Apomixis (asexual reproduction by seeds) has the considerable potential in agriculture and crop breeding due to its ability to produce genetically identical progenies in a form of persistent propagules, i.e. seeds. However, the processes laying behind the origin of apomixis and connected molecular mechanisms are still unknown. Despite the fact, that apomicts are considered to be an evolutionary dead-ends, they are often more widely distributed than their sexual relatives (this phenomenon is commonly referred to as geographical parthenogenesis (GP). Although this phenomenon is studied for decades, its causes are still not fully understood. Importantly, several recent studies pointed out that apomicts with limited genetic variability can at some extent react to changing environment through changes in gene transcription by epigenetic modifications. It is generally assumed, that hybridisation and polyploidization played a crucial role in the emergence of apomixis. For this reason, presented studies test the putative origin of selected polyploid apomicts and if the interspecific hybridisation between diploid sexuals triggers polyploidization using predominantly polyploid and apomictic genus Hieracium s. str. Surprisingly, the presented study demonstrates the hybrid origin of almost all investigated...

Les systèmes reproducteurs déterminent comment le matériel génétique est transmis d’une génération à la suivante […]. Les espèces qui combinent de la reproduction sexuée et asexuée/clonale sont très répandues [… mais] l’effet de leur système reproducteur sur leur évolution reste énigmatique et discuté.L’objectif de cette thèse est de modéliser la dynamique des fréquences génotypiques d’une population avec une combinaison de reproduction sexuée et/ou clonale dans des cycles de vie principalement diploïdes [. … Un] modèle du type chaine de Markov avec temps et états discrets sert de base mathématique pour décrire [leurs] changements […] au cours du temps.Les résultats montrent que la reproduction partiellement asexuée peut en effet modifier la dynamique de la diversité génomique par rapport à une reproduction strictement sexuée ou strictement asexuée. […] L’histoire démographique a un rôle important pour les organismes partiellement clonaux et doit être prise en compte dans toute analyse […].Cette thèse fait des recommandations pour la collecte des données et une hypothèse de base pour l’interprétation des données de génétique/génomique […]. Ces résultats ont des retombées dans plusieurs domaines, allant de la recherche fondamentale […] à des applications en agriculture […], pêche […] et protection de la nature […]. / Reproductive systems determine how genetic material is passed from one generation to the next, making them an important factor for evolution. Organisms that combine sexual and asexual/clonal reproduction are very widespread [… yet] the effects of their reproductive system on their evolution are still controversial and poorly understood.The aim of this thesis was to model the dynamics of genotype frequencies under combined sexual/clonal reproduction in dominantly diploid life cycles [. … A] state and time discrete Markov chain model served as the mathematical basis to describe [their] changes […] through time.The results demonstrate that partial clonality may indeed change the dynamics of genomic diversity compared to either exclusively sexual or exclusively clonal populations. […] Time has a crucial role in partially clonal populations and needs to be taken into account in any analysis of their genomic diversity.This thesis provides recommendations for data collection and a null hypothesis for the interpretation of population genetic/genomic data […]. Moreover, it includes new methods for the analysis of genotype-based population genetic Markov chain models. These results have a high potential relevance in several areas, ranging from basic research […] to applications in agriculture […], fisheries […] and nature conservation […].