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1	Cis-regulatory variation and divergence in Capsella Steige, Kim A. January 2016 (has links) Cis-regulatory changes in e.g. promoters or enhancers that affect the expression of a linked focal gene have long been thought to be important for adaptation. In this thesis, I investigate the selective importance and genomic correlates of cis-regulatory variation and divergence in the genus Capsella, using massively parallel sequencing data. This genus provides an opportunity to investigate cis-regulatory changes in response to polyploidization and mating system shifts, as it harbors three diploid species, the outcrosser Capsella grandiflora and the selfers Capsella orientalis and Capsella rubella, as well as the tetraploid Capsella bursa-pastoris. We first identify cis-regulatory changes associated with adaptive floral evolution in connection with the recent switch to self-fertilization in C. rubella and show that cis-regulatory changes between C. rubella and its outcrossing close relative C. grandiflora are associated with differences in transposable element content. Second, we show that variation in positive and purifying selection is important for the distribution of cis-regulatory variation across the genome of C. grandiflora. Interestingly, the presence of polymorphic transposable elements is strongly associated with cis-regulatory variation in C. grandiflora. Third, we show that the tetraploid C. bursa-pastoris is of hybrid origin and investigate the contribution of both parental species to gene expression. We show that gene expression in the tetraploid is partly explained by cis-regulatory divergence between the parental species. Nonetheless, within C. bursa-pastoris there is a great deal of variation in homeolog expression. In summary, this thesis explores the role of cis-regulatory changes for adaptive morphological changes in connection to a shift in mating system, the role of cis-regulatory divergence between progenitor species for an allopolyploid as well as the impact of positive and purifying selection on cis-regulatory variation within a species. Capsella Shepherd's Purse cis-regulatory changes allele-specific expression mating system shift floral evolution polyploidy positive selection purifying selection transposable elements small RNA methylation transposable element silencing distribution of fitness effects
2	Demography of Birch Populations across Scandinavia Sendrowski, Janek January 2022 (has links) Boreal forests are particularly vulnerable to climate change, experiencing a much more drastic increase in temperatures and having a limited amount of more northern refugia. The trees making up these vast and important ecosystems already had to adapt previously to environmental pressures brought about by the repeated glaciations during past ice ages. Studying the patterns of adaption of these trees can thus provide valuable insights on how to mitigate future damage. This thesis presents and analyses population structure, demo- graphic history and the distribution of fitness effects (DFE) of the diploid Betula pendula and tetraploid B. pubescens across Scandinavia. Birches–being widespread in boreal forests as well as having great economical importance–constitute superb model species. The analyses of this work confirm the expectations on postglacial population expansion and diploid-tetraploid introgression. They furthermore ascertain the presence of two genetic clusters and a remarkably similar DFE for the species. This work also contributes with a transparent, reproducible and reusable pipeline which facilitates running similar analyses for related species. birch betula pubescens pendula betula pubescens betula pendula silver birch downy birch demography population structure distribution of fitness effects DFE dadi UMAP PCA ADMIXTURE polyDFE ice age glaciation tree boreal forest climate change adaption tetraploid diploid-tetraploid introgression Scandinavia genetic cluster pipeline snakemake bioinformatics reproducible population genetics postglacial population expansion demographic history FEEMS site-frequency spectrum SFS last glacial maximum LGM workflow python population expansion population growth EST-SFS 0-fold degenerate 4-fold degenerate maximum likelihood estimation MLE variant call format VCF single-nucleotide polymorphism SNP Bioinformatics (Computational Biology) Bioinformatik (beräkningsbiologi)

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Cis-regulatory variation and divergence in Capsella

Demography of Birch Populations across Scandinavia