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Résumé Abstract RÉSUMÉ ABSTRACT Effets de la reproduction partiellement asexuée sur la dyna- Effects of partial asexuality on the dynamics of genotype frequen- mique des fréquences génotypiques en populations majori- cies in dominantly diploid populations tairement diploïdes Reproductive systems determine how genetic material is passed Les systèmes reproducteurs déterminent comment le matériel from one generation to the next, making them an important fac- génétique est transmis d’une génération à la suivante […]. Les tor for evolution. Organisms that combine sexual and asexual/ espèces qui combinent de la reproduction sexuée et asexuée/clo- clonal reproduction are very widespread [… yet] the effects of nale sont très répandues [… mais] l’effet de leur système repro- their reproductive system on their evolution are still controversial ducteur sur leur évolution reste énigmatique et discuté. and poorly understood. L’objectif de cette thèse est de modéliser la dynamique des fré- The aim of this thesis was to model the dynamics of genotype quences génotypiques d’une population avec une combinaison frequencies under combined sexual/clonal reproduction in domi- de reproduction sexuée et/ou clonale dans des cycles de vie prin- nantly diploid life cycles [. … A] state and time discrete Markov cipalement diploïdes [. … Un] modèle du type chaine de MarKov chain model served as the mathematical basis to describe [their] avec temps et états discrets sert de base mathématique pour changes […] through time. décrire [leurs] changements […] au cours du temps. The results demonstrate that partial clonality may indeed change Les résultats montrent que la reproduction partiellement asexuée the dynamics of genomic diversity compared to either exclusively peut en effet modifi er la dynamique de la diversité génomique sexual or exclusively clonal populations. […] Time has a crucial par rapport à une reproduction strictement sexuée ou strictement role in partially clonal populations and needs to be taken into asexuée. […] L’histoire démographique a un rôle important pour account in any analysis of their genomic diversity. les organismes partiellement clonaux et doit être prise en compte This thesis provides recommendations for data collection and a dans toute analyse […]. null hypothesis for the interpretation of population genetic/geno- Cette thèse fait des recommandations pour la collecte des don- mic data […]. Moreover, it includes new methods for the analy- nées et une hypothèse de base pour l’interprétation des données sis of genotype-based population genetic Markov chain models. de génétique/génomique […]. Ces résultats ont des retombées These results have a high potential relevance in several areas, dans plusieurs domaines, allant de la recherche fondamentale ranging from basic research […] to applications in agriculture […], […] à des applications en agriculture […], pêche […] et protection fi sheries […] and nature conservation […]. de la nature […]. Katja REICHEL • 10 décembre 2015 Mots-clés : évolution, biologie théorique, diversité génétique, Keywords: evolution, theoretical biology, genetic diversity, micro- microsatellites, polymorphismes nucléotidiques, génomique, satellites, single nucleotide polymorphisms, genomics, apomixis, Thèse AGROCAMPUS OUEST ÉCOLE DOCTORALE • Vie-Agro-Santé (VAS) apomixie, agamospermie, multiplication végétative, parthénoge- agamospermy, vegetative multiplication, parthenogenesis, sous le label de l’Université Européenne de Bretagne LABORATOIRE D’ACCUEIL nèse, mutation, dérive génétique, démographie, hybridation mutation, genetic drift, demography, hybridization • UMR INRA - AGROCAMPUS OUEST - pour obtenir le grade de Université de Rennes 1 : Institut de génétique, environnement DOCTEUR D’AGROCAMPUS OUEST et protection des plantes (IGEPP) Spécialité Biologie et Agronomie Effets de la reproduction partiellement asexuée sur la dynamique des fréquences génotypiques génotypiques partiellement fréquences des sur la dynamique la reproduction de Effets asexuée diploïdes populations majoritairement en David CAUSEUR Effets de la reproduction Professeur, AGROCAMPUS OUEST, Laboratoire de mathématiques AGROCAMPUS OUEST • Institut supérieur des sciences agronomiques, appliquées / président agroalimentaires, horticoles et du paysage Sylvain GLEMIN 65 rue de Saint-Brieuc – CS84215 – F-35042 Rennes Cedex partiellement asexuée Directeur de recherche, CNRS Montpellier, Uppsala Universitet / Tél. : 02 23 48 50 00 rapporteur www.agrocampus-ouest.fr Katja REICHEL sur la dynamique des • Christoph HAAG Chargé de recherche, CNRS Montpellier / rapporteur fréquences génotypiques Emmanuelle PORCHER 2015-29 Professeur, MNHN Paris / examinatrice — en populations Denis ROZE Chargé de recherche, CNRS Roscoff / examinateur C-123 majoritairement diploïdes Timothy SHARBEL Professeur, IPK Gatersleben, University of Saskatchewan / examinateur Thèse Jean-Christophe SIMON Directeur de recherche, UMR INRA-AO-UR1 IGEPP / directeur de thèse Solenn STOECKEL Chargé de recherche, UMR INRA-AO-UR1 IGEPP / co-directeur de thèse EFFECTS OF PARTIAL ASEXUALITY ON THE DYNAMICS OF GENOTYPE FREQUENCIES IN DOMINANTLY DIPLOID POPULATIONS EFFETS DE LA REPRODUCTION PARTIELLEMENT ASEXUEE SUR LA DYNAMIQUE DES FREQUENCES GENOTYPIQUES EN POPULATIONS MAJORITAIREMENT DIPLOIDES Thesis submitted by Katja Reichel to obtain a doctoral degree in biology from the Institut Supérieur des Sciences Agronomiques, Agro- Alimentaires, Horticoles et du Paysage (Agrocampus Ouest) Defended in Rennes, 10th December 2015 Jury members Sylvain GLEMIN CNRS Montpellier, Uppsala Universitet rapporteur Christoph HAAG CNRS Montpellier rapporteur Emmanuelle PORCHER MNHN Paris examiner Denis ROZE CNRS Roscoff examiner Timothy SHARBEL IPK Gatersleben, University of Saskatchewan examiner David CAUSEUR Agrocampus Ouest Rennes examiner Solenn STOECKEL INRA Le Rheu adviser Jean-Christophe SIMON INRA Le Rheu senior adviser Seht ihr den Mond dort stehen? Er ist nur halb zu sehen, Und ist doch rund und schön! So sind wohl manche Sachen, Die wir getrost belachen, Weil unsre Augen sie nicht sehn. Der Mond ist aufgegangen Matthias Claudius (1778) 3 4 A Foreword The work presented in this thesis was carried out during three years, from November 2012 to October 2015, at the Institute for Genetics, Environment and Plant Protection (IGEPP), a part of the French National Institute of Agricultural Research (INRA) situated in Le Rheu near Rennes, Brittany. It was co-financed to equal parts by the Doctoral Studies Allowance Programme (ARED) of the Brittany Region, and the Department of Plant Health and Environment (SPE) of the INRA. The subject of the thesis was embedded in the collaborative research project CLONIX (ANR-11-BSV7-0007), financed by the French National Agency for Research (ANR). This document is structured as a thesis by publication based on four manuscripts of research articles. According to the French Government Resolution of 6th January 2005 (NOR: MENS0402905A) and the internal standards of the Life Agronomy Health (VAS) doctoral school, it includes a summary of at least ten percent of the text (by number of pages) in French. In addition, the abstract is provided in German. The progress of this thesis was reported twice to a thesis advisory committee, whose members were: Sophie ARNAUD-HAOND (Ifremer Sète), Stéphane DE MITA (INRA Nancy), Fabien HALKETT (INRA Nancy), Florent MALRIEU (François Rabelais University Tours), Jean- Pierre MASSON (INRA Le Rheu), Denis ROZE (CNRS Roscoff), Jean-Christophe SIMON (INRA Le Rheu, senior advisor), Solenn STOECKEL (INRA Le Rheu, advisor) and Christian WALTER (Agrocampus Ouest Rennes, tutor). Official logo of the CLONIX project, designed by the author. 5 6 B Abstract – Résumé – Kurzfassung Abstract Effects of partial asexuality on the dynamics of genotype frequencies in dominantly diploid populations 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, both throughout the earth’s biomes and on the eukaryotic tree of life. However, 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, with the view of establishing a reference for future field studies. This involves two subtypes of partially clonal reproduction: either both reproductive modes co-occur (“acyclic partial clonality”), or they alternate (“cyclic clonality”). For both, a state and time discrete Markov chain model served as the mathematical basis to describe changes of the genotype frequencies 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. Moreover, both subtypes have different effects under selectively neutral conditions: while acyclic partial clonality leads to increased variation in the frequency of heterozygous genotypes within the population, the patterns observed under cyclic clonality depend on the sampling time (before or after sexual reproduction) and show a stronger effect on allele frequencies. The dynamics of population heterozygosity were also slowed down under acyclic partial clonality, yet this effect did not generally lead to slower adaptation under selection. Time has a crucial role in partially
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