Genetic diversity and fitness in small populations of partially asexual, self-incompatible plants

How self-incompatibility systems are maintained in plant populations is still a debated issue. Theoretical models predict that self-incompatibility systems break down according to the intensity of inbreeding depression and number of S-alleles. Other studies have explored the function of asexual reproduction in the maintenance of self-incompatibility. However, the population genetics of partially asexual, self-incompatible populations are poorly understood and previous studies have failed to consider all possible effects of asexual reproduction or could only speculate on those effects. In this study, we investigated how partial asexuality may affect genetic diversity at the S-locus and fitness in small self-incompatible populations. A genetic model including an S-locus and a viability locus was developed to perform forward simulations of the evolution of populations of various sizes. Drift combined with partial asexuality produced a decrease in the number of alleles at the S-locus. In addition, an excess of heterozygotes was present in the population, causing an increase in mutation load. This heterozygote excess was enhanced by the self-incompatibility system in small populations. In addition, in highly asexual populations, individuals produced asexually had some fitness advantages over individuals produced sexually, because sexual reproduction produces homozygotes of the deleterious allele, contrary to asexual reproduction. Our results suggest that future research on the function of asexuality for the maintenance of self-incompatibility will need to (1) account for whole-genome fitness (mutation load generated by asexuality, self-incompatibility and drift) and (2) acknowledge that the maintenance of self-incompatibility may not be independent of the maintenance of sex itself

Late-acting self-incompatible system, preferential allogamy and delayed selfing in the heteromorphic invasive populations of <i>Ludwigia grandiflora subsp. hexapetala</i>

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Masculinization of the X Chromosome in the Pea Aphid

International audienceEvolutionary theory predicts that sexually antagonistic mutations accumulate differentially on the X chromosome and autosomes in species with an XY sex-determination system, with effects (masculinization or feminization of the X) depending on the dominance of mutations. Organisms with alternative modes of inheritance of sex chromosomes offer interesting opportunities for studying sexual conflicts and their resolution, because expectations for the preferred genomic location of sexually antagonistic alleles may differ from standard systems. Aphids display an XX/X0 system and combine an unusual inheritance of the X chromosome with the alternation of sexual and asexual reproduction. In this study, we first investigated theoretically the accumulation of sexually antagonistic mutations on the aphid X chromosome. Our results show that i) the X is always more favourable to the spread of male-beneficial alleles than autosomes, and should thus be enriched in sexually antagonistic alleles beneficial for males, ii) sexually antagonistic mutations beneficial for asexual females accumulate preferentially on autosomes, iii) in contrast to predictions for standard systems, these qualitative results are not affected by the dominance of mutations. Under the assumption that sex-biased gene expression evolves to solve conflicts raised by the spread of sexually antagonistic alleles, one expects that male-biased genes should be enriched on the X while asexual female-biased genes should be enriched on autosomes. Using gene expression data (RNA-Seq) in males, sexual females and asexual females of the pea aphid, we confirm these theoretical predictions. Although other mechanisms than the resolution of sexual antagonism may lead to sex-biased gene expression, we argue that they could hardly explain the observed difference between X and autosomes. On top of reporting a strong masculinization of the aphid X chromosome, our study highlights the relevance of organisms displaying an alternative mode of sex chromosome inheritance to understanding the forces shaping chromosome evolution

Impact de la propagation asexuée et du système d'auto-incompatibilité gamétophytique sur la structuration et l'évolution de la diversité génétique d'une essence forestière entomophile et disséminée, Prunus avium L.

Les systèmes de reproduction jouent un rôle fondamental dans la structuration spatio-temporelle de la diversité génétique des espèces. Cette thèse, portant sur l'étude de trois populations de merisiers, a pour but de mieux comprendre les implications évolutives d'un système de reproduction mixte chez les plantes combinant à la fois une propagation asexuée et une reproduction sexuée contrôlée par un système d'auto-incompatibilité gamétophytique (GSI).Nous avons étudié les influences de la propagation asexuée et du GSI sur (1) la structuration diversité génétique intra et inter populations et sur (2) l'efficacité de sa transmission d'une génération à l'autre.Confrontant des modèles et concepts théoriques aux réalités biologiques, nos résultats démontrent à la fois un effet de l'asexualité et du GSI sur l'évolution de la diversité génétique de notre espèce. Ces effets sont plus complexes voire contraires à ce que prédisent les modèles ou les concepts actuellement admis

Effets des modes de reproduction sur la diversité génétique et implications pour les stratégies de conservation.

National audience"Que nul n'entre s'il n'est géomètre" : cet exposé illustre comment une formalisation mathématique nourrie d’un dialogue avec les données et les savoirs naturalistes nous a permis des avancées significatives sur la compréhension des trajectoires évolutives des populations partiellement clonales. Les méta-analyses de données de diversité génétique désignent les systèmes de reproduction comme les facteurs les plus influents de l’évolution de la diversité génomique des espèces eucaryotes. En effet, ils conditionnent la transition de la diversité génétique des individus et des populations dans le temps. De nombreux Eucaryotes se reproduisent par clonalité partielle. Ce mode de reproduction implique qu’à l’échelle d’une population, certains descendants sont produits par voie sexuée pendant que d’autres sont formés par voie clonale. C’est notamment le cas de la majorité des espèces structurant les écosystèmes et de celles importantes pour les activités humaines. Pourtant, ce système de reproduction n’a été pris en compte explicitement que récemment dans un modèle formel de génétique des populations. Les modèles développés précédemment considéraient soit des populations purement sexuées, soit des populations purement clonales. Les attendus des effets évolutifs de la clonalité partielle étaient alors imaginés comme une proportion des attendus de chacun de ces deux modèles. Dans un aller-retour d’identifications d’anomalies typiquement kuhniennes entre données et développement algorithmique et mathématiques, je tenterai de montrer comment l’adaptation d’un modèle de Wright-Fisher dans les espaces génotypiques, intégrant les mécanismes génétiques de la clonalité partielle a permis de mieux comprendre, prédire et expliquer les dynamiques évolutives de nombreuses populations partiellement clonales dont l’étude évolutive était jusqu’à présent uniquement abordée par des expertises empiriques. Ce modèle montre que l’évolution de ces populations est différente des populations purement clonales ou sexuées, et ne peut se prédire à l’aide d’une règle simple combinant modèles pour organismes purement clonaux et purement sexués. Enfin, si le temps le permet, je montrerai comment l’utilisation de ce modèle mécaniste utilisé pour calculer des vraisemblances dans une approche statistique nous permet désormais d’inférer quantitativement les taux de reproduction clonale en populations de terrain échantillonnées deux fois dans le temps

The dynamics of genetic diversity in partially clonal populations

International audienceMost clonal Eukaryote species develop sexual events cyclically or concomitantly over time and space, and are therefore partially clonal. The relative importance of clonality versus sexuality is thus a key feature of their reproductive system, expected to impact their evolution. Understanding the specificities of partial clonality on the dynamics of genetic diversity would enable rationalization of many biological applications and population managements. It would also allow identifying the discernible signal of partial clonality on genomes, enabling inferences of clonal rates from genotypings and identifying gene-specific history. We developed a Wright-Fisher-like population genetics model that explicitly accounts for partial clonality. Analysing its exact mathematical form as Markov chain and its Îto-like approximation for large populations as stochastic differential equations allowed predicting the specific impacts of partial clonality from low rates on genetic diversity, computing the times to reach stationary distributions (i.e., equilibrium) and delimit domains where partial clonality contributes driving genetic diversity. Our results show that partial clonality impacts genetic diversity and its dynamics from low rates, and should be considered as specific reproductive system, with deep consequences for population evolution and ecology. We identified the discernible signals that can be exploited for inferring rates of clonality using low-cost population genotypings, democratizing the systematic search for some clonal reproductions in populations and species. We will discuss those results in the light of the increasing number of acquired datasets on species long and newly known to be partially clonal

Stochastic models help understanding the evolution of partially clonal species and inferring rate of clonality from genetic diversity

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The exact distributions of F(IS) under partial asexuality in small finite populations with mutation.

Reproductive systems like partial asexuality participate to shape the evolution of genetic diversity within populations, which is often quantified by the inbreeding coefficient F IS. Understanding how those mating systems impact the possible distributions of F IS values in theoretical populations helps to unravel forces shaping the evolution of real populations. We proposed a population genetics model based on genotypic states in a finite population with mutation. For populations with less than 400 individuals, we assessed the impact of the rates of asexuality on the full exact distributions of F IS, the probabilities of positive and negative F IS, the probabilities of fixation and the probabilities to observe changes in the sign of F IS over one generation. After an infinite number of generations, we distinguished three main patterns of effects of the rates of asexuality on genetic diversity that also varied according to the interactions of mutation and genetic drift. Even rare asexual events in mainly sexual populations impacted the balance between negative and positive F IS and the occurrence of extreme values. It also drastically modified the probability to change the sign of F IS value at one locus over one generation. When mutation prevailed over genetic drift, increasing rates of asexuality continuously increased the variance of F IS that reached its highest value in fully asexual populations. In consequence, even ancient asexual populations showed the entire F IS spectrum, including strong positive F IS. The prevalence of heterozygous loci only occurred in full asexual populations when genetic drift dominated