Global ETD Search

1	Fitness effects of new mutations and adaptive evolution in house mice Kousathanas, Athanasios January 2013 (has links) Knowledge of the distribution of fitness effects of new mutations (DFE) can enable us to quantify the amount of genetic change between species that is driven by natural selection and contributes to adaptive evolution. The primary focus of this thesis is the study of methods to infer the DFE and the study of adaptive evolution in the house mouse subspecies Mus musculus castaneus. Firstly, I extended previous methodology to model the DFE based on polymorphism data. Methods that have previously been used to infer the DFE from polymorphism data have relied on the assumption of a unimodal distribution. I developed new models that can be used to fit DFEs of arbitrary complexity, and found that multimodality can be detected by these models given enough data. I used these new models to analyse polymorphism data from Drosophila melanogaster and M. m. castaneus, and found evidence for a unimodal DFE for D. melanogaster and a bimodal DFE for M. m. castaneus. Secondly, I investigated the contribution of change in coding and non-coding DNA to evolutionary adaptation. I used a polymorphism dataset of ~80 loci from M. m. castaneus sequenced in 15 individuals to investigate selection in protein-coding genes and putatively regulatory DNA close to these genes. I found that, although protein-coding genes are much more selectively constrained than non-coding DNA, they experience similar rates of adaptive substitution. These results suggest that change in functional non-coding DNA sequences might be as important as protein-coding genes to evolutionary adaptation. Thirdly, I used whole genome data from 10 M. m. castaneus individuals to compare the rate of adaptive substitution in autosomal and X-linked genes. I found that, on average, X-linked genes have a 1.8 times faster rate of adaptive substitution than autosomal genes. I also found that faster-X evolution is more pronounced for male-specific genes. I used previously developed theory to show that these observations can be explained if new advantageous mutations are recessive, with an average dominance coefficient less than or equal to 0.25. These results can help to explain the long-studied phenomenon of the large effect of the X chromosome in speciation. 572.8
2	Experimental Evolution : and Fitness Effects of Mutations Knöppel, Anna January 2016 (has links) Bacteria have small, streamlined genomes and evolve rapidly. Their large population sizes allow selection to be the main driver of evolution. With advances in sequencing technologies and precise methods for genetic engineering, many bacteria are excellent models for studying elementary questions in evolutionary biology. The work in this thesis has broadly been devoted to adaptive evolution and fitness effects of different types of mutations. In Paper I we experimentally tested the fitness constrains of horizontal gene transfer (HGT), which could be used to predict how the fixation of HGT events are affected by selection and fitness effects. We found that the majority of the examined HGT inserts were indistinguishable from neutral, implying that extra DNA transferred by HGT, even though it does not confer an immediate selective advantage, could be maintained at transfer-selection balance and serve as a reservoir for the evolution of novel beneficial functions. Paper II examined why four synonymous mutations in rpsT (encoding ribosomal protein S20) reduced fitness, and how this cost could be genetically compensated. We found that the cause for the fitness reduction was low S20 levels and that this lead to a defective subpopulation of 30S subunits lacking S20. In an adaptive evolution experiment, these impairments were compensated by up-regulation of S20 though various types of mutations. In Paper III we continued the studies of how the deleterious rpsT mutations could be compensated. The mutations either down-regulated the global regulator Fis or altered a subunit of the RNA polymerase (rpoA). We found that the decreased S20 levels in the cells causes an assembly defect of the 30S particles and that the fis and rpoA mutations restored the skewed S20:ribosome ratio by both increasing S20 levels and decreasing other ribosomal components. Paper IV examined adaptation of two bacterial species to different growth media. A total of 142 different adaptive mutations were identified and 112 mutants were characterized in terms of fitness. We found that the experimental variation in fitness measurements could be reduced 10-fold by introducing some adaptive mutations prior to the experiment, allowing measurements of fitness differences as small as 0.04%. Experimental evolution Fitness effects mutations S20 fis ribosome horizontal gene transfer adaptation synonymous mutations
3	Processes and Rates of Bacterial Evolution Delaney, Nigel Francis 07 December 2013 (has links) A long-standing question in evolutionary biology is whether adaptation will typically proceed through a few mutations with large selective effects or many mutations with small effects. Many studies have implicated few loci of major effect, but it has been predicted that small-effect mutations should exist and contribute to adaptation. However, such mutations have not been found in many studies, either because they do not exist or because the experimental design limited their detection. To determine the effects and types of mutations contributing to adaptation, I studied laboratory and wild populations of bacteria. I characterized the distribution of the effect sizes in laboratory populations of an aerobic bacterium, Methylobacterium extorquens, and studied the types of genetic changes associated with adaptation to a novel host in wild populations of Mycoplasma gallisepticum. Biology Evolution & development Genetics Automation Fitness Effects Medium Development Methylobacterium
4	Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina Laenen, B., Tedder, Andrew, Nowak, M.D., Toräng, P., Wunder, J., Wötsel, S., Steige, K.A., Kourmpetis, Y., Odong, T., Drouzas, A.D., Bink, M.C.A.M., Ågren, J., Coupland, G., Slotte, T. 13 September 2019 (has links) Yes / Plant mating systems have profound effects on levels and structuring of genetic variation and can affect the impact of natural selection. Although theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population-genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina. We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles, whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, mating system and demography shape the impact of purifying selection on genomic variation in A. alpina. These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies. / This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1707492115/-/DCSupplemental. Arabis alpina Self-fertilisation Demographic history Bottleneck Fitness effects Genetic load
5	Interactions between natural enemies and the dioecious herb Silene dioica Pettersson, Viktoria January 2009 (has links) About 6% of all angiosperms are dioecious. This separation of sexual function to male and female individuals, and the fundamentally different patterns of reproductive resource allocation that follows that separation, are thought to have important ecological and evolutionary consequences for plant enemy interactions. I have studied whether intersexual differences in susceptibility to natural enemies can be explained by intersexual differences in resource allocation. In cases when sexual dimorphic traits form the target resource of a particular enemy I expected the enemy to select the best resource. The study system is the perennial dioecious herb, Silene dioica (Caryophyllaceae) and three of its specialist natural enemies, two insect herbivores the fly Delia criniventris (Anthomyiidae) and the twirler moth Caryocolum viscariella (Gelechiidae) and one systemic anther smut fungus Microbotryum violaceum. All three share the same food recourse, the floral stems, of their host plant. I studied the interaction on nine islands in a rising Bothinan archipelago over seven consecutive years. Both herbivores attacked female plants more than male plants (D. criniventris, 32.8% females, 30.7% males; C. viscariella, 4% females, 2% males). This attack pattern was consistent over years and islands and also correlated with a number of sexually dimorphic traits suggesting that females offer the better resource. Herbivore attack had no effect on plant survival but a significant effect on re-flowering the following year. Non-attacked females had an estimated mean re-flowering rate of 30.2%, and non-attacked males of 31%. Herbivore-attacked females had an estimated re-flowering rate of 46% compared with 38.4% for males. Females showed a stronger compensatory response to attack and tended to re-flower more often than males. Attack rates differed markedly in the different stages of primary succession. They were consistently higher in the youngest zone and decreased in parallel to progressing succession. This zonal pattern of decreasing attack rates correlated with several plant attributes, a decrease in plant size and nitrogen content, and an increased content of secondary compounds, but not to host plant density. We failed to come up with a simple explanation for the spatial structure with chronic high attack rates in the younger zones. However, the consistent patterns in attack rate suggest that a suite of abiotic and biotic factors interact and reinforce the strength and direction of selection. In general females were more frequently diseased by the anther smut Microbotryum violaceum than males with two exceptions. Disease frequencies were male biased on islands with low disease levels and in one of the seven study years. The change in disease frequencies from male to female bias confirm earlier studies suggesting that the relative contribution of the two components of infection risk, disease encounter and per contact infection probability can vary with population disease level. The change in the proportions of diseased males and females that was observed in one of the study years, followed a year of extreme weather conditions (prolonged drought). Both sexes showed a similar decline in flowering but diseased females decreased more than diseased males. This difference in response can be explained if considering that disease is more resource demanding in females than in males. Except for resources needed for mycelial growth and spore production, in females resources are also needed to restructure their sex expression and produce anthers. My study shows (i) that in dioecious species traits that are sexually dimorphic are of great importance for understanding the outcome of interactions with natural enemies, (ii) that the strengths and directions of enemy-host plant interactions are strongly shaped by both biotic and abiotic conditions. Silene dioica Delia criniventris Caryocolum viscariella Microbotryum violaceum plant-herbivore interactions plant -pathogen interactions sex bias sex rato successional gradients fitness effects Skeppsvik Archipelago Terrestrial ecology Terrestisk ekologi
6	Investigating Evolutionary Innovation in Yeast Heat Shock Protein 90 Cote-Hammarlof, Pamela 30 July 2020 (has links) The Heat Shock Protein 90 (Hsp90) is an essential and highly conserved chaperone that facilitates the maturation of a wide array of client proteins, including many kinases. These clients in turn regulate a wide array of cellular processes, such as signal transduction, and transcriptional reprogramming. As a result, the activity of Hsp90 has the potential to influence physiology, which in turn may influence the ability to adapt to new environments. Previous studies using a deep mutational scanning approach, (EMPIRIC) identified multiple substitutions within a 9 amino acid substrate-binding loop of yeast Hsp90 that provides a growth advantage for yeast under elevated salinity conditions and costs of adaptation under alternate environments. These results demonstrate that genetic alterations to a small region of Hsp90 can contribute to evolutionary change and promote adaptation to specific environments. However, because Hsp90 is a large, highly dynamic and multi-functional protein the adaptive potential and evolutionary constraints of Hsp90 across diverse environments requires further investigation. In this dissertation I used a modified version of EMPIRIC to examine the impact of environmental stress on the adaptive potential, costs and evolutionary constraints for a 118 amino acid functional region of the middle domain of yeast Hsp90 under endogenous expression levels and the entire Hsp90 protein sequence under low expression levels. Endogenous Hsp90 expression levels were used to observe how environment may affect Hsp90 mutant fitness effects in nature, while low expression levels were used as a sensitive readout of Hsp90 function and fitness. In general, I found that mutations within the middle domain of Hsp90 have similar fitness effects across many environments, whereas, under low Hsp90 expression I found that the fitness effects of Hsp90 mutants differed between environments. Under individual conditions multiple variants provided a growth advantage, however these variants exhibited growth defects in other environments, indicating costs of adaptation. When comparing experimental results to 261 extant eukaryotic sequences I find that natural variants of Hsp90 support growth in all environments. I identified protein regions that are enriched in beneficial, deleterious and costly mutations that coincides with residues involved in co-chaperone-client-binding interactions, stabilization of Hsp90 client-binding interfaces, stabilization of Hsp90 interdomains and ATPase chaperone activity. In summary, this thesis uncovers the adaptive potential, costs of adaptation and evolutionary constraints of Hsp90 mutations across several environments. These results complement and extend known structural and functional information, highlighting potential adaptive mechanisms. Furthermore, this work elucidates the impact environment can have on shaping Hsp90 evolution and suggests that fluctuating environments may have played a role in the long-term evolution of Hsp90. systematic mutant scans in yeast environmental adaptation in yeast Biochemistry Molecular Biology
7	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
8	Estimation et analyse du taux de substitution adaptatif chez les animaux / Estimation and analysis of the adaptive substitution rate in animals Rousselle, Marjolaine 26 November 2018 (has links) Comprendre les déterminants du taux d’adaptation est une question primordiale en évolution moléculaire. En particulier, l’influence de la taille efficace de population sur la sélection positive, ainsi que la nature des changements d’acides aminés qui mènent à de l’adaptation sont des questions encore débattues. Pour y répondre, la méthode DFE-α, dérivée du test fondateur de McDonald & Kreitman, est un outil puissant pour mesurer le taux de substitution adaptatif. Elle est néanmoins sensible à certains biais. Au cours de cette thèse, nous avons identifié deux biais majeurs de cette méthode, les fluctuations de long-terme du régime de sélection-dérive via des fluctuations démographiques, et la conversion génique biaisée vers GC (gBGC). Via des simulations, nous avons montré que divers scénarios plausibles de fluctuations démographiques peuvent mener à une sur-estimation du taux de substitution adaptatif. Nous avons aussi obtenu des indications empiriques que le régime de sélection-dérive récent ne reflète pas le régime de sélection-dérive de long-terme chez diverses espèces animales, ce qui représente une violation d’une hypothèse forte de la méthode DFE-α. D’autre part, nous avons montré que la gBGC entraîne une sur-estimation du taux de substitution adaptatif chez les primates et les oiseaux. Via un jeu de données de neuf taxons de métazoaires et un total de 40 espèces, nous avons d’une part initié une analyse visant à identifier la nature des changements d’acides aminés qui mènent à l’adaptation, et montré que les changements radicaux sont soumis à une plus forte sélection purificatrice que les changements conservatifs. D’autre part, nous avons pu évaluer le lien entre la taille efficace et le taux de substitution adaptatif tout en prenant en compte les deux sources de biais explorées précédemment. Nous avons mis en évidence pour la première fois une relation négative entre le taux de substitution adaptatif et des traits d’histoire de vie représentatifs de la taille de population de long-terme. Ce résultat va à l’encontre de l’hypothèse canonique d’une adaptation plus efficace en grandes populations. / Understanding the determinants of the adaptive substitution rate is a central question inmolecular evolution. In particular, the influence of the effective population size N e on positiveselection as well as the nature of amino acid changes that lead to adaptation are still debated. TheDFE-α method, which was derived from the seminal McDonald & Kreitman test, is a powerful toolfor estimating the adaptive substitution rate. However, it is sensitive to various sources of bias. Inthis thesis, we identified two major sources of bias of this test, long-term fluctuations of theselective-drift regime through demographic fluctuations, and GC-biased gene conversion (gBGC).Using simulations, we showed that under plausible scenarios of fluctuating demography, the DFE-αmethod can lead to a severe over-estimation of the adaptive substitution rate. We also showed thatpolymorphism data reflect a transient selective-drift regime which is unlikely to correspond to theaverage regime experienced by genes and genomes during the long-term divergence betweenspecies. This violates an important assumption of the DFE-α method. Our results also indicate thatgBGC leads to an over-estimation of the adaptive substitution rate in primates and birds. Using adataset of nine metazoan taxa for a total of 40 species, we started an analysis aiming at identifyingthe type of amino acid changes that are more prone to adaptation, and evaluated the link between N eand the adaptive substitution rate while accounting for the two sources of bias previously explored.We reveal for the first time a negative relationship between the adaptive substitution rate and life-history traits representative of long-term N e . This result is in contradiction with the widespreadhypothesis that adaptation is more efficient in large populations. Adaptation moléculaire Test de McDonald & Kreitman Conversion génique biaisée vers GC Effets en fitness des mutations Fluctuations démographiques Animaux Molecular adaptation McDonald & Kreitman test GC-Biased gene conversion Fitness effects of mutation Demographic fluctutations Animals
9	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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