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- Andersson, Bea Angelica, 1992-
(författare)
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Finding fitness : empirical and theoretical explorations of inferring fitness effects from population-level SNP data
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The distribution of fitness effects (DFE) describes the likelihood that a new mutation has a specific effect on the fitness of an individual in a given population. The shape of the DFE is a result of several factors such as population size, mating system and selective environment, and can in turn influence the evolutionary potential of a species. The DFE has long been a field of intense research, but particularly since molecular methods enabled us to study of genetic variation in organisms empirically. This research has led to the development of several statistical methods that use population-level frequencies of single nucleotide polymorphisms (SNPs) to infer the DFE. However, these methods rely on assumptions about the data and the organism itself, which could potentially affect the accuracy of the inferences. In this thesis, I describe how two major factors – data quality and inbreeding – can affect the accuracy of DFE inferences. I also show how and when to (and when not to) use DFE inference methods based on SNP frequencies.All genomic datasets contain inaccuracies and some level of uncertainty. The data sets are therefore often treated to remove the gaps or less reliable information, such as genotypes with low coverage. Some data sets need heavy filtering, which could reduce the amount of data available for analysis. We show that the choice of filter method affects the size of the final data set and the accuracy of the estimated DFE.Many DFE estimation software assumes random mating within the study population. Unfortunately, this assumption induces some error when trying to estimate the DFE in inbred or selfing species. Some have assumed that this is a result of high rates of homozygosity in the data, and should only be a problem in populations with very high rates of selfing (>99%). We show that accuracy of the estimated DFE decreases already at relatively low rates of selfing (70%) and that removing homozygosity does not improve the accuracy, implying that another mechanism could be causing the error.
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| 2. |
- Bachmann, Jörg Alexander, 1989-
(författare)
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Evolutionary consequences of dominance at the Brassicaceae self-incompatibility locus
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Self-incompatibility (SI) is a genetic mechanism that allows plants to enforce outcrossing by rejecting self-pollen and pollen from close relatives. In the Brassicaceae, SI is sporophytic and controlled by the self-incompatibility locus (S-locus). The S-locus harbors two tightly linked genes SRK and SCR, which encode the female and male SI specificity determinants, respectively. S-locus heterozygotes often only express the S-specificity of the more dominant allele, and at the pollen level such dominance relationships are mediated by small RNAs (sRNAs). The S-locus is thus an example of a locus under strong balancing selection, where dominance modifiers have evolved.In this thesis, I investigate the consequences of S-locus dominance for plant mating system evolution and allopolyploid speciation. I further investigate evolutionary conservation and sequence-level effects of dominance relationships among S-alleles. For this purpose, I used the crucifer genus Capsella as a model system.First, I demonstrated that targeted long-read sequencing results in structurally accurate assemblies of full-length S-haplotype sequences, and that indel errors in such assemblies can be corrected using short reads. Second, I investigated the genetic basis of loss of SI, the first step in the evolution of self-fertilisation, in the self-compatible (SC) Capsella orientalis. I found that loss of SI was dominant and mapped to the S-locus, where C. orientalis harbored a fixed coding frameshift deletion in SCR that is likely to lead to loss of male specificity. I further identified a sRNA-based dominance modifier that is associated with dominant suppression of recessive SCR alleles. Taken together, these results suggest that loss of SI in C. orientalis involved a dominant S-haplotype, suggesting that dominant haplotypes may be favored under conditions that select for loss of SI. Third, I show that a dominant S-haplotype may also have contributed to the shift to SC in the widespread allotetraploid Capsella bursa-pastoris. Fourth, I showed that dominance relationships at the S-locus are largely conserved between the SI outcrossing species C. grandiflora and Arabidopsis halleri which diverged ~8 Mya. I also found that dominant S-haplotypes accumulate more transposable elements than recessive S-haplotypes, in line with expected sequence-level consequences of S-locus dominance. In sum, this thesis provides new insights into the broad conservation of dominance hierarchies at the Brassicaceae S-locus, and the role of dominant S-alleles in allopolyploid speciation and plant mating system shifts.
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| 3. |
- Horvath, Robert, 1988-
(författare)
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Population genomic analyses of regulatory variation and selection in Brassicaceae species
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The impact of selection on regulatory variation and the contribution of regulatory changes to phenotypic variation has long been debated in evolutionary genetics. Because cis-regulatory elements such as promoters and enhancers can be difficult to identify, it has been more challenging to quantify the impact of selection on variation in cis-regulatory regions than in protein-coding regions. In this thesis, I use genomic tools to investigate gene expression variation and selection in Brassicaceae species. First, I investigated the genomic impact of selection on putative cis-regulatory regions in the genome of the crucifer species Capsella grandiflora (Brassicaceae) (Paper I). I used an assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) to empirically identify putative cis-regulatory regions as those located in accessible chromatin regions (ACRs) in the genome of the crucifer species Capsella grandiflora. Based on whole-genome resequencing data from a natural population, I then showed that ACRs are under stronger purifying selection than other intergenic regions and that they are depleted for transposable element (TE) insertions and enriched for expression quantitative trait loci (eQTL), as would be expected if ACRs are enriched for functional elements affecting gene expression. Second, I explored how the location and silencing of transposable elements (TEs) affects selection against TEs (Paper II). Specifically, I tested a trade-off model on epigenetic TE silencing, according to which the positive effects of TE silencing on preventing TE movement conflict with negative effects of TE silencing on nearby gene expression. I found that TE silencing through the RNA-directed DNA methylation (RdDM) pathway affects selection against TEs close to genes in C. grandiflora, which is consistent with the trade-off model. Third, I used Arabidopsis thaliana single-cell expression data to investigate the relationship between gene body methylation (gbM) and transcriptional regulation (Paper III). I found that there was an indirect correlation between gbM and gene expression noise as well as a direct correlation between gbM and gene expression consistency and potentially intron retention in Arabidopsis thaliana. Fourth, I investigated the impact of demographic history on genomic signatures of selection at linked sites (linked selection) (Paper IV). This study revealed that neutral genetic diversity in C. grandiflora with a stable effective population size is influenced by linked selection whereas in Arabidopsis lyrata, which underwent a recent and strong bottleneck, neutral diversity is mainly affected by population size change. In summary, this thesis offers new insights into determinants of gene expression variation, selection on genomic features linked to gene expression alteration, as well as on the effect of demographic history on linked selection patterns in Brassicaceae.
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| 4. |
- Gutiérrez-Valencia, Juanita, 1991-
(författare)
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Genomic studies of mating system variation in flowering plants
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The striking diversity of reproductive strategies that flowering plants exhibit remains one of the most intriguing conundrums in evolutionary biology. Pollination-related traits and mating system strategies have a major impact on the processes shaping plant evolution through their effects on genetic diversity and selection. In this thesis, I use population genomic methods to investigate the genetic underpinnings and genomic impact of cross- and self-fertilization in flowering plants. I first study the evolution and breakdown of the supergene that governs the balanced floral polymorphism of distyly in a wild flaxseed species (Linum tenue). Then I assess the consequences of shifts to self-fertilization on the intensity of sexual selection that populations experience, using the crucifer species Arabis alpina as a model. In chapters I, II and III, I investigated how the evolution of supergenes is impacted by their genetic architecture. Building on a de novo genome assembly, I used population genomic data to identify and characterize the distyly supergene in Linum tenue (chapter II). I found that the dominant allele at the distyly S-locus is defined by the presence of a 260-kb region carried in hemizygosity by thrum individuals. Importantly, the hemizygous region harbors, among others, a strong candidate gene for style length. S-linked genes did not exhibit signatures of relaxed purifying selection, consistent with expectations from previous empirical studies and forward simulations (chapter I) in suggesting that hemizygosity might slow down genetic degeneration of non-recombining haplotypes. In the light of similar studies conducted in independently evolved distylous lineages (reviewed in chapter I), our results indicate that distyly supergenes show convergent evolution at the molecular level. By conducting comparative studies of the genome sequences of L. tenue and closely related homostylous L. trigynum (chapter III), I identified candidate mutations for distyly breakdown at S-linked genes. I also investigated the genome-wide effects of the evolutionary transition to homostyly and self-fertilization in L. trigynum. I found that L. trigynum populations are highly inbred, and show significantly lower genetic diversity and more marked population structure than the obligately outcrossing L. tenue. However, I found only weak signatures of relaxed purifying selection in L. trigynum at the genome-wide scale, suggesting that self-fertilization has not had a major effect on the impact of selection. Finally, by analyzing whole-genome sequences from individuals of populations of A. alpina with contrasting mating strategies, I investigated if shifts to self-fertilization have a particularly marked impact on the evolution of genes involved in pollen-pollen competition (chapter IV). The results indicate that the reduced intensity of sexual selection that self-fertilizing populations experience translate into more pronounced signatures of relaxed purifying selection on genes expressed in male gametophyte components. Overall, this thesis contributes to our understanding of the genetic basis and evolution of plant reproductive strategies, and how they impact selection both locally and broadly across the genome.
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| 5. |
- Steige, Kim A.
(författare)
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Cis-regulatory variation and divergence in Capsella
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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