Proefschrift--Utrecht. / Bibliography: p. 198-200.

The study of population biology and genetic diversity provides insights to the potential for colonization and can detect geographic patterns of invasion and range expansion, which is essential to predict how species might react to dynamic environments and the global climate change. An outstanding example for a successful colonizer is the Shepherd’s Purse (Capsella bursa-pastoris (L.) Medik.). It is closely related to Arabidopsis thaliana, the “lab rat“ of plant scientists, and originated 100-300 kya from the hybridization between an ancestral C. orientalis and an ancestor from the C. grandiflora/rubella lineage according to the current literature (Douglas et al., 2015). Many species invasions are the direct or indirect consequence of human activities, and the worldwide distribution of the Shepherd’s Purse is partially associated with prehistorical human migration (e.g. Neuffer & Hurka, 1999; Cornille et al., 2016). With the novel genome-wide restriction site-associated DNA sequencing (RADseq) it is possible to perform population genetic studies of unprecedented depth and complexity and allowed the exploration of evolutionary history, range expansion and invasion patterns of this plant species. I will show here that a large number of loci and a wide global sampling area, using seed collections from nearly all over the world covering a large part of the whole distribution area of this ubiquitous weed, reveal finer-scale population structure of C. bursa-pastoris than has previously been detected. The work proposed here generates a comprehensive picture of phenotypic diversity in relationship to genetic variation within C. bursa-pastoris. Genetic variation is clearly geographically structured and split into two lineages apparently adapted to different environments, with one population predominantly distributed in Mediterranean climate regions and the other predominantly in temperate climate regions. The worldwide distribution patterns of the genetic variation can be explained by intra- and intercontinental migration, but environmental filtering due to climate pre-adaption seems also involved. The two clusters point to an early diversification into two lineages or may even suggest multiple origins of the species.This dissertation consists of three papers and manuscripts written during my time as a doctoral student at the Osnabrück University.

The aim of this diploma thesis is determination of alfalfa (Medicago sativa) infestation in Agricaltural company Kvasicko a. s. The monitoring of infestation was doing from 2013 to 2016 on land Odšenkovna, sawn on 29. 8. 2013, and on land Novina levá, sawn on 11. 4. 2014. Evaluation was made by counting method. The results of this evaluation were processed with DCA analysis and canonical corespondence analysis (CCA). It was found 11 species of weeds on observed lands during the monitoring. The most frequently weeds were: Capsella bursa-pastoris, Stellaria media, Taraxacum sec. Ruderalia and Veronica.

Yes / Capsella bursa-pastoris (L.) Medik. is a species with a cosmopolitan distribution which shows considerable morphological variation. Numerous authors have recognised widely differing numbers of varieties, microspecies or other infraspecific subdivisions (segregates) of this species. In an attempt to clarify this situation, we grew British material of the species under controlled conditions through to the F) generation to remove environmental variation, and assessed the plants on the basis of a range of morphological criteria, namely leaf shape, capsule size and also length of time taken to flower. Analysis of these characteristics consistently produced four basic groups, which had been previously described. Herbarium specimens could also nearly always be assigned to one of these groups. Limited chromosome counts suggest that two of these groups are diploid and two are tetraploid. We suggest this fourfold division into broad groups reflects the major genetic separations within the species, but that there is also considerable phenotypic plasticity shown by C. bursapastoris in response to factors such as shade or trampling. These four groups appear to differ in their geographic.al distribution in Britain. KEYWORDS: Shepherd's Purse, morphological variation, leaf characters, capsule characters, chromosome

No

Yes / Rapid advances in short-read DNA sequencing technologies have revolutionized population genomic studies, but there are genomic regions where this technology reaches its limits. Limitations mostly arise due to the difficulties in assembly or alignment to genomic regions of high sequence divergence and high repeat content, which are typical characteristics for loci under strong long-term balancing selection. Studying genetic diversity at such loci therefore remains challenging. Here, we investigate the feasibility and error rates associated with targeted long-read sequencing of a locus under balancing selection. For this purpose, we generated bacterial artificial chromosomes (BACs) containing the Brassicaceae S-locus, a region under strong negative frequency-dependent selection which has previously proven difficult to assemble in its entirety using short reads. We sequence S-locus BACs with single-molecule long-read sequencing technology and conduct de novo assembly of these S-locus haplotypes. By comparing repeated assemblies resulting from independent long-read sequencing runs on the same BAC clone we do not detect any structural errors, suggesting that reliable assemblies are generated, but we estimate an indel error rate of 5.7×10−5. A similar error rate was estimated based on comparison of Illumina short-read sequences and BAC assemblies. Our results show that, until de novo assembly of multiple individuals using long-read sequencing becomes feasible, targeted long-read sequencing of loci under balancing selection is a viable option with low error rates for single nucleotide polymorphisms or structural variation. We further find that short-read sequencing is a valuable complement, allowing correction of the relatively high rate of indel errors that result from this approach. / This study was supported by a grant from the Swedish Research Council to T.S.

No

Yes / A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male speci-ficity components, encoded by the genesSRKandSCRat the self-incompatibility locus (S-lo-cus). Theory predicts thatS-linked mutations, and especially dominant mutations inSCR, arelikely to contribute to loss of SI. However, few studies have investigated the contribution ofdominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer speciesCapsella orientalis, by combining genetic mapping, long-read sequencing of completeS-hap-lotypes, gene expression analyses and controlled crosses. We show that loss of SI inC. orientalisoccurred<2.6 Mya and maps as a dominant trait totheS-locus. We identify a fixed frameshift deletion in the male specificity geneSCRand con-firm loss of male SI specificity. We further identify anS-linked small RNA that is predicted tocause dominance of self-compatibility. Our results agree with predictions on the contribution of dominantS-linked mutations toloss of SI, and thus provide new insights into the molecular basis of mating system transitions. / Work at Uppsala Genome Center is funded by 550 RFI / VR and Science for Life Laboratory, Sweden. The SNP&SEQ Platform is supported by 551 the Swedish Research Council and the Knut and Alice Wallenberg Foundation. V.C. 552 acknowledges support by a grant from the European Research Council (NOVEL project, 553 grant #648321). The authors thank the French Ministère de l’Enseignement Supérieur et de la 554 Recherche, the Hauts de France Region and the European Funds for Regional Economical 555 Development for their financial support to this project. This work was supported by a grant 556 from the Swedish Research Council (grant #D0432001) and by a grant from the Science for 557 Life Laboratory, Swedish Biodiversity Program to T.S. The Swedish Biodiversity Program is 558 supported by the Knut and Alice Wallenberg Foundation.

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.