The Impact of Dominance on Adaptation in Changing Environments

Determinants of rapid adaptation in species with large variance in offspring production

The speed of population adaptation to changing biotic and abiotic environments is determined by the interaction between genetic drift, positive selection and linkage effects. Many marine species (fish, crustaceans), invertebrates and pathogens of humans and crops, exhibit sweepstakes reproduction characterized by the production of a very large amount of offspring (fecundity phase) from which only a small fraction may survive to the next generation (viability phase). Using stochastic simulations, we investigate whether the occurrence of sweepstakes reproduction affects the efficiency of a positively selected unlinked locus, and thus, the speed of adaptation since fecundity and/or viability have distinguishable consequences on mutation rate, probability and fixation time of advantageous alleles. We observe that the mean number of mutations at the next generation is always the function of the population size, but the variance increases with stronger sweepstakes reproduction when mutations occur in the parents. On the one hand, stronger sweepstakes reproduction magnifies the effect of genetic drift thus increasing the probability of fixation of neutral allele and decreasing that of selected alleles. On the other hand, the time to fixation of advantageous (as well as neutral) alleles is shortened by stronger sweepstakes reproduction. Importantly, fecundity and viability selection exhibit different probabilities and times to fixation of advantageous alleles under intermediate and weak sweepstakes reproduction. Finally, alleles under both strong fecundity and viability selection display a synergistic efficiency of selection. We conclude that measuring and modelling accurately fecundity and/or viability selection are crucial to predict the adaptive potential of species with sweepstakes reproduction.

Effect of beneficial sweeps and background selection on genetic diversity in changing environments

Neutral theory predicts that the genetic diversity within a population is proportional to the effective population size. In contrast, the observed genetic diversity for various species vary in a narrow range for several orders of magnitude change in the population sizes (Lewontin's paradox). The selective sweeps and background selection, reduce the genetic variation at the linked neutral sites and have been studied considering the environment to be selectively constant. However, in a natural population, the selective environment varies with time. Here, we investigate the impact of selective sweeps and background selection on neutral genetic diversity when the selection coefficient changes periodically over time. The reduction in genetic variation due to selective sweeps is known to depend on the conditional fixation time. Here, we find that the effect of changing environment on conditional mean fixation time is most substantial for the randomly mating population than the inbreeding population with arbitrary inbreeding coefficient. We also study the effect of background selection on neutral sites when the selection coefficient of linked deleterious mutation change periodically in time. In the slowly changing environment, we find that neutral heterozygosity is significantly different, and the site frequency spectrum has a different shape than that in the static environment.

Joint effect of changing selection and demography on the site frequency spectrum

The site frequency spectrum (SFS) is an important statistic that summarizes the molecular variation in a population, and is used to estimate population-genetic parameters and detect natural selection. Here, we study the SFS in a randomly mating, diploid population in which both the population size and selection coefficient vary periodically with time using a diffusion theory approach, and derive simple analytical expressions for the time-averaged SFS in slowly and rapidly changing environments. We show that for strong selection and in slowly changing environments where the population experiences both positive and negative cycles of the selection coefficient, the time-averaged SFS differs significantly from the equilibrium SFS in a constant environment. The deviation is found to depend on the time spent by the population in the deleterious part of the selection cycle and the phase difference between the selection coefficient and population size, and can be captured by an effective population size.

Time to fixation in changing environments

Although many experimental and theoretical studies on natural selection have been carried out in a constant environment, as natural environments typically vary in time, it is important to ask if and how the results of these investigations are affected by a changing environment. Here, we study the properties of the conditional fixation time defined as the time to fixation of a new mutant that is destined to fix in a finite, randomly mating diploid population with intermediate dominance that is evolving in a periodically changing environment. It is known that in a static environment, the conditional mean fixation time of a co-dominant beneficial mutant is equal to that of a deleterious mutant with the same magnitude of selection coefficient. We find that this symmetry is not preserved, even when the environment is changing slowly. More generally, we find that the conditional mean fixation time of an initially beneficial mutant in a slowly changing environment depends weakly on the dominance coefficient and remains close to the corresponding result in the static environment. However, for an initially deleterious mutant under moderate and slowly varying selection, the fixation time differs substantially from that in a constant environment when the mutant is recessive. As fixation times are intimately related to the levels and patterns of genetic diversity, our results suggest that for beneficial sweeps, these quantities are only mildly affected by temporal variation in environment. In contrast, environmental change is likely to impact the patterns due to recessive deleterious sweeps strongly.

Adaptive introgression facilitate adaptation to high latitudes in European aspen (Populus tremula L.)

Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems, and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole-genome resequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum, we detected an adaptive introgression event in a genome region of ∼500 kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of Northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin—probably Russian—of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results, therefore, emphasize the importance of migration–selection balance underlying the genetic architecture of key adaptive quantitative traits.