Reintroduction Du Cisco De Fumage (Coregonus Hoyi) Dans Le Lac Ontario : Diversité Génétique Et Consanguinité

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Reintroduction Du Cisco De Fumage (Coregonus Hoyi) Dans Le Lac Ontario : Diversité Génétique Et Consanguinité MARIE-JULIE FAVE REINTRODUCTION DU CISCO DE FUMAGE (COREGONUS HOYI) DANS LE LAC ONTARIO : DIVERSITÉ GÉNÉTIQUE ET CONSANGUINITÉ Mémoire présenté à la Faculté des études supérieures de l'Université Laval dans le cadre du programme de maîtrise en biologie pour l'obtention du grade de maître es sciences (M.Se.) Département de biologie FACULTÉ DES SCIENCES ET GÉNIE UNIVERSITÉ LAVAL QUÉBEC Octobre 2006 © Marie-Julie Favé, 2006 RESUME La gestion active des populations est souvent désirée et doit être réalisée de façon à minimiser les risques génétiques. Afin de déterminer la meilleure source de cisco de fumage (Coregonus hoyi) pour une réintroduction dans le lac Ontario, le polymorphisme de 10 locus microsatellites a été analysé pour des échantillons de C. hoyi des lacs Huron, Michigan, Supérieur et Nipigon ainsi que pour des échantillons de C. artedi et de ciscos des zones profondes du lac Ontario. Les populations de C. hoyi sont génétiquement diversifiées malgré des baisses d'abondance connues et sont différentiées entre les lacs. Aussi, nos résultats suggèrent que les individus du lac Ontario sont plus étroitement liés aux individus des lacs Huron et Michigan qu'à ceux des lacs Supérieur et Nipigon. Par la suite, des simulations montrent qu'un grand nombre de géniteurs, un rapport des sexes équilibré, une haute proportion de croisements efficaces, un pool de géniteurs diversifié ainsi qu'un grand nombre d'individus introduit minimiserait la consanguinité dans la nouvelle population. ABSTRACT Active population management is often desired and should be designed so as to minimize genetic risks. In order to détermine the best source of bloater {Coregonus hoyi) for a reintroduction in Lake Ontario, we analyzed genetic polymorphism at 10 microsatellite loci in samples of C. hoyi from Lakes Huron, Michigan, Superior and Nipigon as well as samples of C. artedi and deepwater ciscoes from Lake Ontario. C. hoyi populations are genetically diversified despite known démographie déclines and they are significantly differentiated among lakes. Also, our results suggest that Lake Ontario ciscoes are more closely related to ciscoes from Lake Huron and Michigan than to ciscoes from Lake Superior or Nipigon. Computer simulations demonstrate that a high number of breeders, a balanced sex ratio, a high proportion of effective crosses, a genetically diverse pool of breeders and a high number of individuals introduced each year would minimize inbreeding in the reintroduced population. H AVANT-PROPOS Une multitude de gens et d'organismes ont contribué, chacun à leur façon, à l'accomplissement de ce projet : Je tiens avant tout à remercier ma directrice Julie Turgeon pour m'avoir accueillie dans son laboratoire après une simple petite rencontre, pour m'avoir accordé sa confiance et guidée dans mes nombreux apprentissages, de la pipette à la rédaction finale. Merci pour toutes les discussions que nous avons eues, scientifiques comme humanistes, sérieuses comme ludiques, critiques comme naïves. Je dois également un gros merci à Pierre Duchesne pour avoir programmé les équations qui ont servi lors des simulations exécutées dans le Chapitre 2, sans qui la réalisation de cette deuxième partie aurait été bien plus laborieuse, voire impossible. Je le remercie pour ses recommandations toujours éclairées, précises et efficaces. Merci aux nombreuses personnes qui ont collaboré à l'échantillonnage des ciscos dans les Grands Lacs, soit Rick Salmon (OMNR), Lloyd Mohr (OMNR), Bruce Morrison (OMNR), Owen Gorman (USGS) et Kim Scribner (Michigan State University). Je remercie la Great Lakes Fishery Commission pour l'initiation du projet ainsi que pour son support financier nécessaire à la réalisation de celui-ci. Je remercie également pour leur soutien financier, le FGÉS-CRSNG et le département de biologie. Merci aux membres du labo JT pour les discussions quotidiennes qui font avancer les choses et qui refont notre petit (ou grand) monde, pour les conseils judicieux ainsi que pour les bons moments passés ensemble: Julien April, Olivier Rey, Cécilia Hernandez, Marie- Claude Gagnon, Ariane Dubé-Linteau, Mélissa Tremblay, Julie Jeukens, Emilie Bilodeau, Milouda Achaboune, Sébastien Bélanger et Kevin Foulché. Pour m'avoir changé les idées aux moments propices, merci à mes amis cépassiens, avec qui les plus fous délires libérateurs sont permis et aux fidèles grimpeurs matinaux, toujours prêts à se dépasser afin d'assouvir notre dépendance aux endorphines, à l'adrénaline et aux grands espaces... Et bien sûr, un merci tout particulier à François et Martine, pour leur continuel support, pour m'avoir appris à poursuivre mes idées et pour toujours m'encourager à accomplir ce qui me rend heureuse. ni Ce mémoire comporte une introduction et une conclusion générales rédigées en français. Les chapitres I et II sont rédigés en anglais car ils sont destinés à être publiés dans des revues spécialisées. IV TABLE DES MATIERES RÉSUMÉ II ABSTRACT II AVANT-PROPOS III TABLE DES MATIERES V LISTE DES TABLEAUX ET FIGURES VII INTRODUCTION GÉNÉRALE 9 RÉINTRODUCTIONS EN NATURE 9 LA FAUNE ICHTHYENNE DES GRANDS LACS LAURENTIENS 12 RÉINTRODUCTION DE C. HOYI DANS LE LAC ONTARIO 13 OBJECTIFS DE RECHERCHE 14 CHAPITRE 1: 16 PATTERNS OF GENETIC DIVERSITY IN GREAT LAKES BLOATERS (COREGONUS HOYI) FOR FUTURE REINTRODUCTION IN LAKE ONTARIO ... 16 RÉSUMÉ 17 ABSTRACT 17 INTRODUCTION 19 Laurentian Great Lakes Fish Fauna 20 Reintroduction ofC. hoyi inLake Ontario 21 MATERIALS AND METHODS 22 Biological material 22 DNA extraction and microsatellite analysis 23 Genetic diversity and historical demography 23 Genetic relationships among Great Lakes bloaters andLake Ontario ciscoes 24 RESULTS 25 Genetic diversity and historical demography 25 Relationships among populations and individual assignment tests 26 DISCUSSION 28 Genetic diversity and bottlenecks 28 Differentiation within and among lakes 31 CONCLUSIONS 32 ACKNOWLEDGMENTS 33 FIGURE LEGEND 34 ANNEXE A : NOMBRE D'INDIVIDUS (N), NOMBRE D'ALLÈLES (A), HÉTÉROZYGOTIE OBSERVÉE (HO) ET ATTENDUE (HE) PAR LOCUS ET MULTILOCUS POUR CHAQUE ÉCHANTILLON 44 CHAPITRE 2: 48 INBREEDING DYNAMICS IN REINTRODUCED, AGE-STRUCTURED POPULATIONS OF HIGHLY FECUND SPECIES 48 RÉSUMÉ 49 ABSTRACT 49 INTRODUCTION 51 MATERIALS AND METHODS 52 Breeding design and inbreeding coefficient. 52 Dynamics of inbreeding coefficient in a reintroduced population 53 RESULTS 55 Effects of breeding design on FH 55 Dynamics ofFwin the reintroduced population 56 DISCUSSION 57 ACKNOWLEDGMENTS 60 FIGURE LEGEND 61 ANNEXE B: DERIVATION OF RECURRENCE EQUATIONS TO COMPUTE F VALUES 64 Discrète générations 64 Three âge classes 65 Nine âge classes 66 CONCLUSION GÉNÉRALE 69 Résumé de la recherche 69 Limites et perspectives .71 BIBLIOGRAPHIE 73 VI LISTE DES TABLEAUX ET FIGURES Liste des tableaux Chapitre 1 Table 1: Information on ciscoe samples, along with détails on genetic diversity (NA: number of alleles; NAR: allelic richness; Ho and He: observed and expected heterozygosity, respectively), and results of démographie tests, (P-values for heterozygosity déficit and excess (Cornuet and Luikart 1996); M ratio of Garza and Williamson (2001)) 35 Table 2: Microsatellite loci used for the characterization of Great Lakes ciscoes: primer séquences with fluorescent label, PCR conditions (primer concentration, TA, and number of cycles), PCR multiplex and migration set, allele size range (bp), and total number of alleles observed 37 Table 3: Pairwise FST values between C. hoyi samples from Potential Donor Lakes (HUR: Lake Huron; MCH: Lake Michigan; SUP: Lake Superior; NIP: Lake Nipigon) and ciscoes from Lake Ontario (ONT-ARTEDI, ONT-DEEP). FST values significantly différent from 0 (Bonferroni corrected) are in bold 38 Table 4: Average probability (LnP(D)) and standard déviation across 20 runs of STRUCTURE for K genetic partitions among bloaters from ail Potential Donor Lakes 39 Table 5: Assignment of individual ciscoes from Lake Ontario a) to three genetic partitions defined by STRUCTURE - see Results-, with mean coefficient of membership (q) in parenthèses and b) to Potential Donor Lakes with GENECLASS, with average first score in parenthèses (HUR: Lake Huron; MCH: Lake Michigan; SUP: Lake Superior; NIP: Lake Nipigon)) 40 Liste des figures Chapitre 1 Figure 1: Sampling locations for C. hoyi in Potential Donor Lakes (•) and for ciscoes in Lake Ontario (•: contemporary and historical scale samples of C. artedi; "*": deepwater ciscoes caught in 2002) 41 Figure 2: Temporal variation in allelic richness (NAR) and demographical index (M ratio) in historical ciscoes from Lake Ontario (Hay Bay, Canada) in relation with relative commercial ciscoes catch in the Canadian waters of Lake Ontario (grey bars; Baldwin et al. 2005) 42 Figure 3: Unrooted DcE-based neighbor-joining phenogram relating ail samples from Potential Donor Lakes and Lake Ontario ciscoes (ONT-ARTEDI: récent sample of C. artedi; ONT-DEEP: deepwater ciscoes caught in 2002). Bootstrap values above 60 are shown 43 vu Chapitre 2 Figure 1: Inbreeding coefficient (FH) generated by crosses with variable numbers of breeders (NB), M:F sex ratios (• ~ 1:1; • ~ 1:4; * ~ 1:20), and pools of breeders characterized by high (a, b, and c; F = 0.24) or weak genetic diversity (d; F = 0.41) as a function of the proportion of effective crosses (PEC). Dashed Unes represent the F value for an infinité Wright-Fisher population of similar diversity. Bars represent variance among 200 simulations. Missing data points represents situations with unrealizable calculations because of excessively stringent
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