Selective Sweep at a QTL in a Randomly Fluctuating Environment

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Adaptation, Plasticity, and Extinction in a Changing Environment: Towards a Predictive Theory

The authors analyze developmental, genetic, and demographic mechanisms by which populations tolerate changing environments and discuss empirical methods for determining the critical rate of sustained environmental change that causes population extinction

Where is the optimum? Predicting the variation of selection along climatic gradients and the adaptive value of plasticity. A case study on tree phenology

International audienceMany theoretical models predict when genetic evolution and phenotypic plasticity allow adaptation to changing environmental conditions. These models generally assume stabilizing selection around some optimal phenotype. We however often ignore how optimal phenotypes change with the environment, which limit our understanding of the adaptive value of phenotypic plasticity. Here, we propose an approach based on our knowledge of the causal relationships between climate, adaptive traits, and fitness to further these questions. This approach relies on a sensitivity analysis of the process-based model Phenofit, which mathematically formalizes these causal relationships, to predict fitness landscapes and optimal budburst dates along elevation gradients in three major European tree species. Variation in the overall shape of the fitness landscape and resulting directional selection gradients were found to be mainly driven by temperature variation. The optimal budburst date was delayed with elevation, while the range of dates allowing high fitness narrowed and the maximal fitness at the optimum decreased. We also found that the plasticity of the budburst date should allow tracking the spatial variation in the optimal date, but with variable mismatch depending on the species, ranging from negligible mismatch in fir, moderate in beech, to large in oak. Phenotypic plasticity would therefore be more adaptive in fir and beech than in oak. In all species, we predicted stronger directional selection for earlier budburst date at higher elevation. The weak selection on budburst date in fir should result in the evolution of negligible genetic divergence, while beech and oak would evolve counter-gradient variation, where genetic and environmental effects are in opposite directions. Our study suggests that theoretical models should consider how whole fitness landscapes change with the environment. The approach introduced here has the potential to be developed for other traits and species to explore how populations will adapt to climate change

Fluctuating optimum and temporally variable selection on breeding date in birds and mammals

International audienceTemporal variation in natural selection is predicted to strongly impact the evolution and demography of natural populations, with consequences for the rate of adaptation, evolution of plasticity, and extinction risk. Most of the theory underlying these predictions assumes a moving optimum phenotype, with predictions expressed in terms of the temporal variance and autocorrelation of this optimum. However, empirical studies seldom estimate patterns of fluctuations of an optimum phenotype, precluding further progress in connecting theory with observations. To bridge this gap, we assess the evidence for temporal variation in selection on breeding date by modeling a fitness function with a fluctuating optimum, across 39 populations of 21 wild animals, one of the largest compilations of long-term datasets with individual measurements of trait and fitness components. We find compelling evidence for fluctuations in the fitness function, causing temporal variation in the magnitude, but not the direction of selection. However, fluctuations of the optimum phenotype need not directly translate into variation in selection gradients, because their impact can be buffered by partial tracking of the optimum by the mean phenotype. Analyzing individuals that reproduce in consecutive years, we find that plastic changes track movements of the optimum phenotype across years, especially in bird species, reducing temporal variation in directional selection. This suggests that phenological plasticity has evolved to cope with fluctuations in the optimum, despite their currently modest contribution to variation in selection

Fluctuations in lifetime selection in an autocorrelated environment

International audiencePrevious theory investigating the effects of environmental autocorrelation on evolution mostly assumed that total fitness resulted from a single selection episode. Yet organisms are likely to experience selection repeatedly along their life, in response to possibly different environmental states. We model the evolution of a quantitative trait in organisms with non-overlapping generations undergoing several episodes of selection in a randomly fluctuating and autocorrelated environment. We show that the evolutionary dynamics depends not directly on fluctuations of the environment, but instead on those of an effective phenotypic optimum that integrates the effects of all selection episodes within each generation. The variance and autocorrelation of the integrated optimum shape the variance and predictability of selection, with substantial qualitative and quantitative deviations from previous predictions considering a single selection episode per generation. We also investigate the consequence of multiple selection episodes per generation on population load. In particular, we identify a new load resulting from within-generation fluctuating selection, generating the death of individuals without significance for the evolutionary dynamics. Our study emphasizes how taking into account fluctuating selection within lifetime unravels new properties of evolutionary dynamics, with crucial implications notably with respect to responses to global changes

The Hitchhiking Effect of an Autosomal Meiotic Drive Gene

Transmission-ratio distortion is a departure from a 1:1 segregation of alleles in the gametes of a heterozygous individual. The so-called driving allele is strongly selected regardless of its effect on the fitness of the carrying individual. It may then have an important impact on neutral polymorphism due to the genetic hitchhiking effect. We study this hitchhiking effect in the case of true meiotic drive in autosomes and show that it is more dependent on the recombination rate than in the classical case of a gene positively selected at the organism level

Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation

ABSTRACT We model selection at a locus affecting a quantitative trait (QTL) in the presence of genetic variance due to other loci. The dynamics at the QTL are related to the initial genotypic value and to the background genetic variance of the trait, assuming that background genetic values are normally distributed, under three different forms of selection on the trait. Approximate dynamics are derived under the assumption of small mutation effect. For similar strengths of selection on the trait (i.e, gradient of directional selection b) the way background variation affects the dynamics at the QTL critically depends on the shape of the fitness function. It generally causes the strength of selection on the QTL to decrease with time. The resulting neutral heterozygosity pattern resembles that of a selective sweep with a constant selection coefficient corresponding to the early conditions. The signature of selection may also be blurred by mutation and recombination in the later part of the sweep. We also study the race between the QTL and its genetic background toward a new optimum and find the conditions for a complete sweep. Overall, our results suggest that phenotypic traits exhibiting clear-cut molecular signatures of selection may represent a biased subset of all adaptive traits

Génétique de l'adaptation (de l'évolution des caractères phénotypiques aux signatures moléculaires de la sélection)

L adaptation est l augmentation du succès reproducteur des organismes vivants sous l effet de leur adéquation croissante à leur environnement. Son mécanisme, la sélection naturelle, agit sur le phénotype mais se répercute sur les gènes. La recherche de gènes impliqués dans l adaptation, et potentiellement d intérêt (agronomique, médical ) suscite actuellement un vif intérêt. Mais les méthodes de détection de signatures moléculaires de la sélection ne prennent souvent pas en compte le phénotype, ni la possibilité d une réponse polygénique des caractères à la sélection. J ai développé dans ma thèse plusieurs modèles de génétique des populations incorporant ces aspects. J ai d abord étudié les conséquences d une sélection positive à deux locus proches sur le polymorphisme neutre. Cette situation peut diminuer notre capacité à détecter la sélection, mais peut aussi être exploitée pour obtenir des informations complémentaires sur la chronologie des substitutions favorables ou l interaction entre gènes. Par ailleurs, comme la plupart des caractères adaptatifs varient de manière continue, j ai étudié comment la signature moléculaire d un locus sous sélection était affectée par la sélection à beaucoup d autres locus affectant le même caractère. J ai aussi mis au point une méthode préliminaire pour estimer la distribution des coefficients de sélection des mutations favorables à partir d approches génomiques de détection de la sélection. Enfin, j ai utilisé un modèle de mutation pléiotrope (affectant de nombreux caractères) pour comprendre comment l hétérogénéité phénotypique de la mutation entre locus influe sur la probabilité que chacun d eux soit utilisé lors de l adaptation.Adaptation is the increase in reproductive success of living organisms that results from their growing match to their environment. Its underlying mechanism, natural selection, acts on phenotypes, but is transmitted to the genes. The search for the genes involved in adaptation, and of putative agronomical or medical interest, has been a matter of intense research recently. However, most methods to detect molecular signatures of selection overlook the phenotype, and do not consider the consequences of a possible polygenic response to selection. During this PhD, I developed several population genetic models that allow taking those aspects into account. I first studied the consequence of positive selection at two close loci on neutral polymorphism. This situation can paradoxically hinder our ability to detect selection, but can also be exploited to obtain additional information about the chronology of beneficial substitutions, or the interaction between genes. Since most adaptive traits vary quantitatively, I studied how the molecular signature left by a locus under positive selection is affected by selection at many other loci that affect the same trait. I also designed a preliminary method to estimate the distribution of the selection coefficients of beneficial mutations from genome scans for selection. Finally, I used a model of pleiotropic mutation to understand how the phenotypic heterogeneity of mutation across loci influences the probability that each locus is used during adaptation.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Genetic adaptation counters phenotypic plasticity in experimental evolution

International audienceA recommendation of:Huang Y, Agrawal AF. 2016. Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes. PLoS Genetics 12: e1006336. doi: 10.1371/journal.pgen.100633

Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation

We model selection at a locus affecting a quantitative trait (QTL) in the presence of genetic variance due to other loci. The dynamics at the QTL are related to the initial genotypic value and to the background genetic variance of the trait, assuming that background genetic values are normally distributed, under three different forms of selection on the trait. Approximate dynamics are derived under the assumption of small mutation effect. For similar strengths of selection on the trait (i.e, gradient of directional selection β) the way background variation affects the dynamics at the QTL critically depends on the shape of the fitness function. It generally causes the strength of selection on the QTL to decrease with time. The resulting neutral heterozygosity pattern resembles that of a selective sweep with a constant selection coefficient corresponding to the early conditions. The signature of selection may also be blurred by mutation and recombination in the later part of the sweep. We also study the race between the QTL and its genetic background toward a new optimum and find the conditions for a complete sweep. Overall, our results suggest that phenotypic traits exhibiting clear-cut molecular signatures of selection may represent a biased subset of all adaptive traits