Inférences sur l'histoire des populations à partir de leur diversité génétique : étude de séquences démographiques de type fondation-explosion

Studying demography in a historical perspective can help understand evolutionary processes. Through their genealogical and mutational history, population samples at genetic markers record (with loss of information) this demographic history. This potential and the increasing ease of genotyping have recently motivated development of new statistical tools aimed at extracting demographic information from raw molecular data.In this thesis, the Bayesian inference method proposed in 1999 by M.Beaumont is extended to more general demographic and mutational models. As the original method, the extended one (i) is based on Kingman's coalescent with variable population size, (ii) uses Metropolis-Hastings algorithm to sample from the posterior distribution of parameters of interest, and (iii) allows to analyse genetic data at several unliked microsatellite loci. The demographic model underlying the extended version is that of a sudden size change, immediately followed by an exponential size change until sampling time ---instead of a monotonic size change. The mutational model supposed is a two-phase model. It is the first time a fully-probabilistic method allows microsatellite mutations with amplitude greater than one.The demographic and mutational model is explored. Simulated data sets are used to compare the posterior distribution of the parameters, for several historical scenarios: for example a stable size history, an exponential increase for a time period and a founder-flush history. A typology is proposed for posterior distribution. Advice is given about the sampling and genotyping effort in empirical studies that aim at using the method: a unique microsatellite marker can lead to a strongly structured posterior distribution. However, with monolocus samples, highest posterior density domains always comprise scenarios of several kinds (for example not only founder-flush, but also exponential decline or increase). A sample of moderate size (50 haploid genomes typed at 5 microsatellite markers), were shown to strongly support a founder-flush history (99% of the posterior sample), with parameter values used to simulate the data in the 95% highest posterior density domain. Consequences of the violation of some hypothesis underlying the method are discussed: the shape of the demographic explosion is shown to be especially important. It is established that simplifying a TPM mutation process by a SMM model can lead to the detection of a false genetic disequilibrium. Interestingly, the modelisation of the TPM allows to erase this false signal.The method is succinctly applied to the study of two founder-flush histories: the introduction of cat Felis catus on the Kerguelen archipelago, and the introduction of the brown rat Rattus norvegicus on Brittany islands. It is first shown that the frequentist method of Cornuet and Luikart (1996) does not detect any significant departure from mutation-drift equilibrium, despite the strong founder events these populations experienced. This is probably due to cancelling effects of the founder and flush, on the summary statistics the method is based on. Probably for the same reason, the Bayesian method does not detect any disequilibrium signal if a step-like size change is supposed. The foundation and subsequent explosion become both detectable if they are parameterized. However, correlations between parameters make it impossible to infer a single parameter with precision less than several orders of magnitude. Prior information on some parameters (for example the time of the foundation) considerably constraint the possible values of others (for example the mutation rate). This confirms the potential of populations with documented history, to indirectly estimate the parameters of a mutational model for microsatellite markers.L'étude de la démographie dans une perspective historique participe à la compréhension des processus évolutifs. Les données de diversité génétique sont potentiellement informatives quant au passé démographique des populations: en effet, ce passé est enregistré avec perte d'information par les marqueurs moléculaires, par l'intermédiaire de leur histoire généalogique et mutationnelle. L'acquisition de données de diversité génétique est de plus en plus rapide et aisée, et concerne potentiellement n'importe quel organisme d'intérêt. D'où un effort dans la dernière décennie pour développer les outils statistiques permettant d'extraire l'information démographique des données de typage génétique.La présente thèse propose une extension de la méthode d'inférence bayésienne développée en 1999 par M. Beaumont. Comme la méthode originale, (i) elle est basée sur le coalescent de Kingman avec variations d'effectif, (ii) elle utilise l'algorithme de Metropolis-Hastings pour échantillonner selon la loi a posteriori des paramètres d'intérêt et (iii) elle permet de traiter des données de typage à un ou plusieurs microsatellites indépendants. La version étendue généralise les modèles démographique et mutationnel supposés dans la méthode initiale: elle permet d'inférer les paramètres d'un modèle de fondation-explosion pour la population échantillonnée et d'un modèle mutationnel à deux phases, pour les marqueurs microsatellites typés. C'est la première fois qu'une méthode probabiliste exacte incorpore pour les microsatellites un modèle mutationnel autorisant des sauts.Le modèle démographique et mutationnel est exploré. L'analyse de jeux de données simulés permet d'illustrer et de comparer la loi a posteriori des paramètres pour des scénarios historiques: par exemple une stabilité démographique, une croissance exponentielle et une fondation-explosion. Une typologie des lois a posteriori est proposée. Des recommandations sur l'effort de typage dans les études empiriques sont données: un unique marqueur microsatellite peut conduire à une loi a posteriori très structurée. Toutefois, les zones de forte densité a posteriori représentent des scénarios de différents types. 50 génomes haploides typés à 5 marqueurs microsatellites suffisent en revanche à détecter avec certitude (99% de la probabilité a posteriori) une histoire de fondation-explosion tranchée. Les conséquences de la violation des hypothèses du modèle démographique sont discutées, ainsi que les interactions entre processus et modèle mutationnel. En particulier, il est établi que le fait de supposer un processus mutationnel conforme au modèle SMM, alors que ce processus est de type TPM, peut générer un faux signal de déséquilibre génétique. La modélisation des sauts mutationnels permet de supprimer ce faux signal.La méthode est succinctement appliquée à l'étude de deux histoires de fondation-explosion: l'introduction du chat Felis catus sur les îles Kerguelen et celle du surmulot Rattus norvegicus sur les îles du large de la Bretagne. Il est d'abord montré que la méthode fréquentiste développée par Cornuet et Luikart (1996) ne permet pas de détecter les fondations récentes et drastiques qu'ont connu ces populations. Cela est vraisemblablement dû à des effets contraires de la fondation et de l'explosion, sur les statistiques utilisées dans cette méthode.La méthode bayésienne ne détecte pas non plus la fondation si l'on force une histoire démographique en marche d'escalier, pour la même raison. La fondation et l'explosion deviennent détectables si le modèle démographique les autorise. Toutefois, les dépendances entre les paramètres du modèle empêchent de les inférer marginalement avec précision. Toute information a priori sur un paramètre contraint fortement les valeurs des autres paramètres. Ce constat confirme le potentiel de populations d'histoire documentée pour l'estimation indirecte des paramètres d'un modèle de mutation des marqueurs

Inférences sur l'histoire des populations à partir de leur diversité génétique (étude de séquences démographiques de type fondation-explosion)

PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Exploring the Evolution of Wolbachia Compatibility Types: A Simulation Approach

Wolbachia-induced cytoplasmic incompatibility (CI) is observed when males bearing the bacterium mate with uninfected females or with females bearing a different Wolbachia variant; in such crosses, paternal chromosomes are lost at the first embryonic mitosis, most often resulting in developmental arrest. The molecular basis of CI is currently unknown, but it is useful to distinguish conceptually the male and female sides of this phenomenon: in males, Wolbachia must do something, before it is shed from maturing sperm, that will disrupt paternal chromosomes functionality [this is usually termed “the modification (mod) function”]; in females, Wolbachia must somehow restore embryonic viability, through what is usually called “the rescue (resc) function.” The occurrence of CI in crosses between males and females bearing different Wolbachia variants demonstrates that the mod and resc functions interact in a specific manner: different mod resc pairs make different compatibility types. We are interested in the evolutionary process allowing the diversification of compatibility types. In an earlier model, based on the main assumption that the mod and resc functions can mutate independently, we have shown that compatibility types can evolve through a two-step process, the first involving drift on mod variations and the second involving selection on resc variations. This previous study has highlighted the need for simulation-based models that would include the effects of nondeterministic evolutionary forces. This study is based on a simulation program fulfilling this condition, allowing us to follow the evolution of compatibility types under mutation, drift, and selection. Most importantly, simulations suggest that in the frame of our model, the evolution of compatibility types is likely to be a gradual process, with new compatibility types remaining partially compatible with ancestral ones

Cryogenian glaciation and the onset of carbon-isotope decoupling

Global carbon cycle perturbations throughout Earth history are frequently linked to changing paleogeography, glaciation, ocean oxygenation, and biological innovation. A pronounced carbonate carbon-isotope excursion during the Ediacaran Period (635 to 542 million years ago), accompanied by invariant or decoupled organic carbon-isotope values, has been explained with a model that relies on a large oceanic reservoir of organic carbon. We present carbonate and organic matter carbon-isotope data that demonstrate no decoupling from approximately 820 to 760 million years ago and complete decoupling between the Sturtian and Marinoan glacial events of the Cryogenian Period (approximately 720 to 635 million years ago Growth of the organic carbon pool may be related to iron-rich and sulfate-poor deep-ocean conditions facilitated by an increase in the Fe:S ratio of the riverine flux after Sturtian glacial removal of a long-lived continental regolith.</p

Possible animal-body fossils in pre-Marinoan limestones from South Australia

The Neoproterozoic era was punctuated by the Sturtian (about 710 million years ago) and Marinoan (about 635 million years ago) intervals of glaciation. In South Australia, the rocks left behind by the glaciations are separated by a succession of limestones and shales, which were deposited at tropical latitudes. Here we describe millimetre- to centimetre-scale fossils from the Trezona Formation, which pre-dates the Marinoan glaciation. These weakly calcified fossils occur as anvil, wishbone, ring and perforated slab shapes and are contained within stromatolitic limestones. The Trezona Formation fossils pre-date the oldest known calcified fossils of this size by 90 million years, and cannot be separated from the surrounding calcite matrix or imaged by traditional X-ray-based tomographic scanning methods. Instead, we have traced cross-sections of individual fossils by serially grinding and scanning each sample at a resolution of 50.8 μm. From these images we constructed three-dimensional digital models of the fossils. Our reconstructions show a population of ellipsoidal organisms without symmetry and with a network of interior canals that lead to circular apertures on the fossil surface. We suggest that several characteristics of these reef-dwelling fossils are best explained if the fossils are identified as sponge-grade metazoans.</p

Possible animal-body fossils in pre-Marinoan limestones from South Australia

The Neoproterozoic era was punctuated by the Sturtian (about 710 million years ago) and Marinoan (about 635 million years ago) intervals of glaciation. In South Australia, the rocks left behind by the glaciations are separated by a succession of limestones and shales, which were deposited at tropical latitudes. Here we describe millimetre- to centimetre-scale fossils from the Trezona Formation, which pre-dates the Marinoan glaciation. These weakly calcified fossils occur as anvil, wishbone, ring and perforated slab shapes and are contained within stromatolitic limestones. The Trezona Formation fossils pre-date the oldest known calcified fossils of this size by 90 million years, and cannot be separated from the surrounding calcite matrix or imaged by traditional X-ray-based tomographic scanning methods. Instead, we have traced cross-sections of individual fossils by serially grinding and scanning each sample at a resolution of 50.8 μm. From these images we constructed three-dimensional digital models of the fossils. Our reconstructions show a population of ellipsoidal organisms without symmetry and with a network of interior canals that lead to circular apertures on the fossil surface. We suggest that several characteristics of these reef-dwelling fossils are best explained if the fossils are identified as sponge-grade metazoans.</p