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(Abies Balsamea [L.] Mill.) Et De Ses Relations Avec Le Sapin Subalpin (Abies Lasiocarpa [Hook] Nutt.) Dans L’Ouest Du Canada

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(Abies Balsamea [L.] Mill.) Et De Ses Relations Avec Le Sapin Subalpin (Abies Lasiocarpa [Hook] Nutt.) Dans L’Ouest Du Canada Étude phylogéographique pancanadienne du sapin baumier (Abies balsamea [L.] Mill.) et de ses relations avec le sapin subalpin (Abies lasiocarpa [Hook] Nutt.) dans l’ouest du Canada Thèse Benjamin Cinget Doctorat en sciences forestières Philosophiæ Doctor (Ph. D.) Québec, Canada © Benjamin Cinget, 2015 Résumé La structure phylogéographique et l’histoire postglaciaire du sapin baumier (Abies balsamea), ont été étudiées en utilisant l’ADN mitochondrial (ADNmt) et l’ADN chloroplastique (ADNcp). La différenciation génétique entre populations est ainsi apparue importante pour l’ADNmt (dispersé par les graines) et pour l’ADNcp (dispersé par le pollen puis par les graines), impliquant donc un flux de gènes par le pollen plus restreint chez le sapin baumier que celui habituellement observé chez d’autres conifères boréaux. Cette faible dispersion du pollen est supposée due aux propriétés structurales et la faible production de pollen, mais aussi à la récurrence des épidémies de tordeuse du bourgeon de l’épinette limitant les efforts reproductifs du sapin baumier. Par ailleurs, les polymorphismes de l’ADNmt et de l’ADNcp sont apparus géographiquement structurés, mettant en évidence une concordance incomplète d’au moins cinq lignées chloroplastiques et cinq lignées mitochondriales, résultante des flux de gènes chloroplastiques en place depuis l’Holocène. Enfin, de nouvelles combinaisons de génomes cytoplasmiques ont été observées permettant la détection de plusieurs cas de capture de génome cytoplasmique. L’étude de l’étendue et de la direction de l’introgression cytoplasmique est utile pour comprendre la dynamique des zones hybrides entre espèces interfécondes. L’introgression cytoplasmique entre Abies lasiocarpa x Abies balsamea a été caractérisée en utilisant des marqueurs de l’ADNmt et de l’ADNcp. L’utilisation des données génétiques et paléobotaniques a permis de définir la dynamique de la zone hybride en évaluant la concordance entre les localisations actuelle et historique de la zone hybride. Les flux de gènes de l’ADNcp sont apparus plus importants que ceux de l’ADNmt et la distribution géographique des mitotypes était plus concordante avec la répartition des espèces. Ces évidences génétiques, en accord avec un modèle de zone hybride stable, ont été confirmées par la chronologie de colonisation postglaciaire dérivée de données fossiles publiées, contrastant avec les attendus d’un scénario de zone hybride mobile et les observations habituellement faites chez les conifères. Enfin, bien que les flux de gènes interspécifiques de l’ADNcp semblent principalement conditionnés par les vents d’ouest dominants, des facteurs non-neutres pourraient aussi jouer un rôle dans le maintien de cette zone hybride stable. III Abstract The phylogeographic structure and postglacial history of balsam fir (Abies balsamea) were inferred using mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA). Population differentiation was high for both mtDNA (dispersed by seeds only) and cpDNA (dispersed by both seeds and pollen), implying a more restricted pollen gene flow in balsam fir than usually observed for other boreal conifers. Reduced pollen dispersal due to its structural properties and the recurrence of spruce budworm outbreaks limiting the reproductive effort of balsam fir are likely related to this trend. Polymorphisms from the mtDNA and cpDNA genomes were geographically structured, indicating the existence of at least five genetically distinct glacial lineages. The concordance between mtDNA and cpDNA lineages was not complete, reflecting restricted but nonetheless detectable cpDNA gene flow between lineages since the Holocene recolonization. New cpDNA and mtDNA genome combinations resulting from this recent gene flow and cytoplasmic genome capture were also observed. Studying the extent and direction of cytoplasmic introgression is useful to unravel the dynamics of hybrid zones between interbreeding species. The extent of cytoplasmic introgression in the Abies lasiocarpa x Abies balsamea species complex was characterized using markers from the mitochondrial (mtDNA) and chloroplast (cpDNA) genomes. Hybrid zone dynamics since postglacial colonization was inferred by assessing the concordance between current and historical locations of the hybrid zone using genetic and paleoecological data. Interspecific gene flow was higher for cpDNA than mtDNA markers and the geographic distribution of mitotypes was thus more congruent with species distributions than chlorotypes. This genetic signature was contrary to expectations under a moving hybrid zone scenario, as well as empirical observations in conifers. Genetic evidence for a stable hybrid zone was corroborated by the colonization chronology derived from published fossil data. While cpDNA interspecific gene flow seemed primarily driven by westerly winds, non- neutral factors may also play a role in maintaining of this complex yet stable hybrid zone. V Table des matières Résumé .............................................................................................................................................. III Abstract .............................................................................................................................................. V Table des matières .......................................................................................................................... VII Liste des tableaux ............................................................................................................................. XI Liste des figures ............................................................................................................................. XIII Remerciements .............................................................................................................................. XVII Avant-propos .................................................................................................................................. XIX Chapitre 1 : Introduction générale ............................................................................ 1 1.1. HISTOIRE DE CHANGEMENTS CLIMATIQUES ......................................................................... 1 1.1.1. La dernière glaciation : l’Amérique du Nord sous la glace ............................................................ 1 1.1.2. Les espèces face aux changements ................................................................................................ 3 1.1.3. Écologie et biologie : sapin baumier et sapin subalpin ................................................................. 5 1.2. LA DIVERSITÉ GÉNÉTIQUE, COMPOSANTE DE LA BIODIVERSITÉ .................................... 11 1.2.1. Diversité génétique en conservation ............................................................................................. 11 1.2.2. Diversité génétique, dimension spatio-temporelle ....................................................................... 11 1.3. PHYLOGÉOGRAPHIE, DISCIPLINE MULTIDIMENSIONNELLE .............................................. 13 1.3.1. Sur les traces du passé : survie à l’Âge glaciaire ......................................................................... 13 1.3.2. Mécanismes de la colonisation postglaciaire ............................................................................... 15 1.3.3. Les arbres en phylogéographie ...................................................................................................... 16 1.3.4. Tripartisme de la cellule végétale : les trois génomes ................................................................. 17 1.3.5. Méthodes d’analyse de la diversité génétique .............................................................................. 19 1.4. OBJECTIFS ET HYPOTHÈSES DE RECHERCHE .................................................................... 21 1.5. RÉFÉRENCES ............................................................................................................................ 22 Chapitre 2 : Phylogéographie du sapin baumier ................................................... 35 2.1. RÉSUMÉ ..................................................................................................................................... 36 2.2. ABSTRACT ................................................................................................................................. 38 2.3. INTRODUCTION ......................................................................................................................... 39 2.4. MATERIALS AND METHODS .................................................................................................... 40 2.4.1. Ethics Statement .............................................................................................................................. 40 2.4.2. Population sampling and DNA extraction ..................................................................................... 41 2.4.3. Screening of mtDNA polymorphism, PCR conditions and genotyping ...................................... 42 2.4.4. Screening of cpDNA polymorphism, PCR conditions and genotyping ...................................... 43 VII 2.4.5. Data analysis .................................................................................................................................... 44 2.5. RESULTS .................................................................................................................................... 45 2.5.1. MtDNA polymorphisms ..................................................................................................................
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