Hitchhiking of deleterious alleles and the cost of adaptation in partially selfing species

Signatures of selective sweeps in continuous-space populations

Selective sweeps describe the process by which an adaptive mutation arises and rapidly fixes in the population, thereby removing genetic variation in its genomic vicinity. The expected signatures of selective sweeps are relatively well understood in panmictic population models, yet natural populations often extend across larger geographic ranges where individuals are more likely to mate with those born nearby. To investigate how such spatial population structure can affect sweep dynamics and signatures, we simulated selective sweeps in populations inhabiting a two-dimensional continuous landscape. The maximum dispersal distance of offspring from their parents can be varied in our simulations from an essentially panmictic population to scenarios with increasingly limited dispersal. We find that in low-dispersal populations, adaptive mutations spread more slowly than in panmictic ones, while recombination becomes less effective at breaking up genetic linkage around the sweep locus. Together, these factors result in a trough of reduced genetic diversity around the sweep locus that looks very similar across dispersal rates. We also find that the site frequency spectrum around hard sweeps in low-dispersal populations becomes enriched for intermediate-frequency variants, making these sweeps appear softer than they are. Furthermore, haplotype heterozygosity at the sweep locus tends to be elevated in low-dispersal scenarios as compared to panmixia, contrary to what we observe in neutral scenarios without sweeps. The haplotype patterns generated by these hard sweeps in low-dispersal populations can resemble soft sweeps from standing genetic variation that arose from substantially older alleles. Our results highlight the need for better accounting for spatial population structure when making inferences about selective sweeps.

Polygenic selection to a changing optimum under self-fertilisation

Many traits are polygenic, affected by multiple genetic variants throughout the genome. Selection acting on these traits involves co-ordinated allele-frequency changes at these underlying variants, and this process has been extensively studied in random-mating populations. Yet many species self-fertilise to some degree, which incurs changes to genetic diversity, recombination and genome segregation. These factors cumulatively influence how polygenic selection is realised in nature. Here, we use analytical modelling and stochastic simulations to investigate to what extent self-fertilisation affects polygenic adaptation to a new environment. Our analytical solutions show that while selfing can increase adaptation to an optimum, it incurs linkage disequilibrium that can slow down the initial spread of favoured mutations due to selection interference, and favours the fixation of alleles with opposing trait effects. Simulations show that while selection interference is present, high levels of selfing (at least 90%) aids adaptation to a new optimum, showing a higher long-term fitness. If mutations are pleiotropic then only a few major-effect variants fix along with many neutral hitchhikers, with a transient increase in linkage disequilibrium. These results show potential advantages to self-fertilisation when adapting to a new environment, and how the mating system affects the genetic composition of polygenic selection.

Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana

The phenotype of an individual can be affected by the genes of its conspecifics through indirect genetic effects (IGEs). IGEs have been studied across different organisms including wild and domesticated animals and plants, but little is known about their genetic architecture. Here, in a large-scale intraspecific interaction experiment, we show that the contribution of IGEs to the biomass variation of Arabidopsis thaliana is comparable to values classically reported in animals. Moreover, we identify 11 loci explaining 85.1% of the variability in IGEs. We find that positive IGE alleles (that is, those with positive effects on neighbour biomass) occur both in relict accessions from southern Eurasia and in post-glacial colonizers from northern Scandinavia, and that they are likely to have two divergent origins: for nine loci, they evolved in the post-glacial colonizers independently from the relicts, while the two others were introgressed in the post-glacial colonizer from the relicts. Finally, we find that variation in IGEs probably reflects divergent adaptations to the contrasting environments of the edges and the centre of the native range of the species. These findings reveal a surprisingly tractable genetic basis of IGEs in A. thaliana that is shaped by the ecology and the demographic history of the species.

Influence of the mutation load on the genomic composition of hybrids between outcrossing and self-fertilizing species

Hybridization is a natural process whereby two diverging evolutionary lineages reproduce and create offspring of mixed ancestry. Differences in mating systems (e.g., self-fertilization and outcrossing) are expected to affect the direction and extent of hybridization and introgression in hybrid zones. Among other factors, selfers and outcrossers are expected to differ in their mutation loads. This has been studied both theoretically and empirically; however, conflicting predictions have been made on the effects mutation loads of parental species with different mating systems can have on the genomic composition of hybrids. Here, we develop a multi-locus, selective model to study how the different mutation load built up in selfers and outcrossers as a result of selective interference and homozygosity impact the long-term genetic composition of hybrid populations. Notably, our results emphasize that genes from the parental population with lesser mutation load get rapidly overrepresented in hybrid genomes, regardless of the hybrids own mating system. When recombination tends to be more important than mutation, outcrossers' genomes tend to be of higher quality and prevail. When recombination rates are low, however, selfers' genomes may reach higher quality than outcrossers' genomes and prevail in the hybrids. Taken together, these results provide concrete insights into one of the multiple factors influencing hybrid genome ancestry and introgression patterns in hybrid zones containing species with different mating systems.

Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes

Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being tenfold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. The results illustrate how genome organization and selection play a crucial role in shaping the genomic pattern of diversity whereas demographic processes scale the level of diversity across the genome as a whole.

On the hidden temporal dynamics of plant adaptation

Adaptation to a wide range of environments is a major driver of plant diversity. It is now possible to catalog millions of potential adaptive genomic differences segregating between environments within a plant species in a single experiment. Understanding which of these changes contributes to adaptive phenotypic divergence between plant populations is a major goal of evolutionary biologists and crop breeders. In this review, we briefly highlight the approaches frequently used to understand the genetic basis of adaptive phenotypes in plants, and we discuss some of the limitations of these methods. We propose that direct observation of the process of adaptation using multigenerational studies and whole genome sequencing is a crucial missing component of recent studies of plant adaptation because it complements several shortcomings of sampling-based techniques.

The genetic basis of selfing rate evolution

Evolution of selfing is common in plant populations, but the genetic basis of selfing rate evolution remains unclear. Although the effects of genetic properties on fixation for mating-unrelated alleles have been investigated, loci that modify the selfing rate (selfing modifiers) differ from mating-unrelated loci in several aspects. Using population genetic models, I investigate the genetic basis of selfing rate evolution. For mating-unrelated alleles, selfing promotes fixation only for recessive mutations, but for selfing modifiers, because the selection coefficient depends on the background selfing rate, selfing can promote fixation even for dominant modifiers. For mating-unrelated alleles, the fixation probability from standing variation is independent of dominance and decreases with an increased background selfing rate. However, for selfing modifiers, the fixation probability peaks at an intermediate selfing rate and when alleles are recessive, because a change of its selection coefficient necessarily involves a change of the inbreeding coefficient, because both depend on the level of inbreeding depression. Furthermore, evolution of selfing involving multiple modifier loci is more likely when selfing is controlled by few large-effect rather than many slight-effect modifiers. I discuss how these characteristics of selfing modifiers have implications for the unidirectional transition from outcrossing to selfing and other empirical patterns.

Interplay between extreme drift and selection intensities favors the fixation of beneficial mutations in selfing maize populations

Population and quantitative genetic models provide useful approximations to predict long-term selection responses sustaining phenotypic shifts, and underlying multilocus adaptive dynamics. Valid across a broad range of parameters, their use for understanding the adaptive dynamics of small selfing populations undergoing strong selection intensity (thereafter High Drift-High selection regime, HDHS) remains to be explored. Saclay Divergent Selection Experiments (DSEs) on maize flowering time provide an interesting example of populations evolving under HDHS, with significant selection responses over 20 generations in two directions. We combined experimental data from Saclay DSEs, forward individual-based simulations, and theoretical predictions to dissect the evolutionary mechanisms at play in the observed selection responses. We asked two main questions: How do mutations arise, spread, and reach fixation in populations evolving under HDHS? How does the interplay between drift and selection influence observed phenotypic shifts? We showed that the long-lasting response to selection in small populations is due to the rapid fixation of mutations occurring during the generations of selection. Among fixed mutations, we also found a clear signal of enrichment for beneficial mutations revealing a limited cost of selection. Both environmental stochasticity and variation in selection coefficients likely contributed to exacerbate mutational effects, thereby facilitating selection grasp and fixation of small-effect mutations. Together our results highlight that despite a small number of polymorphic loci expected under HDHS, adaptive variation is continuously fueled by a vast mutational target. We discuss our results in the context of breeding and long-term survival of small selfing populations.

Balancing selection in self-fertilizing populations

Self-fertilization commonly occurs in hermaphroditic species, either occasionally or as the main reproductive mode. It strongly affects the genetic functioning of a population by increasing homozygosity and genetic drift and reducing the effectiveness of recombination. Balancing selection is a form of selection that maintains polymorphism, which has been extensively studied in outcrossing species. Yet, despite recent developments, the analysis of balancing selection in partially selfing species is limited to specific cases and a general treatment is still lacking. In particular, it is unclear whether selfing globally reduced the efficacy of balancing selection as in the well-known case of overdominance. I provide a unifying framework, quantify how selfing affects the maintenance of polymorphism and the efficacy of the different form of balancing selection, and show that they can be classified into two main categories: overdominance-like selection (including true overdominance, selection variable in space and time, and antagonistic selection), which is strongly affected by selfing, and negative frequency dependent selection, which is barely affected by selfing, even at multiple loci. I also provide simple analytical results for all cases under the assumption of weak selection. This framework provides theoretical background to analyze the genomic signature of balancing selection in partially selfing species. It also sheds new light on the evolution of selfing species, including the evolution of selfing syndrome, the interaction with pathogens, and the evolutionary fate of selfing lineages.

Selective Sweeps Under Dominance and Inbreeding

A major research goal in evolutionary genetics is to uncover loci experiencing positive selection. One approach involves finding 'selective sweeps' patterns, which can either be 'hard sweeps' formed by de novo mutation, or 'soft sweeps' arising from recurrent mutation or existing standing variation. Existing theory generally assumes outcrossing populations, and it is unclear how dominance affects soft sweeps. We consider how arbitrary dominance and inbreeding via self-fertilization affect hard and soft sweep signatures. With increased self-fertilization, they are maintained over longer map distances due to reduced effective recombination and faster beneficial allele fixation times. Dominance can affect sweep patterns in outcrossers if the derived variant originates from either a single novel allele, or from recurrent mutation. These models highlight the challenges in distinguishing hard and soft sweeps, and propose methods to differentiate between scenarios.

Population Genomics of Transitions to Selfing in Brassicaceae Model Systems

Many plants harbor complex mechanisms that promote outcrossing and efficient pollen transfer. These include floral adaptations as well as genetic mechanisms, such as molecular self-incompatibility (SI) systems. The maintenance of such systems over long evolutionary timescales suggests that outcrossing is favorable over a broad range of conditions. Conversely, SI has repeatedly been lost, often in association with transitions to self-fertilization (selfing). This transition is favored when the short-term advantages of selfing outweigh the costs, primarily inbreeding depression. The transition to selfing is expected to have major effects on population genetic variation and adaptive potential, as well as on genome evolution. In the Brassicaceae, many studies on the population genetic, gene regulatory, and genomic effects of selfing have centered on the model plant Arabidopsis thaliana and the crucifer genus Capsella. The accumulation of population genomics datasets have allowed detailed investigation of where, when and how the transition to selfing occurred. Future studies will take advantage of the development of population genetics theory on the impact of selfing, especially regarding positive selection. Furthermore, investigation of systems including recent transitions to selfing, mixed mating populations and/or multiple independent replicates of the same transition will facilitate dissecting the effects of mating system variation from processes driven by demography.

Mating system impacts the genetic architecture of adaptation to heterogeneous environments

Self-fertilisation has consequences for variation across the genome as it reduces effective population size, effect recombination rates and pollen flow, with implications for local adaptation. We conducted simulations of divergent stabilising selection on a quantitative trait with drift, pollen flow, mutation, recombination and different outcrossing rates. We quantified trait divergence and the genetic architecture of adaptation. We conducted an F_ST outlier analysis to identify candidate loci and quantified the impact of mating system on detectability. Selfing promoted trait divergence mainly through reductions in pollen flow. Moreover, trait architecture became more diffuse with selfing. Average effect size of trait loci was lower, while the number of loci, and their clustering distance increased. The genetic architecture of selfers was also more diffuse than outcrossers for equivalent migration rates. However, when deleterious alleles were included, architectures became more concentrated in selfers, likely to be because of reductions in population size caused by mutational meltdown and impacts of background selection on N_e . Our simulations demonstrate that mating system has important impacts on adaptive divergence of traits and the genetic landscape underlying that divergence. Selfing has a significant effect on detectability of regions of the genome important for adaptation because of neutral divergence and diffuse trait architecture.

Effect of partial selfing and polygenic selection on establishment in a new habitat

This article analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the inbreeding history model to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple nonidentical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection is discussed.

Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum (Sorghum bicolor)

Sorghum (Sorghum bicolor (L.) Moench) is a major staple food cereal for millions of people worldwide. Valluru et al. identify putative deleterious mutations among ∼5.5M segregating variants of 229 diverse sorghum...

Sorghum (Sorghum bicolor L.) is a major food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. The lack of recombination, drift, and the coupling with favorable loci impede the removal of deleterious mutations from the genome by selection. To study how deleterious variants impact phenotypes, we identified putative deleterious mutations among ∼5.5 M segregating variants of 229 diverse biomass sorghum lines. We provide the whole-genome estimate of the deleterious burden in sorghum, showing that ∼33% of nonsynonymous substitutions are putatively deleterious. The pattern of mutation burden varies appreciably among racial groups. Across racial groups, the mutation burden correlated negatively with biomass, plant height, specific leaf area (SLA), and tissue starch content (TSC), suggesting that deleterious burden decreases trait fitness. Putatively deleterious variants explain roughly one-half of the genetic variance. However, there is only moderate improvement in total heritable variance explained for biomass (7.6%) and plant height (average of 3.1% across all stages). There is no advantage in total heritable variance for SLA and TSC. The contribution of putatively deleterious variants to phenotypic diversity therefore appears to be dependent on the genetic architecture of traits. Overall, these results suggest that incorporating putatively deleterious variants into genomic models slightly improves prediction accuracy because of extensive linkage. Knowledge of deleterious variants could be leveraged for sorghum breeding through either genome editing and/or conventional breeding that focuses on the selection of progeny with fewer deleterious alleles.

Prediction of deleterious mutations in coding regions of mammals with transfer learning

The genomes of mammals contain thousands of deleterious mutations. It is important to be able to recognize them with high precision. In conservation biology, the small size of fragmented populations results in accumulation of damaging variants. Preserving animals with less damaged genomes could optimize conservation efforts. In breeding of farm animals, trade-offs between farm performance versus general fitness might be better avoided if deleterious mutations are well classified. In humans, the problem of such a precise classification has been successfully solved, in large part due to large databases of disease-causing mutations. However, this kind of information is very limited for other mammals. Here, we propose to better use information available on human mutations to enable classification of damaging mutations in other mammalian species. Specifically, we apply transfer learning-machine learning methods-improving small dataset for solving a focal problem (recognizing damaging mutations in our companion and farm animals) due to the use of much large datasets available for solving a related problem (recognizing damaging mutations in humans). We validate our tools using mouse and dog annotated datasets and obtain significantly better results in companion to the SIFT classifier. Then, we apply them to predict deleterious mutations in cattle genomewide dataset.

Genome Evolution in Outcrossing vs. Selfing vs. Asexual Species

A major current molecular evolution challenge is to link comparative genomic patterns to species' biology and ecology. Breeding systems are pivotal because they affect many population genetic processes and thus genome evolution. We review theoretical predictions and empirical evidence about molecular evolutionary processes under three distinct breeding systems-outcrossing, selfing, and asexuality. Breeding systems may have a profound impact on genome evolution, including molecular evolutionary rates, base composition, genomic conflict, and possibly genome size. We present and discuss the similarities and differences between the effects of selfing and clonality. In reverse, comparative and population genomic data and approaches help revisiting old questions on the long-term evolution of breeding systems.

The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping

Recombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence-based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome-wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans-acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans-acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low-recombining pericentromeric regions of chromosomes.

The Evolutionary Interplay between Adaptation and Self-Fertilization

Genome-wide surveys of nucleotide polymorphisms, obtained from next-generation sequencing, have uncovered numerous examples of adaptation in self-fertilizing organisms, especially regarding changes to climate, geography, and reproductive systems. Yet existing models for inferring attributes of adaptive mutations often assume idealized outcrossing populations, which risks mischaracterizing properties of these variants. Recent theoretical work is emphasizing how various aspects of self-fertilization affects adaptation, yet empirical data on these properties are lacking. We review theoretical and empirical studies demonstrating how self-fertilization alters the process of adaptation, illustrated using examples from current sequencing projects. We propose ideas for how future research can more accurately quantify aspects of adaptation in self-fertilizers, including incorporating the effects of standing variation, demographic history, and polygenic adaptation.

Analysis of large-scale next-generation sequencing datasets are finding more examples of adaptive evolution at the genomic level.

Advances in theoretical work has demonstrated how self-fertilisation affects different aspects of adaptation in these organisms, compared to outcrossers.

Current software and statistical methods do not take different mating systems into account, which risks mischaracterising the presence or strength of adaptive mutations from genome scans.

Development of new mathematical and statistical methods that explicitly consider self-fertilization and associated demographic effects will enable researchers to more accurately quantify adaptation in these organisms.

Genomic studies of adaptive evolution in outcrossing Arabidopsis species

Large-scale population genomic approaches have very recently been fruitfully applied to the Arabidopsis relatives Arabidopsis halleri, A. lyrata and especially A. arenosa. In contrast to A. thaliana, these species are obligately outcrossing and thus the footprints of natural selection are more straightforward to detect. Furthermore, both theoretical and empirical studies indicate that outcrossers are better able to evolve in response to selection pressure. As a result, recent work in these species serves as a paradigm of population genomic studies of adaptation both to environmental as well as intracellular challenges.

Genetic, Physical and Comparative Mapping of the Powdery Mildew Resistance Gene Pm21 Originating from Dasypyrum villosum

Pm21, originating from wheat wild relative Dasypyrum villosum, confers immunity to all known races of Blumeria graminis f. sp. tritici (Bgt) and has been widely utilized in wheat breeding. However, little is known on the genetic basis of the Pm21 locus. In the present study, four seedling-susceptible D. villosum lines (DvSus-1 ∼ DvSus-4) were identified from different natural populations. Based on the collinearity among genomes of Brachypodium distachyon, Oryza, and Triticeae, a set of 25 gene-derived markers were developed declaring the polymorphisms between DvRes-1 carrying Pm21 and DvSus-1. Fine genetic mapping of Pm21 was conducted by using an extremely large F₂ segregation population derived from the cross DvSus-1/DvRes-1. Then Pm21 was narrowed to a 0.01-cM genetic interval defined by the markers 6VS-08.4b and 6VS-10b. Three DNA markers, including a resistance gene analog marker, were confirmed to co-segregate with Pm21. Moreover, based on the susceptible deletion line Y18-S6 induced by ethyl methanesulfonate treatment conducted on Yangmai 18, Pm21 was physically mapped into a similar interval. Comparative analysis revealed that the orthologous regions of the interval carrying Pm21 were narrowed to a 112.5 kb genomic region harboring 18 genes in Brachypodium, and a 23.2 kb region harboring two genes in rice, respectively. This study provides a high-density integrated map of the Pm21 locus, which will contribute to map-based cloning of Pm21.

Limits to Adaptation in Partially Selfing Species

In outcrossing populations, "Haldane's sieve" states that recessive beneficial alleles are less likely to fix than dominant ones, because they are less exposed to selection when rare. In contrast, selfing organisms are not subject to Haldane's sieve and are more likely to fix recessive types than outcrossers, as selfing rapidly creates homozygotes, increasing overall selection acting on mutations. However, longer homozygous tracts in selfers also reduce the ability of recombination to create new genotypes. It is unclear how these two effects influence overall adaptation rates in partially selfing organisms. Here, we calculate the fixation probability of beneficial alleles if there is an existing selective sweep in the population. We consider both the potential loss of the second beneficial mutation if it has a weaker advantage than the first one, and the possible replacement of the initial allele if the second mutant is fitter. Overall, loss of weaker adaptive alleles during a first selective sweep has a larger impact on preventing fixation of both mutations in highly selfing organisms. Furthermore, the presence of linked mutations has two opposing effects on Haldane's sieve. First, recessive mutants are disproportionally likely to be lost in outcrossers, so it is likelier that dominant mutations will fix. Second, with elevated rates of adaptive mutation, selective interference annuls the advantage in selfing organisms of not suffering from Haldane's sieve; outcrossing organisms are more able to fix weak beneficial mutations of any dominance value. Overall, weakened recombination effects can greatly limit adaptation in selfing organisms.

Lower selfing rates in metallicolous populations than in non-metallicolous populations of the pseudometallophyte Noccaea caerulescens (Brassicaceae) in Southern France

BACKGROUND AND AIMS

The pseudometallophyte Noccaea caerulescens is an excellent model to study evolutionary processes, as it grows both on normal and on heavy-metal-rich, toxic soils. The evolution and demography of populations are critically impacted by mating system and, yet, information about the N. caerulescens mating system is limited.

METHODS

Mean selfing rates were assessed using microsatellite loci and a robust estimation method (RMES) in five metallicolous and five non-metallicolous populations of N. caerulescens in Southern France, and this measure was replicated for two successive reproductive seasons. As a part of the study, the patterns of gene flow among populations were analysed. The mating system was then characterized at a fine spatial scale in three populations using the MLTR method on progeny arrays.

KEY RESULTS

The results confirm that N. caerulescens has a mixed mating system, with selfing rates ranging from 0·2 to 0·5. Selfing rates did not vary much among populations within ecotypes, but were lower in the metallicolous than in the non-metallicolous ecotype, in both seasons. Effective population size was also lower in non-metallicolous populations. Biparental inbreeding was null to moderate. Differentiation among populations was generally high, but neither ecotype nor isolation by distance explained it.

CONCLUSIONS

The consequences of higher selfing rates on adaptation are expected to be weak to moderate in non-metallicolous populations and they are expected to suffer less from inbreeding depression, compared to metallicolous populations.

Obstruction of adaptation in diploids by recessive, strongly deleterious alleles

Recessive deleterious mutations are common, causing many genetic disorders in humans and producing inbreeding depression in the majority of sexually reproducing diploids. The abundance of recessive deleterious mutations in natural populations suggests they are likely to be present on a chromosome when a new adaptive mutation occurs, yet the dynamics of recessive deleterious hitchhikers and their impact on adaptation remains poorly understood. Here we model how a recessive deleterious mutation impacts the fate of a genetically linked dominant beneficial mutation. The frequency trajectory of the adaptive mutation in this case is dramatically altered and results in what we have termed a "staggered sweep." It is named for its three-phased trajectory: (i) Initially, the two linked mutations have a selective advantage while rare and will increase in frequency together, then (ii), at higher frequencies, the recessive hitchhiker is exposed to selection and can cause a balanced state via heterozygote advantage (the staggered phase), and (iii) finally, if recombination unlinks the two mutations, then the beneficial mutation can complete the sweep to fixation. Using both analytics and simulations, we show that strongly deleterious recessive mutations can substantially decrease the probability of fixation for nearby beneficial mutations, thus creating zones in the genome where adaptation is suppressed. These mutations can also significantly prolong the number of generations a beneficial mutation takes to sweep to fixation, and cause the genomic signature of selection to resemble that of soft or partial sweeps. We show that recessive deleterious variation could impact adaptation in humans and Drosophila.

The evolution of selfing is accompanied by reduced efficacy of selection and purging of deleterious mutations

The transition from outcrossing to selfing is predicted to reduce the genome-wide efficacy of selection because of the lower effective population size (Ne) that accompanies this change in mating system. However, strongly recessive deleterious mutations exposed in the homozygous backgrounds of selfers should be under strong purifying selection. Here, we examine estimates of the distribution of fitness effects (DFE) and changes in the magnitude of effective selection coefficients (Nes) acting on mutations during the transition from outcrossing to selfing. Using forward simulations, we investigated the ability of a DFE inference approach to detect the joint influence of mating system and the dominance of deleterious mutations on selection efficacy. We investigated predictions from our simulations in the annual plant Eichhornia paniculata, in which selfing has evolved from outcrossing on multiple occasions. We used range-wide sampling to generate population genomic datasets and identified nonsynonymous and synonymous polymorphisms segregating in outcrossing and selfing populations. We found that the transition to selfing was accompanied by a change in the DFE, with a larger fraction of effectively neutral sites (Nes < 1), a result consistent with the effects of reduced Ne in selfers. Moreover, an increased proportion of sites in selfers were under strong purifying selection (Nes > 100), and simulations suggest that this is due to the exposure of recessive deleterious mutations. We conclude that the transition to selfing has been accompanied by the genome-wide influences of reduced Ne and strong purifying selection against deleterious recessive mutations, an example of purging at the molecular level.

Sexually antagonistic polymorphism in simultaneous hermaphrodites

In hermaphrodites, pleiotropic genetic trade-offs between female and male reproductive functions can lead to sexually antagonistic (SA) selection, where individual alleles have conflicting fitness effects on each sex function. Although an extensive theory of SA selection exists for dioecious species, these results have not been generalized to hermaphrodites. We develop population genetic models of SA selection in simultaneous hermaphrodites, and evaluate effects of dominance, selection on each sex function, self-fertilization, and population size on the maintenance of polymorphism. Under obligate outcrossing, hermaphrodite model predictions converge exactly with those of dioecious populations. Self-fertilization in hermaphrodites generates three points of divergence with dioecious theory. First, opportunities for stable polymorphism decline sharply and become less sensitive to dominance with increased selfing. Second, selfing introduces an asymmetry in the relative importance of selection through male versus female reproductive functions, expands the parameter space favorable for the evolutionary invasion of female-beneficial alleles, and restricts invasion criteria for male-beneficial alleles. Finally, contrary to models of unconditionally beneficial alleles, selfing decreases genetic hitchhiking effects of invading SA alleles, and should therefore decrease these population genetic signals of SA polymorphisms. We discuss implications of SA selection in hermaphrodites, including its potential role in the evolution of "selfing syndromes."

Adaptive gene introgression after secondary contact

By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range.

Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima)

The African cultivated rice (Oryza glaberrima) was domesticated in West Africa 3000 years ago. Although less cultivated than the Asian rice (O. sativa), O. glaberrima landraces often display interesting adaptation to rustic environment (e.g. drought). Here, using RNA-seq technology, we were able to compare more than 12,000 transcripts between 9 O. glaberrima, 10 wild O. barthii and one O. meridionalis individuals. With a synonymous nucleotide diversity πs = 0.0006 per site, O. glaberrima appears as the least genetically diverse crop grass ever documented. Using approximate Bayesian computation, we estimated that O. glaberrima experienced a severe bottleneck during domestication. This demographic scenario almost fully accounts for the pattern of genetic diversity across O. glaberrima genome as we detected very few outliers regions where positive selection may have further impacted genetic diversity. Moreover, the large excess of derived nonsynonymous substitution that we detected suggests that the O. glaberrima population suffered from the 'cost of domestication'. In addition, we used this genome-scale data set to demonstrate that (i) O. barthii genetic diversity is positively correlated with recombination rate and negatively with gene density, (ii) expression level is negatively correlated with evolutionary constraint, and (iii) one region on chromosome 5 (position 4-6 Mb) exhibits a clear signature of introgression with a yet unidentified Oryza species. This work represents the first genome-wide survey of the African rice genetic diversity and paves the way for further comparison between the African and the Asian rice, notably regarding the genetics underlying domestication traits.