The reciprocal evolutionary effects pathogens and their hosts have on each other are one of the most powerful selective forces in evolution, leading to adaptive phenotypic and genetic changes of both antagonists. In nature, bacterial infections often consist of more than one genotype. Since the host represents a limited resource, an interaction between the co-infecting genotypes is likely and potentially has fundamental effects on the interaction with the host. Nevertheless, most studies focus only on the interaction of parasite and host, ignoring within-host dynamics between co-infecting parasite genotypes. In my thesis, I focussed on both, the consequences of long-term host-parasite evolution for the interaction with a host and for parasite-parasite interactions. The first chapter is a comprehensive theoretical overview presenting the effects of multiple infections on virulence towards the host. It summarizes not only potential social interactions between the different co-infecting genotypes, but also discusses the relevance of their relatedness and resulting consequences for virulence. In the second chapter I present the results from a long-term evolution experiment using Caenorhabditis elegans as a multicellular host, singly infected with one of two different strains of its microparasite Bacillus thuringiensis. I found that both, coevolution with and adaptation to the host, led to rapid diversification of the clonal parasite populations into distinct clones. These clones showed strain specific phenotypic changes (i.e., killing rate and production of antagonistic substances) not only within, but also between replicate populations. In the third chapter one of these evolved clones was compared to its ancestral, non-evolved clone on the molecular level. By using next generation genome sequencing, I analysed the underlying genetic mechanisms that led to diversification within the clonal population presented in chapter two. In this study I demonstrated the importance of bacterial genomic plasticity for adaptation: the results revealed that changes were mainly caused by mobile genetic elements (MGEs), especially transposases and plasmids. Overall this thesis shows that the evolutionary selection pressure mediated by a multicellular host causes phenotypic diversification of the parasite. This change within and between parasite populations is reflected on both, the phenotypic and the genetic level.

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The evolutionary relevance of homeotic alterations for the origin of new taxonomic entities is still a controversial objective in plant sciences. In this context, the discovery of a floral homeotic variant of Capsella bursa-pastoris in natural populations offers the unique opportunity to elucidate the evolutionary significance of homeotic mutants in the wild. Since all petals are transformed into additional stamens, the variant was termed Stamenoid petals (Spe). In this thesis, a combination of ecological and molecular characterisation of the variant was performed, to improve the understanding of evolutionary processes in plant populations. Molecular markers were used to analyze genetic differentiation among known provenances and also within a large sympatric population of wild-type and homeotic mutant. The results clearly suggest a repeated evolution of the novel flower morphology. Furthermore, genetic analyses provided substantial evidence, that the two floral variants are well-defined into flower-type dependent sub-samples within one population. The evaluation of phenotypic traits elucidated that the homeotic variant is not hampered in fitness. In greenhouse and field experiments, a significant ecological differentiation in the onset of flowering was detected among variants. Finally, the novel floral phenotype shows a co-dominant inheritance, and a marker-assisted mapping approach exposed a single locus in a genetic map. In conclusion, the comprehensive study of ecological and molecular aspects indicates that the floral homeotic variant may be treated as an established taxonomic entity and proved the predicted role as model for evolutionary objectives. Since morphological alterations like Spe are discussed as a result of macroevolution, the homeotic variant of C. bursa-pastoris provides the opportunity to survey a (macro)evolutionary novelty in association with continuous micro-evolutionary adaptation

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