Doctor of Philosophy (PhD) / A renewed focus on generalised pollinator systems has inspired a conceptual framework which highlights that spatial and temporal interactions among plants and their assemblage of pollinators can vary across the individual, population, regional and species levels. Pollination is clearly a dynamic interaction, varying in the number and interdependence of participants and the strength of the outcome of the interaction. Therefore, the role of variation in pollination is fundamental for understanding ecological dynamics of plant populations and is a major factor in the evolution and maintenance of generalised and specialised pollination systems. My study centred on these basic concepts by addressing the following questions: (1) How variable are pollinators in a generalised pollination system? To what degree do insect visitation rates and assemblage composition vary spatially among populations and temporally among flowering seasons? (2) How does variation in pollinators affect plant reproductive success? I chose to do this using a model system, Trachymene incisa subsp. incisa (Apiaceae), which is a widespread Australian herbaceous species with simple white flowers grouped into umbels that attract a high diversity of insect visitors. The Apiaceae are considered to be highly generalist in terms of pollination, due to their simple and uniform floral display and easily accessible floral rewards. Three populations of T. incisa located between 70 km and 210 km apart were studied over 2-3 years. The few studies investigating spatial and temporal variation simultaneously over geographic and yearly/seasonal scales indicate that there is a trend for more spatial than temporal variation in pollinators of generalist-pollinated plants. My study showed both spatial and temporal variation in assemblage composition among all populations and variation in insect visitation rates, in the form of a significant population by year interaction. However, removing ants from the analyses to restrict the assemblage to flying insects and the most likely pollinators, resulted in a significant difference in overall visitation rate between years but no difference in assemblage composition between the Myall Lakes and Tomago populations. These results indicate more temporal than spatial variation in the flying insect visitor assemblage of T. incisa. Foraging behaviour provides another source of variation in plant-pollinator interactions. Trachymene incisa exhibits umbels that function as either male or female at any one time and offer different floral rewards in each phase. For successful pollination, pollinators must visit both male and female umbels during a foraging trip. Insects showed both preferences and non-preferences for umbel phases in natural patches where the gender ratio was male biased. In contrast, insects showed no bias in visitation during a foraging trip or in time spent foraging on male and female umbels in experimental arrays where the gender ratio was equal. Pollinator assemblages consisting of a mixture of different pollinator types coupled with temporal variation in the assemblages of populations among years maintains generalisation at the population/local level. In addition, spatial variation in assemblages among populations maintains generalisation at the species level. Fire alters pollination in T. incisa by shifting the flowering season and reducing the abundance of flying insects. Therefore, fire plays an important role in maintaining spatial and temporal variation in this fire-prone system. Although insect pollinators are important in determining the mating opportunities of 90% of flowering plant species worldwide, few studies have looked at the effects of variation in pollinator assemblages on plant reproductive success and mating. In T. incisa, high insect visitation rates do not guarantee high plant reproductive success, indicating that the quality of visit is more important than the rate of visitation. This is shown by comparing the Agnes Banks and Myall Lakes populations in 2003: Agnes Banks received the highest visitation rate from an assemblage dominated by ants but produced the lowest reproductive output, and Myall Lakes received the lowest visitation rate by an assemblage dominated by a native bee and produced the highest seedling emergence. Interestingly, populations with different assemblage composition can produce similar percentage seed set per umbel. However, similar percentage seed set did not result in similar percentage seedling emergence. Differences among years in reproductive output (total seed production) were due to differences in umbel production (reproductive effort) and proportion of umbels with seeds, and not seed set per umbel. Trachymene incisa is self-compatible and suffers weak to intermediate levels of inbreeding depression through early stages of the life cycle when seeds are self-pollinated and biparentally inbred. Floral phenology, in the form of synchronous protandry, plays an important role in avoiding self-pollination within umbels and reducing the chance of geitonogamous pollination between umbels on the same plant. Although pollinators can increase the rate of inbreeding in T. incisa by foraging on both male and female phase umbels on the same plant or closely related plants, most consecutive insect movements were between plants not located adjacent to each other. This indicates that inbreeding is mostly avoided and that T. incisa is a predominantly outcrossing species, although further genetic analyses are required to confirm this hypothesis. A new conceptual understanding has emerged from the key empirical results in the study of this model generalised pollination system. The large differences among populations and between years indicate that populations are not equally serviced by pollinators and are not equally generalist. Insect visitation rates varied significantly throughout the day, highlighting that sampling of pollinators at one time will result in an inaccurate estimate and usually underestimate the degree of generalisation. The visitor assemblage is not equivalent to the pollinator assemblage, although non-pollinating floral visitors are likely to influence the overall effectiveness of the pollinator assemblage. Given the high degree of variation in both the number of pollinator species and number of pollinator types, I have constructed a model which includes the degree of ecological and functional specialisation of a plant species on pollinators and the variation encountered across different levels of plant organisation. This model describes the ecological or current state of plant species and their pollinators, as well as presenting the patterns of generalisation across a range of populations, which is critical for understanding the evolution and maintenance of the system. In-depth examination of pollination systems is required in order to understand the range of strategies utilised by plants and their pollinators, and I advocate a complete floral visitor assemblage approach to future studies in pollination ecology. In particular, future studies should focus on the role of introduced pollinators in altering generalised plant-pollinator systems and the contribution of non-pollinating floral visitors to pollinator assemblage effectiveness. Comparative studies involving plants with highly conserved floral displays, such as those in the genus Trachymene and in the Apiaceae, will be useful for investigating the dynamics of generalised pollination systems across a range of widespread and restricted species.

L’haplodiploïdie chez les hyménoptères leur confère une meilleure résistance aux effets délétères de la dépression de consanguinité. Cependant, certains hyménoptères ont un déterminisme du sexe particulier qui les rend sensibles à cette dépression. Chez ces espèces, le genre des individus dépend de la complémentarité des allèles à un locus donné, le single-locus Complementary Sex Determination (sl-CSD). Les oeufs non fécondés se développent en mâles haploïdes alors hémizygotes au locus de CSD. En revanche les oeufs fécondés donnent des femelles diploïdes s’ils sont hétérozygotes au locus du CSD mais deviennent des mâles diploïdes s’ils sont homozygotes pour ce même locus. Ces derniers sont d’autant plus fréquents dans les populations consanguines où le taux d’homozygotes est élevé. Or, les mâles diploïdes sont dans la majorité des cas non viables ou stériles. La production de tels mâles est de ce fait coûteuse pour les femelles. La faible viabilité des mâles diploïdes s’apparente alors à de la dépression de consanguinité. Par des approches liées à l’écologie comportementale et à l’écologie chimique le projet de thèse se concentre sur l’étude des coûts individuels générés par la production de mâles diploïdes et à l’évolution des comportements sélectionnés en réponse à ces coûts. Dans un premier temps, je me suis intéressée à la fitness des mâles diploïdes et aux répercussions de leur production sur les femelles de la population. Dans un second temps, j’ai étudié les comportements permettant de réduire les coûts de la production des mâles diploïdes. Les individus apparentés représentent les partenaires sexuels où le risque de produire des fils diploïdes est le plus élevé. De ce fait, les comportements d’évitement de la consanguinité devraient être sélectionnés dans ces populations / Haplodiploidy in hymenopterans offers a great resistance to the deleterious effect of inbreeding depression. However, some hymenopterans have a specific sex determination which drives them to this depression. Among those species, the sex of individuals depends on allele complementary at a particular locus; the single-locus Complementary Sex Determinatation (sl-CSD). Unfertilized eggs give birth to haploid males which are hemizygotes at the CSD locus. Conversely, fertilized eggs develop into females when heterozygote at the CSD locus but become diploid males when homozygote at the same locus. Diploid males are especially frequent in inbred populations with a high inbreeding rate. Yet diploid males are generally unviable or sterile. Production of such males is therefore costly for females. Reduced viability of diploid males is then similar to inbreeding depression. Linked with behavioural ecology and chemical ecology approaches, the PhD project starts by focusing on individual costs due to production of diploid males, and then on behaviours that have evolved in response to these costs. As a first step, the fitness of diploid males and its impact on females of the population have been measured. If they are unviable, their production is akin to female mortality. As a second step, we studied behaviours that reduce the cost of diploid male production. Related individuals are sexual partners that are most likely to father diploid sons. Therefore, behavioural inbreeding avoidance may be selected in such populations

Les changements globaux récents affectent la physiologie, la distribution et la phénologie des espèces, ainsi que la dynamique des populations et les interactions entre espèces. Les interactions plantes-pollinisateurs sont particulièrement menacées par les changements globaux et la perturbation de ces interactions peut avoir des conséquences importantes sur le système de reproduction des espèces végétales. Dans ce contexte des changements globaux, nous avons déterminé les cortèges de visiteurs de Rhododendron ferrugineum le long de gradients environnementaux et étudié comment la variabilité de leur efficacité affectait le système de reproduction de cette espèce. Nous nous sommes également intéressés à l’histoire biogéographique de cette espèce et comment elle a répondu à des changements passés tels que les dernières glaciations. Nous avons mis en évidence que R. ferrugineum est visité par une large diversité d’espèces d’insectes. L’efficacité des cortèges de visiteurs varie le long de gradients environnementaux mais ne semble pas avoir un impact sur le système de R. ferrugineum. Cette espèce présente un système mixte de reproduction, avec une capacité à l’autofécondation mais les taux élevés de dépression de consanguinité limitent le développement des individus issus d’autofécondation. Cette forte dépression de consanguinité a permis un maintien relativement élevé de la diversité génétique dans les Pyrénées. Un tel niveau de dépression de consanguinité ne permet pas l’évolution de l’autofécondation et maintient ainsi le système mixte de reproduction chez R. ferrugineum. La capacité d’autofécondation de R. ferrugineum pourrait lui permettre de coloniser de nouveaux milieux ou de survivre aux changements globaux. Durant les dernières glaciations, R. ferrugineum a survécu dans de grands refuges de basse altitude ainsi que dans des nunataks (refuges de haute altitude). Quelques populations marginales présentent un taux significatifs de consanguinité (FIS> 0) et des niveaux de diversité génétique particulièrement faibles. Ce patron génétique est consistant avec des évènements de fondation accompagnés de perte de diversité génétique et d’hétérozygotie durant les périodes d’expansion de l’aire de répartition de l’espèce. Ces données suggèrent que la dépression de consanguinité dans ces populations devait être faible et que l’assurance reproductive a joué un rôle fondamental dans l’établissement de ces populations. / Recent global changes affect the physiology, distribution and phenology of species, also they impact population dynamic and interactions among species. Plantpollinators interactions are particularly threated by global changes and perturbations of these interactions may lead to important changes in plant mating system. In this context of globalchanges, we determined the pollinator assemblages of Rhododendron ferrugineum and howthe variability of their efficiencies affects the mating system. We also studied thebiogeographic history of R. ferrugineum and how it responds to past climatic changes.We have shown that R. ferrugineum is visited by a large variety of insects. Visitorassemblages efficiency varied along environmental gradients but did not seem to impact themating system of R. ferrugineum. This species presents a mixed mating system, indeed it isable to self-fecundate but high levels of inbreeding depression are limiting the development of self-fecundate descendants. High levels of inbreeding depression maintain high genetic diversity in the Pyrenees. Also, it did not allow the evolution of selfing and maintain a mixed mating system. The ability to self-fecundate may favor the colonization of new habitats.During the last glaciation, R. ferrugineum survived in large lowland refugia and in nunataks at high altitude. Some marginal populations present a high level of selfing (FIS> 0) and low genetic diversity. This genetic pattern is consistent with foundation events and loss of genetic diversity and heterozygosity along colonization rods. Our data suggest that inbreeding depression in these populations should have been low and the reproductive assurance played akey role in the establishment of these populations.

La population canadienne-française a une histoire démographique unique faisant d’elle une population d’intérêt pour l’épidémiologie et la génétique. Cette thèse vise à mettre en valeur les caractéristiques de la population québécoise qui peuvent être utilisées afin d’améliorer la conception et l’analyse d’études d’épidémiologie génétique. Dans un premier temps, nous profitons de la présence d’information généalogique détaillée concernant les Canadiens français pour estimer leur degré d’apparentement et le comparer au degré d’apparentement génétique. L’apparentement génétique calculé à partir du partage génétique identique par ascendance est corrélé à l’apparentement généalogique, ce qui démontre l'utilité de la détection des segments identiques par ascendance pour capturer l’apparentement complexe, impliquant entre autres de la consanguinité. Les conclusions de cette première étude pourront guider l'interprétation des résultats dans d’autres populations ne disposant pas d’information généalogique. Dans un deuxième temps, afin de tirer profit pleinement du potentiel des généalogies canadienne-françaises profondes, bien conservées et quasi complètes, nous présentons le package R GENLIB, développé pour étudier de grands ensembles de données généalogiques. Nous étudions également le partage identique par ascendance à l’aide de simulations et nous mettons en évidence le fait que la structure des populations régionales peut faciliter l'identification de fondateurs importants, qui auraient pu introduire des mutations pathologiques, ce qui ouvre la porte à la prévention et au dépistage de maladies héréditaires liées à certains fondateurs. Finalement, puisque nous savons que les Canadiens français ont accumulé des segments homozygotes, à cause de la présence de consanguinité lointaine, nous estimons la consanguinité chez les individus canadiens-français et nous étudions son impact sur plusieurs traits de santé. Nous montrons comment la dépression endogamique influence des traits complexes tels que la grandeur et des traits hématologiques. Nos résultats ne sont que quelques exemples de ce que nous pouvons apprendre de la population canadienne-française. Ils nous aideront à mieux comprendre les caractéristiques des autres populations de même qu’ils pourront aider la recherche en épidémiologie génétique au sein de la population canadienne-française. / The French Canadian founder population has a demographic history that makes it an important population for epidemiology and genetics. This work aims to explain what features can be used to improve the design and analysis of genetic epidemiological studies in the Quebec population. First we take advantage of the presence of extended genealogical records among French Canadians to estimate relatedness from those records and compare it to the genetic kinship. The kinship based on identical-by-descent sharing correlates well with the genealogical kinship, further demonstrating the usefulness of genomic identical-by-descent detection to capture complex relatedness involving inbreeding and our findings can guide the interpretation of results in other population without genealogical data. Second to optimally exploit the full potential of these well preserved, exhaustive and detailed French Canadian genealogical data we present the GENLIB R package developed to study large genealogies. We also investigate identical-by-descent sharing with simulations and highlight the fact that regional population structure can facilitate the identification of notable founders that could have introduced disease mutations, opening the door to prevention and screening of founder-related diseases. Third, knowing that French Canadians have accumulated segments of homozygous genotypes, as a result of inbreeding due to distant ancestors, we estimate the inbreeding in French Canadian individuals and investigate its impact on multiple health traits. We show how inbreeding depression influences complex traits such as height and blood-related traits. Those results are a few examples of what we can learn from the French Canadian population and will help to gain insight on other populations’ characteristics as well as help the genetic epidemiological research within the French Canadian population.

No description available.

Only 40 years ago, just three individuals made the journey from Finland/Russia to found the current wolf population in the southwest of Sweden. This population, that to this date descends from less than 10 founders, has a substantial increased extinction risk due to inbreeding. Several previous studies have used SNPs to monitor the level of inbreeding and homozygosity in the population, as well as measure immigration and the inflow of new genetic material. This study uses both short- and long-read data to discover structural variants (SVs) and small indels in the population, so that they may be used to extend the analyses and provide more insight into the current state of the Scandinavian wolf population. After the calling of the SVs, strict filtering and manual curation were applied to the data, thereby removing many false positive calls and increasing confidence in the remaining SVs. Short-read and long-read SV-callers found 31,800 and 57,821 SVs respectively, with relatively little overlap between the two sets. By far, the most common SV-types were deletions and insertions, at about 30,000 each with varying length ranging from a 50 base pairs to several tens of Mbp. Analyses on the data, such as PCAs and parent-offspring trio analyses, reveal high-confidence calls and consistent results between SV-types and SV-callers, as well as a low estimated genotyping error rate. PCAs performed on the SVs resembled those performed on SNPs, which strengthens the credibility of the identified variants. Finally, this study suggests several alternative steps for possible improvement to the dataset, along with some proposals for subsequent research topics that may use the variants discovered in this study.