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Saccharomyces Paradoxus En Tant Que Système D'étude De La Spéciation Dans Les Populations Naturelles

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Saccharomyces Paradoxus En Tant Que Système D'étude De La Spéciation Dans Les Populations Naturelles Saccharomyces paradoxus en tant que système d’étude de la spéciation dans les populations naturelles Mémoire Guillaume Charron Maîtrise en biologie Maître ès sciences (M.Sc.) Québec, Canada © Guillaume Charron, 2015 RÉSUMÉ La spéciation implique l’établissement de barrières à la reproduction entre les espèces en formation. Bien que leurs bases moléculaires soient identifiées, l’émergence de ces barrières dans le temps et la manière dont elles se propagent à l'intérieur des populations reste peu connue. Les objectifs de cette étude sont i) de déterminer la présence de Saccharomyces paradoxus au Québec ii) de déterminer le niveau d’isolement reproducteur post-zygotique entre les lignées américaines de S. paradoxus et iii) de le corréler avec la divergence génétique et les réarrangements chromosomiques. Nous avons échantillonné divers substrats au Québec afin d’isoler S. paradoxus. L’identification des levures au niveau de l’espèce s’est fait à l’aide des séquences ITS. En laboratoire nous avons vérifié le caryotype des souches de S. paradoxus par PFGE, procédé à des croisements entre les lignées et estimé l’isolement reproducteur à l’aide de la survie des spores hybrides. Notre étude confirme la présence des lignées américaines de S. paradoxus au Québec. Un isolement reproducteur est présent entre et à l’intérieur de ces lignées. La variation au niveau des profils chromosomiques à l’intérieur des lignées est corrélée avec l’isolement reproducteur. Nos résultats suggèrent que la variation au niveau des réarrangements chromosomiques ségrégerait au sein des populations et jouerait un rôle dans l’initiation de l’isolement reproducteur. iii ABSTRACT Speciation involves the emergence of reproductive barriers between the incipient species. Although the molecular bases of these barriers have been identified, we lack knowledge about the timing of their emergence and their propagation through populations. The objectives of this project are i) to look for the presence of S. paradoxus in the province of Québec, ii) to determine the level of post-zygotic reproductive isolation between the American lineages of S. paradoxus and iii) to correlate this reproductive isolation with genetic divergence and chromosomal rearrangements. We sampled different substrates through the Province of Québec to isolate S. paradoxus. Yeasts were identified to the species level using ITS sequences. We used a PFGE method to obtain the karyotypes from the S. paradoxus yeast, made experimental crosses and estimated reproductive isolation by counting surviving hybrid spores. Our study confirms the presence of the two S. paradoxus lineages in the province of Québec. We also find that reproductive isolation is not only present between strains of the two lineages but also between strains from the same lineage. A great intra-lineage variation in the chromosomal profiles is correlated with reproductive isolation. Our results suggest that variation of chromosomal rearrangements could segregate between populations and could be involved in the initiation of reproductive isolation. v TABLE DES MATIÈRES RÉSUMÉ ................................................................................................................................ III ABSTRACT .............................................................................................................................. V TABLE DES MATIÈRES.......................................................................................................... VII LISTE DES FIGURES ............................................................................................................... IX LISTE DES ANNEXES ............................................................................................................. XI REMERCIEMENTS ............................................................................................................... XIII AVANT-PROPOS ................................................................................................................... XV INTRODUCTION GÉNÉRALE .................................................................................................... 1 SPÉCIATION ........................................................................................................................... 1 ISOLEMENT REPRODUCTEUR .................................................................................................. 2 ISOLEMENT REPRODUCTEUR POST-ZYGOTIQUE ....................................................................... 4 ISOLEMENT REPRODUCTEUR POST-ZYGOTIQUE INTRINSÈQUE .................................................. 4 RÉARRANGEMENTS CHROMOSOMIQUES .................................................................................. 5 CHANGEMENTS AU NIVEAU DE LA PLOÏDIE .............................................................................. 5 INCOMPATIBILITÉS GÉNÉTIQUES ............................................................................................. 6 INCOMPATIBILITÉ ENTRE GÉNOME NUCLÉAIRE ET ENDOSYMBIOTE ........................................... 7 LES LEVURES DU GENRE SACCHAROMYCES ............................................................................. 8 SACCHAROMYCES PARADOXUS ............................................................................................... 9 DÉMOGRAPHIE DES POPULATIONS DE S. PARADOXUS ............................................................ 10 DIVERGENCE GÉNÉTIQUE ET PHÉNOTYPIQUE CHEZ S. PARADOXUS ........................................ 11 OBJECTIF ............................................................................................................................ 11 CHAPITRE 1: EXPLORING THE NORTHERN LIMIT OF THE DISTRIBUTION OF SACCHAROMYCES CEREVISIAE AND SACCHAROMYCES PARADOXUS IN NORTH AMERICA. ... 13 CHAPITRE 2: CHROMOSOMAL VARIATION SEGREGATES WITHIN INCIPIENT SPECIES AND CORRELATES WITH REPRODUCTIVE ISOLATION. ................................................................. 29 CONCLUSION GÉNÉRALE ...................................................................................................... 49 DISTRIBUTION DES LEVURES SACCHAROMYCES AU QUÉBEC .................................................. 50 ANALYSE DE L’ISOLEMENT REPRODUCTEUR CHEZ S. PARADOXUS .......................................... 50 VARIATION DANS LA VIABILITÉ INTRAGROUPE ........................................................................ 51 PERSPECTIVES ..................................................................................................................... 52 BIBLIOGRAPHIE .................................................................................................................... 55 ANNEXES ............................................................................................................................... 69 vii LISTE DES FIGURES Figure 1: Map of the 29 sites sampled in this study. ........................................................ 26 Figure 2: Effect of temperature on yeast isolation success. ............................................ 27 Figure 3: Season-dependent isolation success. ................................................................. 28 Figure 4: Two diverging lineages of S. paradoxus are partially sympatric in North America. ............................................................................................................................... 44 Figure 5: Reproductive isolation and karyotyping in S. paradoxus North-American strains. .................................................................................................................................. 45 Figure 6: Spore survival (S) among 25 S. paradoxus North-American strains correlates with variation among and within lineages in genetic divergence (Dg) and chromosome profiles (Dc). ................................................................................................. 46 Figure 7: Proposed scenario for the divergence and secondary contact of the North American lineages of Saccharomyces paradoxus. ............................................................. 47 ix LISTE DES ANNEXES Table S1: List of sampling sites. ........................................................................................ 69 Table S2: ANOVA analysis of yeast isolation success ..................................................... 70 Table S3: List of strains isolated in this study. ................................................................. 71 Table S4: Uncharacterized yeasts isolated in this study. ................................................ 79 Table S5: List of yeast strains used in this study. ............................................................ 81 Table S6: List of oligonucleotides and plasmids used for HO locus deletion. ............... 83 Table S7: List of crosses realized in this study. ................................................................ 84 Table S8: Results from linear model (lm) of spore survival (S) variation in function of genetic divergence (Dg) and karyotypic divergence (Dc) and their interaction (Dg*Dc) as additional factors (lm Formula = S ~ dg+dc+ dg*dc). ................................................. 87 Figure S1: Principle of permutation tests used in this study to control for the effects of non-independence of pairwise comparisons and of bias in strain usage in pairwise comparisons. ........................................................................................................................ 88 Figure S2: Violin plots showing the expected distribution
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