erinaceus
Loudová, Miroslava ; Černá Bolfíková, Barbora (advisor) ; Choleva, Lukáš (referee)
Hedgehogs from the genus Erinaceus are an important model organism for studying the postglacial recolonisation of Europe and the processes that take place in the secondary contact zones of their areas of distribution. In this study, five individuals of white-breasted hedgehog (Erinaceus roumanicus), four individuals of western hedgehog (Erinaceus europaeus) and one estimated hybrid were analysed. Geographical distribution of individuals used in the study covers the region of the Central Europe, however in the further research expansion of analsysed individuals will be needed and the whole Palearct should be sampled. The main goal was to implement novel methods in research of hedgehogs, which will enable to map the population-genomic structure of the genus Erinaceus in western Palearct. The method RADSeq (Restriction site associated DNA sequencing) enables to obtain polymorphic markers, e.g., SNPs which we used (Single Nucleotide Polymorphisms) across the genome. In this work it was analyzed 16382 SNPs. Using the binary data which indicates the presence and absence of SNPs for each species, hypotheses raised under classical analyzes of genetic markers from previous studies have not been fully confirmed. In further research it will be necessary to verify possible occurrence of biases connected with...
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Internal structure of the Balkan refugium using Erinaceus roumanicus as a model organism
Eliášová, Kristýna ; Černá Bolfíková, Barbora (advisor) ; Zemanová, Barbora (referee)
The aim of this work was to describe the spatial distribution of genetic variability of the northern white-breasted hedgehog (E. roumanicus), mainly within the Balkan Peninsula and Central Europe, as these areas are crucial for understanding the effects of Pleistocene climate oscillations on the genetic architecture of the species. Based on this spatial distribution, hypotheses about the possible structuring of the Balkan refugia were formulated. A total of 260 individuals and 9 microsatellite loci were used for the analysis. Using the approach of landscape and population genetics several possible isolated subpopulations within the area surveyed were identified. Unique status was proved for a population originating from Crete, probably influenced by mechanisms of island evolution. Differences from the rest of the range were ascertained also in population from the Czech Republic, located in a secondary contact zone with the E. europeaus. The role of interspecific interactions and possible introgression should be considered in this case. In the area of Romania and the area south of the Balkan Peninsula the highest genetic distances between individuals were identified, probably associated with the occurrence of geographical barriers and the possible presence of glacial subrefugia. Other identified...
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Evolutionary history of hedgehogs from genus>Erinaceus
Černá Bolfíková, Barbora ; Hulva, Pavel (advisor) ; Janko, Karel (referee) ; Kryštufek, Boris (referee)
Hedgehogs from the genus Erinaceus are extremely interesting and suitable model organisms for studying impacts of climatic changes during Pleistocene on species and speciation processes. Erinaceus europaeus and E. roumanicus, which have diverged in southern refugia, formed a secondary contact zone in Central Europe. The widest part of this zone is situated in Czech Republic. Our work benefits from this position and processes that take place here such as reinforcement, character displacement and hybridization are discussed. Moreover, we addressed several questions about biological invasions and topics connected to peripatric processes. Using combination of nuclear and mitochondrial DNA we detected differences in population structure between the species and also between sexes. E roumanicus is mainly restricted to lowlands. Ranges of both species expand and hybridization may play role during formation of reproductive isolation. We did not observed ecological character displacement when using 3D geometric morphometry approaches. Populations in sympatry are more similar than in allopatry. Our data are enhanced by description of parasite fauna of sympatrical populations and we discuss the role which they may play in evolution of the hedgehogs. Study proceeded in New Zealand was based on comparison of...
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Genetic structure of mammalian invasive populations on islands
Loudová, Miroslava ; Černá Bolfíková, Barbora (advisor) ; Hájková, Petra (referee)
Biological invasion is understood as introduction, establishment and expansion of organisms into new, non-native area. This is a natural process that is significantly compounded by human activities and is one of the factors that threaten biological diversity and stability of natural ecosystems. Understanding to the evolution and current status of invasive populations is especially important for planning a project to eradicate invasive species from certain areas to avoid their negative impact on the environment. One option for the research of the invasive populations and their history is the analysis of genetic material. This thesis summarizes the current knowledge on invasive populations of small mammals on the islands, with the focus on genetic studies. Specifically, the study of Norway rats (Rattus norvegicus) on Moturemu island and five archipelagos off the coast of Brittany; black rats (Rattus rattus) on Congo Cay, Madagascar, Guadeloupe Archipelago, Sainte Anne Archipelago and Canary Islands; Pacific rats (Rattus exulans) on Tetiaroa Atoll; house mice (Mus musculus) on Marion Island; house mice (Mus musculus domesticus) on Kerguelen Archipelago; red squirrels (Sciurus vulgaris) on Jersey island, West European hedgehogs (Erinaceus europaeus) in New Zealand; pygmy shrews (Sorex minutus) in Ireland and...
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Genetic structure of Central European populations of hedgehogs Erinaceus europaeus and E. roumanicus
Bolfíková, Barbora ; Hulva, Pavel (advisor) ; Bryja, Josef (referee)
In the Czech Republic there is a wide zone of sympatric occurrence of two hedgehog species - Erinaceus europaeus and E. roumanicus, which is of Holocene origin. This work is based on genetic data obtained in 248 specimens, the sampling was focused on the area of Central Europe. We have used 410 bp long partial sequence of mtDNA control region and 9 microsatellite loci. With aid of different methods, we attempted to reveal details of distributions, population structure, demographic history and potential gene flow between both species. We have detected significantly higher occurrence of E. europaeus (3 times) compared to E. roumanicus and the shift of range borders in scale of tens of kilometers in last 30 years. Genetic variability was higher in E. europaeus. In E. roumanicus, there was support for moderate population increase, while the population size in E. europaeus seems to be stable. We have detected deviations from Hardy-Weinberg equilibrium in some loci, which could be ascribed to the Wahlund effect. We did not detect existence of hybridization or introgression, the complete precopulatory reproductive barriers have been formed supposedly. Powered by TCPDF (www.tcpdf.org)
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Colonisation of islands by the insectivorous mammals
Matějů, Petr ; Černá Bolfíková, Barbora (advisor) ; Kristýna, Kristýna (referee)
Biological invasions are a serious problem worldwide. Besides the natural colonizations mediated by tectonic movements or formation of a land bridge connection, there are also the artificial ones. Humans can deliberately or undeliberately translocate species across ecosystems. Recently, mainly because of the buisness and tourism there is a dramatical increase in human-mediated biological invasions. Many authors, who discussed invasions in the past, were focused on rodents. Despite its severe impact on the ecosystems the topic of insectivorous mammals remains relatively untouched by scientists so far. Practical part of this thesis is focused on the Northern white-breasted hedgehog (Erinaceus roumanicus) and his dispersal in the Mediterranean area. Mitochondrial control region sequences of 28 samples were analyzed and compared to already published data from GenBank. Discussion was made through phylogenetical analysis. Main topics of discussion were focused on a possible contemporaneity and a course of transfer of the gene flow. Most of the samples showed haplotype similarity with individuals occupying the closest mainland. On the other hand samples from Skyros did not go with the trend. They matched with haplotype from Crete.
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Population genetics of Grey Wolf (Canis lupus) in Eurasia
Báčová, Alžběta ; Černá Bolfíková, Barbora (advisor) ; Pavel, Pavel (referee)
The grey wolf (Canis lupus) is the largest canine carnivore living on northern
hemisphere of the Earth. Excessive persecution of Canis lupus at the turn of 19th and
20th century has caused nearly extermination of this animal species in the most parts
of its natural habitat. Natural habitat got rapidly smaller at that time. At the end of 20th
century number of individuals of Canis lupus has increased and the grey wolf has
started to return to its natural habitat due to better legal protection. Its natural habitat
is very fragmented especially in Western Europe. The origin of founders of wolf
populations is estimated and the tracks of migrating individuals are followed, by
monitoring the gene flow. In last fifteen years the grey wolf has started to return back
to Czech countryside. Usage of microsatellites proved its presence in Beskyd
Mountains, Czech and Slovakia republic. Comparing DNA samples of Canis lupus with
those of Carpathian wolves showed the same origin of both groups within Europe.
Detailed research points to deeper structure even within subpopulation.
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Methods of Carnivores genetic monitoring in Holarctis
Smutný, Matyáš ; Černá Bolfíková, Barbora (advisor) ; Miroslav, Miroslav (referee)
Genetic monitoring begins to be widely used for monitoring carnivores, in Europe this method is also used for monitoring of other species. In this work I focused on exact definition of genetic monitoring, what is the practical use of this method and function together with other methods of monitoring. In my work I further examined invasive and non-invasive methods of gathering samples and well-known but also less known methods of monitoring of small carnivores in general and large carnivores namely.
For practical part I extracted DNA from thirty three samples of faeces and eight samples of tissue. Thirty blood samples used in this work were extracted in the research From Wolves to Dogs and Back: Genetic Composition of the Czechoslovakian Wolfdog by Smetanová et al. (2015). Scats came from Beskydy and Kokořínsko, tissues were from legal blast in Slovakia and specimen killed in Valašské Meziříčí and Kokořínsko, and blood came from dogs. After extraction I measured the concentration of DNA by spectrophotometer NanoDrop 2000 and using statistical program Statistica 12 I compared their quality. The blood had the highest average concentration od DNA, the lowest in contrast had tissue. In this work I discuss which genetic material is most suitable, in terms of yield of genetic monitoring, and additionally the limits of each method.
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