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Detection of structural variants in genomes of two nightingale species
Halenková, Zuzana ; Reifová, Radka (advisor) ; Jansa, Petr (referee)
Structural variants are mutations in DNA sequence affecting the location, orientation, or the number of copies of regions longer than 50 bp. Although this type of variation has the potential to cause large phenotypic changes, structural variants remain largely understudied compared to other classes of variation (such as single nucleotide polymorphisms) due to the difficulties associated with their detection. Nevertheless, it was suggested that structural variants could play a profound role in the evolution of species. Inversions particularly are considered to be a potent mechanism for both adaptation and speciation due to their ability to suppress recombination. This thesis provides the first insight into the structural variation between two closely related naturally hybridizing species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia). Structural variants were detected using long-read sequence data and high-quality de novo whole genome assemblies from one individual per species. High-confidence sets of structural variants were built by the intersection of results from several structural variant calling methods separately for each reference genome and included 18 839 variants for the common nightingale reference and 19 864 variants for the thrush...
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Speciation genomics in nightingales
Mořkovský, Libor
Speciationisusuallyaslowprocessoccurringoverthousandstomillionsofyears.Thismakes speciation research difficult because no direct observation or manipulation is possible. At best, we can gain some insight by inferring the population history and structure in very fine detail by investigating genetic markers in multiple individuals of the nascent species. Today, speciationresearchisinanunprecedentedpositionthankstotheadventofhigh-throughput sequencingmethods,whichmakeiteasier and cheaper than ever before to evaluate multiple markers in many individuals. Speciation is not a straightforward process that happens in the same way every time, but rather a phenomenon occurring when genetic and ecological circumstancesactinginsymphonyultimatelyleadtoreproductiveisolationoftwosubpopula- tions. This is why it is important to study multiple model systems to understand the general principles behind speciation. We worked with two species of nightingales (Luscinia luscinia andL.megarhynchos)thatdivergedapproximately1.8Mya,likelyduetoglacialfluctuations in Europe. Our main goal was to use these new high-throughput sequencing methods to (1) detect interspecific hybrids between the species, (2) estimate levels of interspecific gene flow,(3)findareasofthenightingalegenomethatunderliereproductiveisolationand,finally, (4)...
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Analysis of karyotype and sex chromosome differentiation in African annual killifish of the genus Nothobranchius (Teleostei: Nothobranchiidae)
Lukšíková, Karolína ; Sember, Alexandr (advisor) ; Zrzavá, Magda (referee)
Teleost fishes (Teleostei) encompass more than half of the extant vertebrate biodiversity. Their genomes display considerable plasticity and flexibility, going hand in hand with polyploidization events and repetitive DNA dynamics. Teleosts also display a striking diversity in mechanisms of sex determination and differentiation. The aim of the present thesis was to study the mechanisms underlying the karyotype and sex chromosome differentiation through cytogenetic mapping of repetitive DNA (by fluorescence in situ hybridization, FISH) in selected representatives of the African annual killifishes of the genus Nothobranchius (Teleostei: Nothobranchiidae). Nothobranchius spp. evolved a unique adaptation to freshwater temporary water pools whose existence is limited to periods of rainy season in African savannahs. Recent diversification, allopatric speciation in non-overlapping generations and small-sized populations together with known cytogenetics collectively suggest fast dynamics of chromosomal changes in Nothobranchius killifishes. The study took advantage of the availability of i) more populations of several closely related species for analysis and ii) data on specific repetitive DNA composition in selected Nothobranchius genomes as revealed by RepeatExplorer analysis. My work showed considerable...
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Karyotype evolution of the family Araneidae
Pajpach, Filip ; Král, Jiří (advisor) ; Sember, Alexandr (referee)
Orb-weavers (Araneidae) are a diversified spider family comprising more than 3,100 species in more than 170 genera. Together with 13 other families, they con- stitute to superfamily Araneoidea. The presented thesis focuses on karyotype evo- lution of Araneidae, including its comparison with a related family Tetragnathidae. The results obtained from 19 araneid and four tetragnathid species confirm previ- ously postulated hypothesis that the ancestral karyotype of Araneoidea (including Araneidae) consists of 24 acrocentric chromosomes in males, including two acro- centric X chromosomes of system X1X20. However, there is a tendency of 2n decrease in some araneids due to centric fusions. In these cases, centric fusions affected most autosomes (and sometimes gonosomes as well); number of chromosome pairs de- creased from 11 to six. Three independent reduction events were detected in this thesis. Furthermore, pattern of nucleolar organizer regions (NORs) was studied in this thesis using fluorescent in situ hybridization, since data on evolution of this marker are scarce in spiders. Striking variability in NORs number was discovered, ranging from one to 13 loci. Remarkably, multiple centric fusions were always ac- companied by considerable increase of NORs number. In araneids and tetragnathids possessing...
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Transformation of trace element speciation in disturbed soil profile
Kochergina, Yulia
Distributions of toxic trace elements were studied in soils before and after disturbation of their profiles.Two areas with different vegetation cover were selected: beech (Fagus sylvatica) and spruce (Picea abies) forests at the Načetín site in the Ore Mts. In the past, this area belonged to places with extreme levels of acidic atmospheric deposition. The studied areas are not placed too far from each other and have thus approximately the same climatic conditions, geological background and pollution input. On the other hand, physicochemical properties of soils (pH, CEC, BS, Ctot, Stot) and concentrations of major and trace elements are different. At selected sites in spruce and beech stand, two soil probes to a depth of 40-50 cm were dug in 2010 and samples of individual soil horizont were collected for chemical analyses (approximately 0.5 kg). Four samples from L, H, A and B horizons were taken in the spruce forest area and five samples from L, H, A, B and C horizons were taken in the beech forest. In 2011, the sites were re-sampled and samples were taken from horizons that were disturbed in 2010, paralleled by samples of undisturbed soil horizons from the same probe sites. Trace element concentrations were determined by ICP-MS, the speciation of individual elements in the soils was determined by...
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Sperm motility and postmating prezygotic isolation in two nightingale species
Baránková, Lucie ; Reifová, Radka (advisor) ; Frolíková, Michaela (referee)
The motility of male gametes (sperm) is one of the important factors influencing the reproductive success of males. Because sperms are often subjected to strong postmating sexual selection and even closely related species often differ in sperm morphology, sperm motility could also differ between species, which may contribute to reproductive isolation between species. As part of my diploma thesis, I studied sperm motility in two closely related species of songbirds, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia). These two species of nightingales are an ideal model system because the areas of these two species overlap in the secondary contact zone across Central and Eastern Europe, where they occasionally hybridize and thus allow the study of speciation mechanisms in the natural environment. Both species also differ greatly in total sperm length. As part of my diploma thesis, I studied the possible influence of different sperm morphology on their motility. I further tested whether the motility of nightingale sperm differs in the fluid from the cloaca of a female of the same species and a different species, which would demonstrate the presence of postmating prezygotic reproductive isolation between species. The results of my work showed that despite the...
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Sex chromosome evolution in ray-finned fishes (Actinopterygii)
Pavlica, Tomáš ; Sember, Alexandr (advisor) ; Knytl, Martin (referee)
Ray-finned fishes (Actinopterygii) possess strikingly diverse sex sex differentiation strategies (including gonochorism, unisexuality and several types of hermaphroditism) and mechanisms of sex determination (both environmental and genetic), including frequent turnovers between abovementioned strategies and mechanisms. Although exhibiting remarkable diversity of sex determination mechanisms, only about 5% of analyzed teleost species possess cytologically recognizable (i.e. heteromorphic) sex chromosomes. Still, nine different male- or female- heterogametic sex chromosome systems at various stages of differentiation have been described along with high rate of inter- and intraspecific variability. Given that early sex chromosome evolution is best studied in evolutionarily young nascent sex chromosomes, ray- finned fishes and especially the teleost lineage (Teleostei) represent vital model group for these investigations offering new insights into the evolution of these rapidly evolving regions of vertebrate genomes. Moreover, handful of studies available so far has provided evidence for a role of emerging sex chromosomes and their turnover in processes such as ecologial adaptation, speciation or genomic conflict. Besides cytogenetic studies, which had a major impact on our current knowledge about fish...
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Speciation genomics in nightingales
Mořkovský, Libor ; Reifová, Radka (advisor) ; Macholán, Miloš (referee) ; Piálek, Lubomír (referee)
Speciationisusuallyaslowprocessoccurringoverthousandstomillionsofyears.Thismakes speciation research difficult because no direct observation or manipulation is possible. At best, we can gain some insight by inferring the population history and structure in very fine detail by investigating genetic markers in multiple individuals of the nascent species. Today, speciationresearchisinanunprecedentedpositionthankstotheadventofhigh-throughput sequencingmethods,whichmakeiteasier and cheaper than ever before to evaluate multiple markers in many individuals. Speciation is not a straightforward process that happens in the same way every time, but rather a phenomenon occurring when genetic and ecological circumstancesactinginsymphonyultimatelyleadtoreproductiveisolationoftwosubpopula- tions. This is why it is important to study multiple model systems to understand the general principles behind speciation. We worked with two species of nightingales (Luscinia luscinia andL.megarhynchos)thatdivergedapproximately1.8Mya,likelyduetoglacialfluctuations in Europe. Our main goal was to use these new high-throughput sequencing methods to (1) detect interspecific hybrids between the species, (2) estimate levels of interspecific gene flow,(3)findareasofthenightingalegenomethatunderliereproductiveisolationand,finally, (4)...
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Why so specious? The role of pollinators and symbionts in plant population structure and speciation along elevational gradients.
SOUTO VILARÓS, Daniel
This thesis explores the role mutualist pollinators and their symbionts play in the genetic structuring and speciation of their host plants along an elevational gradient in Papua New Guinea. Using the fig and fig-wasp mutualism as a model system, we employed high-throughput sequencing techniques to explore fine-scale population genomics of both fig and wasps along their elevational range. We found there to be clear lowland and highland clustering of tree populations along the gradient, often with a mid-elevation contact zone. In the case of the pollinating wasps, we retrieved the same clustering except in this case, the genetic difference between clusters was high enough as to consider them as separate species. This result supports evidence from other studies challenging the cospeciation paradigm of one wasp species per fig species. In addition, we explore ecological traits which may promote, or at least, maintain, reproductive isolation between fig (sub)species along with behavioural preference tests from pollinating wasps. In order to further investigate the mechanisms promoting wasp speciation along the gradient, we describe Wolbachia infection status as well as strain type. Wolbachia-induced cytoplasmic incompatibility (CI) is often invoked as a possible speciation agent since it can rapidly provoke and maintain reproductive isolation between otherwise freely interbreeding insect populations. Finally, we explore non-pollinating fig wasp (NPFW) diversity along the gradient for a subset of our focal species. Our study reveals that there is a tight relationship between NPFW diversity and host species, and a mid-elevation peak.
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