@phdthesis{Folkertsma2020,
  author    = {Folkertsma, Remco},
  title     = {Evolutionary adaptation to climate in microtine mammals},
  doi       = {10.25932/publishup-47680},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-476807},
  school      = {Universit{\"a}t Potsdam},
  pages     = {135},
  year      = {2020},
  abstract  = {Understanding how organisms adapt to their local environment is a major focus of evolutionary biology. Local adaptation occurs when the forces of divergent natural selection are strong enough compared to the action of other evolutionary forces. An improved understanding of the genetic basis of local adaptation can inform about the evolutionary processes in populations and is of major importance because of its relevance to altered selection pressures due to climate change. So far, most insights have been gained by studying model organisms, but our understanding about the genetic basis of local adaptation in wild populations of species with little genomic resources is still limited. With the work presented in this thesis I therefore set out to provide insights into the genetic basis of local adaptation in populations of two voles species: the common vole (Microtus arvalis) and the bank vole (Myodes glareolus). Both voles species are small mammals, they have a high evolutionary potential compared to their dispersal capabilities and are thus likely to show genetic responses to local conditions, moreover, they have a wide distribution in which they experience a broad range of different environmental conditions, this makes them an ideal species to study local adaptation. The first study focused on producing a novel mitochondrial genome to facilitate further research in M. arvalis. To this end, I generated the first mitochondrial genome of M. arvalis using shotgun sequencing and an iterative mapping approach. This was subsequently used in a phylogenetic analysis that produced novel insights into the phylogenetic relationships of the Arvicolinae. The following two studies then focused on the genetic basis of local adaptation using ddRAD-sequencing data and genome scan methods. The first of these involved sequencing the genomic DNA of individuals from three low-altitude and three high-altitude M. arvalis study sites in the Swiss Alps. High-altitude environments with their low temperatures and low levels of oxygen (hypoxia) pose considerable challenges for small mammals. With their small body size and proportional large body surface they have to sustain high rates of aerobic metabolism to support thermogenesis and locomotion, which can be restricted with only limited levels of oxygen available. To generate insights into high-altitude adaptation I identified a large number of single nucleotide polymorphisms (SNPs). These data were first used to identify high levels of differentiation between study sites and a clear pattern of population structure, in line with a signal of isolation by distance. Using genome scan methods, I then identified signals of selection associated with differences in altitude in genes with functions related to oxygen transport into tissue and genes related to aerobic metabolic pathways. This indicates that hypoxia is an important selection pressure driving local adaptation at high altitude in M. arvalis. A number of these genes were linked with high-altitude adaptation in other species before, which lead to the suggestion that high-altitude populations of several species have evolved in a similar manner as a response to the unique conditions at high altitude The next study also involved the genetic basis of local adaptation, here I provided insights into climate-related adaptation in M. glareolus across its European distribution. Climate is an important environmental factor affecting the physiology of all organisms. In this study I identified a large number of SNPs in individuals from twelve M. glareolus populations distributed across Europe. I used these, to first establish that populations are highly differentiated and found a strong pattern of population structure with signal of isolation by distance. I then employed genome scan methods to identify candidate loci showing signals of selection associated with climate, with a particular emphasis on polygenic loci. A multivariate analysis was used to determine that temperature was the most important climate variable responsible for adaptive genetic variation among all variables tested. By using novel methods and genome annotation of related species I identified the function of genes of candidate loci. This showed that genes under selection have functions related to energy homeostasis and immune processes. Suggesting that M. glareolus populations have evolved in response to local temperature and specific local pathogenic selection pressures. The studies presented in this thesis provide evidence for the genetic basis of local adaptation in two vole species across different environmental gradients, suggesting that the identified genes are involved in local adaptation. This demonstrates that with the help of novel methods the study of wild populations, which often have little genomic resources available, can provide unique insights into evolutionary processes.},
  language  = {en}
}
@phdthesis{Derežanin2023,
  author    = {Derežanin, Lorena},
  title     = {Contribution of structural variation to adaptive evolution of mammalian genomes},
  doi       = {10.25932/publishup-59144},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-591443},
  school      = {Universit{\"a}t Potsdam},
  pages     = {188},
  year      = {2023},
  abstract  = {Following the extinction of dinosaurs, the great adaptive radiation of mammals occurred, giving rise to an astonishing ecological and phenotypic diversity of mammalian species. Even closely related species often inhabit vastly different habitats, where they encounter diverse environmental challenges and are exposed to different evolutionary pressures. As a response, mammals evolved various adaptive phenotypes over time, such as morphological, physiological and behavioural ones. Mammalian genomes vary in their content and structure and this variation represents the molecular mechanism for the long-term evolution of phenotypic variation. However, understanding this molecular basis of adaptive phenotypic variation is usually not straightforward. The recent development of sequencing technologies and bioinformatics tools has enabled a better insight into mammalian genomes. Through these advances, it was acknowledged that mammalian genomes differ more, both within and between species, as a consequence of structural variation compared to single-nucleotide differences. Structural variant types investigated in this thesis - such as deletion, duplication, inversion and insertion, represent a change in the structure of the genome, impacting the size, copy number, orientation and content of DNA sequences. Unlike short variants, structural variants can span multiple genes. They can alter gene dosage, and cause notable gene expression differences and subsequently phenotypic differences. Thus, they can lead to a more dramatic effect on the fitness (reproductive success) of individuals, local adaptation of populations and speciation. In this thesis, I investigated and evaluated the potential functional effect of structural variations on the genomes of mustelid species. To detect the genomic regions associated with phenotypic variation I assembled the first reference genome of the tayra (Eira barbara) relying on linked-read sequencing technology to achieve a high level of genome completeness important for reliable structural variant discovery. I then set up a bioinformatics pipeline to conduct a comparative genomic analysis and explore variation between mustelid species living in different environments. I found numerous genes associated with species-specific phenotypes related to diet, body condition and reproduction among others, to be impacted by structural variants. Furthermore, I investigated the effects of artificial selection on structural variants in mice selected for high fertility, increased body mass and high endurance. Through selective breeding of each mouse line, the desired phenotypes have spread within these populations, while maintaining structural variants specific to each line. In comparison to the control line, the litter size has doubled in the fertility lines, individuals in the high body mass lines have become considerably larger, and mice selected for treadmill performance covered substantially more distance. Structural variants were found in higher numbers in these trait-selected lines than in the control line when compared to the mouse reference genome. Moreover, we have found twice as many structural variants spanning protein-coding genes (specific to each line) in trait-selected lines. Several of these variants affect genes associated with selected phenotypic traits. These results imply that structural variation does indeed contribute to the evolution of the selected phenotypes and is heritable. Finally, I suggest a set of critical metrics of genomic data that should be considered for a stringent structural variation analysis as comparative genomic studies strongly rely on the contiguity and completeness of genome assemblies. Because most of the available data used to represent reference genomes of mammalian species is generated using short-read sequencing technologies, we may have incomplete knowledge of genomic features. Therefore, a cautious structural variation analysis is required to minimize the effect of technical constraints. The impact of structural variants on the adaptive evolution of mammalian genomes is slowly gaining more focus but it is still incorporated in only a small number of population studies. In my thesis, I advocate the inclusion of structural variants in studies of genomic diversity for a more comprehensive insight into genomic variation within and between species, and its effect on adaptive evolution.},
  language  = {en}
}
@phdthesis{Cheng2024,
  author    = {Cheng, Feng},
  title     = {Evolution and ontogeny of electric organ discharge in African weakly electric fish genus Campylomormyrus: a genomic and transcriptomic perspective},
  doi       = {10.25932/publishup-63017},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-630172},
  school      = {Universit{\"a}t Potsdam},
  pages     = {176},
  year      = {2024},
  abstract  = {The African weakly electric fishes (Mormyridae) exhibit a remarkable adaptive radiation possibly due to their species-specific electric organ discharges (EODs). It is produced by a muscle-derived electric organ that is located in the caudal peduncle. Divergence in EODs acts as a pre-zygotic isolation mechanism to drive species radiations. However, the mechanism behind the EOD diversification are only partially understood. The aim of this study is to explore the genetic basis of EOD diversification from the gene expression level across Campylomormyrus species/hybrids and ontogeny. I firstly produced a high quality genome of the species C. compressirostris as a valuable resource to understand the electric fish evolution. The next study compared the gene expression pattern between electric organs and skeletal muscles in Campylomormyrus species/hybrids with different types of EOD duration. I identified several candidate genes with an electric organ-specific expression, e.g. KCNA7a, KLF5, KCNJ2, SCN4aa, NDRG3, MEF2. The overall genes expression pattern exhibited a significant association with EOD duration in all analyzed species/hybrids. The expression of several candidate genes, e.g. KCNJ2, KLF5, KCNK6 and KCNQ5, possibly contribute to the regulation of EOD duration in Campylomormyrus due to their increasing or decreasing expression. Several potassium channel genes showed differential expression during ontogeny in species and hybrid with EOD alteration, e.g. KCNJ2. I next explored allele specific expression of intragenus hybrids by crossing the duration EOD species C. compressirostris with the medium duration EOD species C. tshokwe and the elongated duration EOD species C. rhynchophorus. The hybrids exhibited global expression dominance of the C. compressirostris allele in the adult skeletal muscle and electric organ, as well as in the juvenile electric organ. Only the gene KCNJ2 showed dominant expression of the allele from C. rhynchophorus, and this was increasingly dominant during ontogeny. It hence supported our hypothesis that KCNJ2 is a key gene of regulating EOD duration. Our results help us to understand, from a genetic perspective, how gene expression effect the EOD diversification in the African weakly electric fish.},
  language  = {en}
}
@phdthesis{Autenrieth2020,
  author    = {Autenrieth, Marijke},
  title     = {Population genomics of two odontocetes in the North Atlantic and adjacent waters},
  school      = {Universit{\"a}t Potsdam},
  pages     = {IX, 110},
  year      = {2020},
  abstract  = {Due to continuously intensifying human usage of the marine environment worldwide ranging cetaceans face an increasing number of threats. Besides whaling, overfishing and by-catch, new technical developments increase the water and noise pollution, which can negatively affect marine species. Cetaceans are especially prone to these influences, being at the top of the food chain and therefore accumulating toxins and contaminants. Furthermore, they are extremely noise sensitive due to their highly developed hearing sense and echolocation ability. As a result, several cetacean species were brought to extinction during the last century or are now classified as critically endangered. This work focuses on two odontocetes. It applies and compares different molecular methods for inference of population status and adaptation, with implications for conservation. The worldwide distributed sperm whale (Physeter macrocephalus) shows a matrilineal population structure with predominant male dispersal. A recently stranded group of male sperm whales provided a unique opportunity to investigate male grouping for the first time. Based on the mitochondrial control region, I was able to infer that male bachelor groups comprise multiple matrilines, hence derive from different social groups, and that they represent the genetic variability of the entire North Atlantic. The harbor porpoise (Phocoena phocoena) occurs only in the northern hemisphere. By being small and occurring mostly in coastal habitats it is especially prone to human disturbance. Since some subspecies and subpopulations are critically endangered, it is important to generate and provide genetic markers with high resolution to facilitate population assignment and subsequent protection measurements. Here, I provide the first harbour porpoise whole genome, in high quality and including a draft annotation. Using it for mapping ddRAD seq data, I identify genome wide SNPs and, together with a fragment of the mitochondrial control region, inferred the population structure of its North Atlantic distribution range. The Belt Sea harbors a distinct subpopulation oppose to the North Atlantic, with a transition zone in the Kattegat. Within the North Atlantic I could detect subtle genetic differentiation between western (Canada-Iceland) and eastern (North Sea) regions, with support for a German North Sea breading ground around the Isle of Sylt. Further, I was able to detect six outlier loci which show isolation by distance across the investigated sampling areas. In employing different markers, I could show that single maker systems as well as genome wide data can unravel new information about population affinities of odontocetes. Genome wide data can facilitate investigation of adaptations and evolutionary history of the species and its populations. Moreover, they facilitate population genetic investigations, providing a high resolution, and hence allowing for detection of subtle population structuring especially important for highly mobile cetaceans.},
  language  = {en}
}