Genealogy-dependent variation in viability among self-incompatibility genotypes

The genetic architecture of the load linked to dominant and recessive self-incompatibility alleles in Arabidopsis halleri and Arabidopsis lyrata

The long-term balancing selection acting on mating types or sex-determining genes is expected to lead to the accumulation of deleterious mutations in the tightly linked chromosomal segments that are locally 'sheltered' from purifying selection. However, the factors determining the extent of this accumulation are poorly understood. Here, we took advantage of variations in the intensity of balancing selection along a dominance hierarchy formed by alleles at the sporophytic self-incompatibility system of the Brassicaceae to compare the pace at which linked deleterious mutations accumulate among them. We first experimentally measured the phenotypic manifestation of the linked load at three different levels of the dominance hierarchy. We then sequenced and phased polymorphisms in the chromosomal regions linked to 126 distinct copies of S-alleles in two populations of Arabidopsis halleri and three populations of Arabidopsis lyrata. We find that linkage to the S-locus locally distorts phylogenies over about 10-30 kb along the chromosome. The more intense balancing selection on dominant S-alleles results in greater fixation of linked deleterious mutations, while recessive S-alleles accumulate more linked deleterious mutations that are segregating. Hence, the structure rather than the overall magnitude of the linked genetic load differs between dominant and recessive S-alleles. Our results have consequences for the long-term evolution of new S-alleles, the evolution of dominance modifiers between them, and raise the question of why the non-recombining regions of some sex and mating type chromosomes expand over evolutionary times while others, such as the S-locus of the Brassicaceae, remain restricted to small chromosomal regions.

Joint estimation of selection intensity and mutation rate under balancing selection with applications to HLA

A composite likelihood method is introduced for jointly estimating the intensity of selection and the rate of mutation, both scaled by the effective population size, when there is balancing selection at a single multi-allelic locus in an isolated population at demographic equilibrium. The performance of the method is tested using simulated data. Average estimated mutation rates and selection intensities are close to the true values but there is considerable variation about the averages. Allowing for both population growth and population subdivision does not result in qualitative differences but the estimated mutation rates and selection intensities do not in general reflect the current effective population size. The method is applied to three class I (HLA-A, HLA-B and HLA-C) and two class II loci (HLA-DRB1 and HLA-DQA1) in the 1000 Genomes populations. Allowing for asymmetric balancing selection has only a slight effect on the results from the symmetric model. Mutations that restore symmetry of the selection model are preferentially retained because of the tendency of natural selection to maximize average fitness. However, slight differences in selective effects result in much longer persistence time of some alleles. Trans-species polymorphism (TSP), which is characteristic of major-histocompatibility loci in vertebrates, is more likely when there are small differences in allelic fitness than when complete symmetry is assumed. Therefore, variation in allelic fitness expands the range of parameter values consistent with observations of TSP.

Evolution of self-incompatibility in the Brassicaceae: Lessons from a textbook example of natural selection

Self-incompatibility (SI) is a self-recognition genetic system enforcing outcrossing in hermaphroditic flowering plants and results in one of the arguably best understood forms of natural (balancing) selection maintaining genetic variation over long evolutionary times. A rich theoretical and empirical population genetics literature has considerably clarified how the distribution of SI phenotypes translates into fitness differences among individuals by a combination of inbreeding avoidance and rare-allele advantage. At the same time, the molecular mechanisms by which self-pollen is specifically recognized and rejected have been described in exquisite details in several model organisms, such that the genotype-to-phenotype map is also pretty well understood, notably in the Brassicaceae. Here, we review recent advances in these two fronts and illustrate how the joint availability of detailed characterization of genotype-to-phenotype and phenotype-to-fitness maps on a single genetic system (plant self-incompatibility) provides the opportunity to understand the evolutionary process in a unique perspective, bringing novel insight on general questions about the emergence, maintenance, and diversification of a complex genetic system.

Genetic architecture and balancing selection: the life and death of differentiated variants

Balancing selection describes any form of natural selection, which results in the persistence of multiple variants of a trait at intermediate frequencies within populations. By offering up a snapshot of multiple co-occurring functional variants and their interactions, systems under balancing selection can reveal the evolutionary mechanisms favouring the emergence and persistence of adaptive variation in natural populations. We here focus on the mechanisms by which several functional variants for a given trait can arise, a process typically requiring multiple epistatic mutations. We highlight how balancing selection can favour specific features in the genetic architecture and review the evolutionary and molecular mechanisms shaping this architecture. First, balancing selection affects the number of loci underlying differentiated traits and their respective effects. Control by one or few loci favours the persistence of differentiated functional variants by limiting intergenic recombination, or its impact, and may sometimes lead to the evolution of supergenes. Chromosomal rearrangements, particularly inversions, preventing adaptive combinations from being dissociated are increasingly being noted as features of such systems. Similarly, due to the frequency of heterozygotes maintained by balancing selection, dominance may be a key property of adaptive variants. High heterozygosity and limited recombination also influence associated genetic load, as linked recessive deleterious mutations may be sheltered. The capture of deleterious elements in a locus under balancing selection may reinforce polymorphism by further promoting heterozygotes. Finally, according to recent genomewide scans, balanced polymorphism might be more pervasive than generally thought. We stress the need for both functional and ecological studies to characterize the evolutionary mechanisms operating in these systems.

How Have Self-Incompatibility Haplotypes Diversified? Generation of New Haplotypes during the Evolution of Self-Incompatibility from Self-Compatibility

I developed a gametophytic self-incompatibility (SI) model to study the conditions leading to diversification in SI haplotypes. In the model, the SI system is assumed to be incomplete, and the pollen expressing a given specificity is not fully rejected by the pistils expressing the same specificity. I also assumed that mutations can occur that enhance the rejection of pollen by pistils with the same haplotype variant and reduce rejection by pistils with other variants in the same haplotype. I found that if such mutations occur, the new haplotypes (mutant variants) can stably coexist with the ancestral haplotype in which the mutant arose. This is because pollen bearing the new haplotype is most strongly rejected by pistils bearing the same new haplotype among the pistils in the population; hence, negative frequency-dependent selection prevents their fixation. I also performed simulations and found that the nearly complete SI system evolves from completely self-compatible populations and that SI haplotypes can increase to about 40-50 within a few thousand generations. On the basis of my findings, I propose that diversification of SI haplotypes occurred during the evolution of SI from self-compatibility.

Trait transitions in explicit ecological and genomic contexts: plant mating systems as case studies

Plants are astonishingly diverse in how they reproduce sexually, and the study of plant mating systems provides some of the most compelling cases of parallel and independent evolutionary transitions. In this chapter, we review how the massive amount of genomic data being produced is allowing long-standing predictions from ecological and evolutionary theory to be put to test. After a review of theoretical predictions about the importance of considering the genomic architecture of the mating system, we focus on a set of recent discoveries on how the mating system is controlled in a variety of model and non-model species. In parallel, genomic approaches have revealed the complex interaction between the evolution of genes controlling mating systems and genome evolution, both genome-wide and in the mating system control region. In several cases, major transitions in the mating system can be clearly associated with important ecological changes, hence illuminating an important interplay between ecological and genomic approaches. We also list a number of major unsolved questions that remain for the field, and highlight foreseeable conceptual developments that are likely to play a major role in our understanding of how plant mating systems evolve in Nature.

Gradual molecular evolution of a sex determination switch through incomplete penetrance of femaleness

Some genes regulate phenotypes that are either present or absent. They are often important regulators of developmental switches and are involved in morphological evolution. We have little understanding of the molecular mechanisms by which these absence/presence gene functions have evolved, because the phenotype and fitness of molecular intermediate forms are unknown. Here, we studied the sex-determining switch of 14 natural sequence variants of the csd gene among 76 genotypes of the honeybee (Apis mellifera). Heterozygous genotypes (different specificities) of the csd gene determine femaleness, while hemizygous genotypes (single specificity) determine maleness. Homozygous genotypes of the csd gene (same specificity) are lethal. We found that at least five amino acid differences and length variation between Csd specificities in the specifying domain (PSD) were sufficient to regularly induce femaleness. We estimated that, on average, six pairwise amino acid differences evolved under positive selection. We also identified a natural evolutionary intermediate that showed only three amino acid length differences in the PSD relative to its parental allele. This genotype showed an intermediate fitness because it implemented lethality regularly and induced femaleness infrequently (i.e., incomplete penetrance). We suggest incomplete penetrance as a mechanism through which new molecular switches can gradually and adaptively evolve.

The population genetics of sporophytic self-incompatibility in three hybridizing senecio (asteraceae) species with contrasting population histories

Hybridization generates evolutionary novelty and spreads adaptive variation. By promoting outcrossing, plant self-incompatibility (SI) systems also favor interspecific hybridization because the S locus is under strong negative frequency-dependent balancing selection. This study investigates the SI mating systems of three hybridizing Senecio species with contrasting population histories. Senecio aethnensis and S. chrysanthemifolius native to Sicily, form a hybrid zone at intermediate altitudes on Mount Etna, and their neo-homoploid hybrid species, S. squalidus, has colonized disturbed urban habitats in the UK during the last 150 years. We show that all three species express sporophytic SI (SSI), where pollen incompatibility is controlled by the diploid parental genome, and that SSI is inherited and functions normally in hybrids. Large-scale crossing studies of wild sampled populations allowed direct comparison of SSI between species and found that the main impacts of colonization in S. squalidus compared to Sicilian Senecio was a reduced number of S alleles, increased S allele frequencies, and increased interpopulation S allele sharing. In general, many S alleles were shared between species and the S locus showed reduced intra- and interspecific population genetic structure compared to molecular genetic markers, indicative of enhanced effective gene flow due to balancing selection.

Inbreeding depression in self-incompatible North-American Arabidopsis lyrata: disentangling genomic and S-locus-specific genetic load

Newly formed selfing lineages may express recessive genetic load and suffer inbreeding depression. This can have a genome-wide genetic basis, or be due to loci linked to genes under balancing selection. Understanding the genetic architecture of inbreeding depression is important in the context of the maintenance of self-incompatibility and understanding the evolutionary dynamics of S-alleles. We addressed this using North-American subspecies of Arabidopsis lyrata. This species is normally self-incompatible and outcrossing, but some populations have undergone a transition to selfing. The goals of this study were to: (1) quantify the strength of inbreeding depression in North-American populations of A. lyrata; and (2) disentangle the relative contribution of S-linked genetic load compared with overall inbreeding depression. We enforced selfing in self-incompatible plants with known S-locus genotype by treatment with CO(2), and compared the performance of selfed vs outcrossed progeny. We found significant inbreeding depression for germination rate (δ=0.33), survival rate to 4 weeks (δ=0.45) and early growth (δ=0.07), but not for flowering rate. For two out of four S-alleles in our design, we detected significant S-linked load reflected by an under-representation of S-locus homozygotes in selfed progeny. The presence or absence of S-linked load could not be explained by the dominance level of S-alleles. Instead, the random nature of the mutation process may explain differences in the recessive deleterious load among lineages.

Inbreeding depression in Solanum carolinense (Solanaceae) under field conditions and implications for mating system evolution

The clonal weed Solanum carolinense exhibits plasticity in the strength of its self-incompatibility (SI) system and suffers low levels of inbreeding depression (δ) in the greenhouse. We planted one inbred and one outbred plant from each of eight maternal plants in a ring (replicated twice) and monitored clonal growth, herbivory, and reproduction over two years. Per ramet δ was estimated to be 0.63 in year one and 0.79 in year two, and outbred plants produced 2.5 times more ramets than inbred plants in the spring of year two. Inbred plants also suffered more herbivore damage than outbred plants in both fields, suggesting that inbreeding compromises herbivore resistance. Total per genet δ was 0.85 over the two years, indicating that S. carolinense is unlikely to become completely self-compatible, and suggesting that plasticity in the SI system is part of a stable mixed-mating system permitting self-fertilization when cross pollen limits seed production.

Microevolution of S-allele frequencies in wild cherry populations: respective impacts of negative frequency dependent selection and genetic drift

Negative frequency dependent selection (NFDS) is supposed to be the main force controlling allele evolution at the gametophytic self-incompatibility locus (S-locus) in strictly outcrossing species. Genetic drift also influences S-allele evolution. In perennial sessile organisms, evolution of allelic frequencies over two generations is mainly shaped by individual fecundities and spatial processes. Using wild cherry populations between two successive generations, we tested whether S-alleles evolved following NFDS qualitative and quantitative predictions. We showed that allelic variation was negatively correlated with parental allelic frequency as expected under NFDS. However, NFDS predictions in finite population failed to predict more than half S-allele quantitative evolution. We developed a spatially explicit mating model that included the S-locus. We studied the effects of self-incompatibility and local drift within populations due to pollen dispersal in spatially distributed individuals, and variation in male fecundity on male mating success and allelic frequency evolution. Male mating success was negatively related to male allelic frequency as expected under NFDS. Spatial genetic structure combined with self-incompatibility resulted in higher effective pollen dispersal. Limited pollen dispersal in structured distributions of individuals and genotypes and unequal pollen production significantly contributed to S-allele frequency evolution by creating local drift effects strong enough to counteract the NFDS effect on some alleles.

Expression and trans-specific polymorphism of self-incompatibility RNases in coffea (Rubiaceae)

Self-incompatibility (SI) is widespread in the angiosperms, but identifying the biochemical components of SI mechanisms has proven to be difficult in most lineages. Coffea (coffee; Rubiaceae) is a genus of old-world tropical understory trees in which the vast majority of diploid species utilize a mechanism of gametophytic self-incompatibility (GSI). The S-RNase GSI system was one of the first SI mechanisms to be biochemically characterized, and likely represents the ancestral Eudicot condition as evidenced by its functional characterization in both asterid (Solanaceae, Plantaginaceae) and rosid (Rosaceae) lineages. The S-RNase GSI mechanism employs the activity of class III RNase T2 proteins to terminate the growth of "self" pollen tubes. Here, we investigate the mechanism of Coffea GSI and specifically examine the potential for homology to S-RNase GSI by sequencing class III RNase T2 genes in populations of 14 African and Madagascan Coffea species and the closely related self-compatible species Psilanthus ebracteolatus. Phylogenetic analyses of these sequences aligned to a diverse sample of plant RNase T2 genes show that the Coffea genome contains at least three class III RNase T2 genes. Patterns of tissue-specific gene expression identify one of these RNase T2 genes as the putative Coffea S-RNase gene. We show that populations of SI Coffea are remarkably polymorphic for putative S-RNase alleles, and exhibit a persistent pattern of trans-specific polymorphism characteristic of all S-RNase genes previously isolated from GSI Eudicot lineages. We thus conclude that Coffea GSI is most likely homologous to the classic Eudicot S-RNase system, which was retained since the divergence of the Rubiaceae lineage from an ancient SI Eudicot ancestor, nearly 90 million years ago.

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.

The sheltered genetic load linked to the s locus in plants: new insights from theoretical and empirical approaches in sporophytic self-incompatibility

Inbreeding depression and mating systems evolution are closely linked, because the purging of deleterious mutations and the fitness of individuals may depend on outcrossing vs. selfing rates. Further, the accumulation of deleterious mutations may vary among genomic regions, especially for genes closely linked to loci under balancing selection. Sporophytic self-incompatibility (SSI) is a common genetic mechanism in angiosperm that enables hermaphrodite plants to avoid selfing and promote outcrossing. The SSI phenotype is determined by the S locus and may depend on dominance relationships among alleles. Since most individuals are heterozygous at the S locus and recombination is suppressed in the S-locus region, it has been suggested that deleterious mutations could accumulate at genes linked to the S locus, generating a "sheltered load." In this article, we first theoretically investigate the conditions generating sheltered load in SSI. We show that deleterious mutations can accumulate in linkage with specific S alleles, and particularly if those S alleles are dominant. Second, we looked for the presence of sheltered load in Arabidopsis halleri using CO(2) gas treatment to overcome self-incompatibility. By examining the segregation of S alleles and measuring the relative fitness of progeny, we found significant sheltered load associated with the most dominant S allele (S15) of three S alleles tested. This sheltered load seems to be expressed at several stages of the life cycle and to have a larger effect than genomic inbreeding depression.

A new theory of MHC evolution: beyond selection on the immune genes

The major histocompatibility complex (MHC) is a dense region of immune genes with high levels of polymorphism, which are arranged in haplotype blocks. Traditional models of balancing selection (i.e. overdominance and negative frequency dependence) were developed to study the population genetics of single genes. However, the MHC is a multigene family surrounded by linked (non-neutral) polymorphisms, and not all of its features are well explained by these models. For example, (i) the high levels of polymorphism in small populations, (ii) the unexpectedly large genetic differentiation between populations, (iii) the shape of the allelic genealogy associated with trans-species evolution, and (iv) the close associations between particular MHC (human leucocyte antigen, HLA) haplotypes and the approximately 100 pathologies in humans. Here, I propose a new model of MHC evolution named Associative Balancing Complex evolution that can explain these phenomena. The model proposes that recessive deleterious mutations accumulate as a 'sheltered load' nearby MHC genes. These mutations can accumulate because (i) they are rarely expressed as homozygotes given the high MHC gene diversity and (ii) purifying selection is inefficient with low recombination rates (cf. Muller's ratchet). Once fixed, these mutations add to balancing selection and further reinforce linkage through epistatic selection against recombinants.

Modeling multiallelic selection using a Moran model

We present a Moran-model approach to modeling general multiallelic selection in a finite population and show how it may be used to develop theoretical models of biological systems of balancing selection such as plant gametophytic self-incompatibility loci. We propose new expressions for the stationary distribution of allele frequencies under selection and use them to show that the continuous-time Markov chain describing allele frequency change with exchangeable selection and Moran-model reproduction is reversible. We then use the reversibility property to derive the expected allele frequency spectrum in a finite population for several general models of multiallelic selection. Using simulations, we show that our approach is valid over a broader range of parameters than previous analyses of balancing selection based on diffusion approximations to the Wright-Fisher model of reproduction. Our results can be applied to any model of multiallelic selection in which fitness is solely a function of allele frequency.

Antagonism between local dispersal and self-incompatibility systems in a continuous plant population

Many self-incompatible plant species exist in continuous populations in which individuals disperse locally. Local dispersal of pollen and seeds facilitates inbreeding because pollen pools are likely to contain relatives. Self-incompatibility promotes outbreeding because relatives are likely to carry incompatible alleles. Therefore, populations can experience an antagonism between these forces. In this study, a novel computational model is used to explore the effects of this antagonism on gene flow, allelic diversity, neighbourhood sizes, and identity by descent. I confirm that this antagonism is sensitive to dispersal levels and linkage. However, the results suggest that there is little to no difference between the effects of gametophytic and sporophytic self-incompatibility systems (GSI and SSI) on unlinked loci. More importantly, both GSI and SSI affect unlinked loci in a manner similar to obligate outcrossing without mating types. This suggests that the primary evolutionary impact of self-incompatibility systems may be to prevent selfing, and prevention of biparental inbreeding might be a beneficial side-effect.

Ancient trans-specific polymorphism at pheromone receptor genes in basidiomycetes

In the majority of sexual organisms, reproduction occurs almost exclusively through the combination of distinct and alternate forms, called sexes or mating types. In some fungi, there can be dozens to hundreds of alternate alleles that determine compatible mating types. Such extensive polymorphism is expected to be maintained by balancing selection, and in extreme cases may give rise to trans-specific polymorphism. Here, we analyzed sequences of two pheromone receptors in the Microbotryum fungal species complex (Basidiomycota), which has only two alternate mating types. Several lines of evidence strongly suggest that the pheromone receptors are two allelic sequences acting to determine the alternate A1 and A2 mating types required for mating in Microbotryum. Phylogenetic trees of pheromone receptors in the Microbotryum species complex indicated a trans-specific polymorphism: the Microbotryum sequences from a given mating type were all more similar to the pheromone receptors of distantly related classes of fungi than to the alternate pheromone receptor in the Microbotryum species. A phylogenetic tree built using other known pheromone receptors from basidiomycetes showed that trans-specific polymorphism is widespread. The pheromone receptor alleles from Microbotryum appeared as the oldest, being at least 370 million years old. This represents the oldest known trans-specific polymorphism known in any organism so far, which may be due to the existence of sex chromosomes, obligate sexuality, mitochondrial inheritance linked to the mating type, and a highly selfing mating system in Microbotryum.

Ecological and evolutionary genomics in the wild tomatoes (Solanum sect. Lycopersicon)

The plant group Solanum section Lycopersicon (the clade containing the domesticated tomato and its wild relatives) is ideal for integrating genomic tools and approaches into ecological and evolutionary research. Wild species within Lycopersicon span broad morphological, physiological, life history, mating system, and biochemical variation, and are separated by substantial, but incomplete postmating reproductive barriers, making this an ideal system for genetic analyses of these traits. This ecological and evolutionary diversity is matched by many logistical advantages, including extensive historical occurrence records for all species in the group, publicly available germplasm for hundreds of known wild accessions, demonstrated experimental tractability, and extensive genetic, genomic, and functional tools and information from the tomato research community. Here I introduce the numerous advantages of this system for Ecological and Evolutionary Functional Genomics (EEFG), and outline several ecological and evolutionary phenotypes and questions that can be fruitfully tackled in this system. These include biotic and abiotic adaptation, reproductive trait evolution, and the genetic basis of speciation. With the modest enhancement of some research strengths, this system is poised to join the best of our currently available model EEFG systems.

Unequal segregation of SRK alleles at the S locus in Brassica cretica

In the Brassicaceae plant family, which includes the Arabidopsis and Brassica genera, self-incompatibility (SI) is controlled by genes at the S locus. Using experimental crosses, we studied the pattern of inheritance of S-locus alleles in the wild species Brassica cretica. Four full-sib families were established and unequal segregation of alleles at the SRK SI gene was found in one family. The segregation distortion acted in favour of a recessive (class II) allele and was best explained by some form of gametic-level selection. Our findings are discussed in the light of theoretical predictions of differential accumulation of deleterious mutations among S-locus alleles.

Genomic consequences of selection on self-incompatibility genes

Frequency-dependent selection at plant self-incompatibility systems is inherent and well understood theoretically. A self-incompatibility locus leads to a strong peak of diversity in the genome, to a unique distribution of diversity across the species and possibly to increased introgression between closely related species. We review recent empirical studies demonstrating these features and relate the empirical findings to theoretical predictions. We show how these features are being exploited in searches for other genes under multi-allelic balancing selection and for inference on recent breakdown of self-incompatibility.

Segregation analyses of partial self-incompatibility in self and cross progeny of Solanum carolinense reveal a leaky S-allele

Natural populations of self-incompatible species often exhibit marked phenotypic variation among individuals in the strength of self-incompatibility (SI). In previous studies, we found that the strength of the SI response in Solanum carolinense, a weedy invasive with RNase-mediated SI, is a plastic trait. Selfing can be particularly important for weeds and other successional species that typically undergo repeated colonization and local extinction events and whose population sizes are often small. We applied a PCR-based protocol to identify the S-alleles present in 16 maternal genotypes and their offspring and performed a two-generation greenhouse study to determine whether variation in the strength of SI is due to the existence of weak and strong S-alleles differing in their ability to recognize and reject self-pollen. We found that allele S9 sets significantly more self seed than the other S-alleles in the population we sampled and that its ability to self is not dependent on interactions with other S-alleles. Our data suggest that the observed variations in self-fertility are likely due to factors that directly influence the expression of SI by altering the translation, turnover, or activity of the S-RNase. The variability in the strength of SI among individuals that we have observed in this and our previous studies raises the possibility that plasticity in the strength of SI in S. carolinense may play a role in the colonization and establishment of this weedy species.

Variability patterns and positively selected sites at the gametophytic self-incompatibility pollen SFB gene in a wild self-incompatible Prunus spinosa (Rosaceae) population

Current models for the generation of new gametophytic self-incompatibility specificities require that neutral variability segregates within specificity classes. Furthermore, one of the models predicts greater ratios of nonsynonymous to synonymous substitutions in pollen than in pistil specificity genes. All models assume that new specificities arise by mutation only. To test these models, 21 SFB (the pollen S-locus) alleles from a wild Prunus spinosa (Rosaceae) population were obtained. For seven of these, the corresponding S-haplotype was also characterized. The SFB data set was also used to identify positively selected sites. Those sites are likely to be the ones responsible for defining pollen specificities. Of the 23 sites identified as being positively selected, 21 are located in the variable (including a new region described here) and hypervariable regions. Little variability is found within specificity classes. There is no evidence for selective sweeps being more frequent in pollen than in pistil specificity genes. The S-RNase and the SFB genes have only partially correlated evolutionary histories. None of the models is compatible with the variability patterns found in the SFB and the S-haplotype data.

Historical events and allelic polymorphism at the gametophytic self-incompatibility locus in Solanaceae

The historical migration rate of a species is often difficult to estimate with neutral markers, because the relationship between the turnover time of the markers and the age of the species commonly remains unknown. Compared with neutral markers, the plant self-incompatibility locus (S) provides a much better source of data for migration-rate estimation due to its high allelic polymorphism and antiquity. Here, the results from extensive surveys of S alleles in two wild solanaceous species, Solanum carolinense and Physalis longifolia, indicate that historical migration rates have differed significantly between the species; the higher migration rate found in S. carolinense appears to have interacted with the balancing selection at the S locus to result in fewer S alleles being maintained in the species. Historical population growth rates estimated via a modified coalescent approach also suggest a faster growing population for S. carolinense than for P. longifolia, which would have further widened their interspecific difference in S-allelle polymorphism. These historical factors may have reduced the probability of new S alleles to prevailing in S. carolinense, leaving old ones segregating at the S locus with little signature of positive selection being currently detectable.

The evolutionary dynamics of self-incompatibility systems

Self-incompatible flowering plants reject pollen that expresses the same mating specificity as the pistil (female reproductive tract). In most plant families, pollen and pistil mating specificities segregate as a single locus, the S locus. In at least two self-incompatibility systems, distinct pollen and pistil specificity genes are embedded in an extensive nonrecombining tract. To facilitate consideration of how new S locus specificities arise in systems with distinct pollen and pistil genes, we present a graphical model for the generation of hypotheses. It incorporates the evolutionary principle that nonreciprocal siring success (cross-pollinations between two plants produce seeds in only one direction) tends to favor the rejecting partner. This model suggests that selection within S-allele specificity classes could accelerate the rate of nonsynonymous (amino acid-changing) substitutions, with periodic selective sweeps removing segregating variation within classes. Accelerated substitution within specificity classes could also promote the origin of new S-allele specificities.

Rapid recent radiation of S-RNase lineages in Witheringia solanacea (Solanaceae)

Strong frequency-dependent selection as found in the self-incompatibility loci of flowering plants maintains allelic lineages for extremely long time scales, such that allelic genealogies can shed insight into long-term demographic patterns of species. Effective mutation rate, as well as demographic change such as population bottlenecks, can influence genealogical structure. In addition, loss of functionality at the self-incompatibility locus is likely to affect radiation rates. Partial sequences for 21 S-RNase alleles of the mid-elevation tropical species Witheringia solanacea were obtained in order to compare their substitution rates and genealogy with those of Witheringia maculata and two species in the closely related genus Physalis. Sequences for W. solanacea fell into the three clades within the Solanaceae already identified for the genus. Terminal branch lengths for W. solanacea, scaled to the total depth of its phylogeny, were intermediate between the unusually short terminal branches of W. maculata and those of the two Physalis species. In contrast to the Physalis species, where interspecific dN/dS for closely related alleles exceeded 1.0 to the same degree as did intraspecific dN/dS, in Witheringia only intraspecific comparisons showed an excess of nonsynonymous substitutions, suggesting postspeciation radiation of alleles. Alleles associated with lowered S-RNase production and self-compatibility showed extremely short terminal branches. In summary, it appears that rapid recent diversification of alleles characterizes the Witheringia lineages. In some cases, this rapid diversification can be attributed to relaxed constraints due to breakdown of self-incompatibility.

Maximum-likelihood estimation of rates of recombination within mating-type regions

Features common to many mating-type regions include recombination suppression over large genomic tracts and cosegregation of genes of various functions, not necessarily related to reproduction. Model systems for homomorphic self-incompatibility (SI) in flowering plants share these characteristics. We introduce a method for the exact computation of the joint probability of numbers of neutral mutations segregating at the determinant of mating type and at a linked marker locus. The underlying Markov model incorporates strong balancing selection into a two-locus coalescent. We apply the method to obtain a maximum-likelihood estimate of the rate of recombination between a marker locus, 48A, and S-RNase, the determinant of SI specificity in pistils of Nicotiana alata. Even though the sampled haplotypes show complete allelic linkage disequilibrium and recombinants have never been detected, a highly significant deficiency of synonymous substitutions at 48A compared to S-RNase suggests a history of recombination. Our maximum-likelihood estimate indicates a rate of recombination of perhaps 3 orders of magnitude greater than the rate of synonymous mutation. This approach may facilitate the construction of genetic maps of regions tightly linked to targets of strong balancing selection.

Evolution under tight linkage to mating type

Recent large-scale sequencing studies of mating type loci in a number of organisms offer insight into the origin and evolution of these genomic regions. Extensive tracts containing genes with a wide diversity of functions typically cosegregate with mating type. Cases in which mating type determination entails complementarity between distinct transcription units may descend from systems in which close physical linkage facilitated the coordinated expression and cosegregation of the interacting genes. In response to the particular selection pressures associated with the maintenance of more than one mating type, this nucleus of low recombination may expand over evolutionary time, engulfing neighboring tracts bearing genes with no direct role in reproduction. This scenario is consistent with the present-day structure of some mating type loci, including regulators of homomorphic self-incompatibility in angiosperms (S-loci). Recombination suppression and enforced S-locus heterozygosity accelerate the accumulation of genetic load and promote genetic associations between S-alleles and degenerating genes in cosegregating tracts. This S-allele-specific load may influence the evolution of self-incompatibility systems.

Plant self-incompatibility in natural populations: a critical assessment of recent theoretical and empirical advances

Self-incompatibility systems in plants are genetic systems that prevent self-fertilization in hermaphrodites through recognition and rejection of pollen expressing the same allelic specificity as that expressed in the pistils. The evolutionary properties of these self-recognition systems have been revealed through a fascinating interplay between empirical advances and theoretical developments. In 1939, Wright suggested that the main evolutionary force driving the genetic and molecular properties of these systems was strong negative frequency-dependent selection acting on pollination success. The empirical observation of high allelic diversity at the self-incompatibility locus in several species, followed by the discovery of very high molecular divergence among alleles in all plant families where the locus has been identified, supported Wright's initial theoretical predictions as well as many of its later developments. In the last decade, however, advances in the molecular characterization of the incompatibility reaction and in the analysis of allelic frequencies and allelic divergence from natural populations have stimulated new theoretical investigations that challenged some important assumptions of Wright's model of gametophytic self-incompatibility. We here review some of these recent empirical and theoretical advances that investigated: (i) the hypothesis that S-alleles are selectively equivalent, and the evolutionary consequences of genetic interactions between alleles; (ii) the occurrence of frequency-dependent selection in female fertility; (iii) the evolutionary genetics of self-incompatibility systems in subdivided populations; (iv) the evolutionary implications of the self-incompatibility locus's genetic architecture; and (v) of its interactions with the genomic environment.

Uneven segregation of sporophytic self-incompatibility alleles in Arabidopsis lyrata

Self-incompatibility in Arabidopsis lyrata is sporophytically controlled by the multi-allelic S-locus. Self-incompatibility alleles (S-alleles) are under strong negative frequency dependent selection because pollen carrying common S-alleles have fewer mating opportunities. Population genetics theory predicts that deleterious alleles can accumulate if linked to the S-locus. This was tested by studying segregation of S-alleles in 11 large full sib families in A. lyrata. Significant segregation distortion leading to an up to fourfold difference in transmission rates was found in six families. Differences in transmission rates were not significantly different in reciprocal crosses and the distortions observed were compatible with selection acting at the gametic stage alone. The S-allele with the largest segregation advantage is also the most recessive, and is very common in natural populations concordant with its apparent segregation advantage. These results imply that frequencies of S-alleles in populations of A. lyrata cannot be predicted based on simple models of frequency-dependent selection alone.

A simple method for computing exact probabilities of mutation numbers

We describe a method for the recursive computation of exact probability distributions for the number of neutral mutations segregating in samples of arbitrary size and configuration. Construction of the recursions requires only characterization of evolutionary changes as a Markov process and determination of one-step transition matrices. We address the pattern of nucleotide diversity at a neutral marker locus linked to a determinant of mating type. Under a reformulation of parameters, the method also applies directly to metapopulation models with island migration among demes. Characterization of complete probability distributions facilitates parameter estimation and hypothesis testing by likelihood- as well as moment-based approaches.

Sheltered load associated with S-alleles in Solanum carolinense

Bud pollinations allowed me to examine the effects of homozygosity at loci in the area of suppressed recombination around the S-locus in Solanum carolinense, whose S-alleles show surprisingly low diversification rates. The total number of seeds produced was lower for incompatible than compatible pollinations, revealing that self-incompatibility was only somewhat overcome by bud pollination. However, low seed set in incompatible crosses was not due solely to the incompatibility response; crosses between distinct plants sharing the same alleles at the S-locus led to dramatically high seed abortion, nearly equal to that found upon selfing. An excess of heterozygotes in the surviving progeny supports the supposition that these high abortion rates are due to sheltered load, that is, previously unexpressed load accumulated due to enforced heterozygosity and recombination suppression around the S-locus. Of the seven alleles examined in total, two showed evidence of severe load and five did not. The magnitude of load was consistent with terminal branch length in some, but not all, cases.