Sheltered load associated with S-alleles in Solanum carolinense

Genetic load: genomic estimates and applications in non-model animals

Genetic variation, which is generated by mutation, recombination and gene flow, can reduce the mean fitness of a population, both now and in the future. This 'genetic load' has been estimated in a wide range of animal taxa using various approaches. Advances in genome sequencing and computational techniques now enable us to estimate the genetic load in populations and individuals without direct fitness estimates. Here, we review the classic and contemporary literature of genetic load. We describe approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations. We show that splitting the load into its two components - the realized load (or expressed load) and the masked load (or inbreeding load) - can improve our understanding of the population genetics of deleterious mutations.

Whole-genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self-incompatibility

Whole‐genome sequencing of non‐model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are of high biological interest remain problematic for assembly and data‐handling. Three such regions are the major histocompatibility complex (MHC), sex‐determining regions (SDRs) and the plant self‐incompatibility locus (S‐locus). Using these as examples, we illustrate the challenges of both assembling and resequencing these highly polymorphic regions and how bioinformatic and technological developments are enabling new approaches to their study. Mapping short‐read sequences against multiple alternative references improves genotyping comprehensiveness at the S‐locus thereby contributing to more accurate assessments of allelic frequencies. Long‐read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S‐locus haplotypes. These advances are adding value to short‐read genome resequencing approaches by allowing, for example, more accurate haplotype phasing across longer regions. Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches.

Inbreeding depression is difficult to purge in self-incompatible populations of Leavenworthia alabamica

The extent to which inbreeding depression can be purged is a major determinant of mating system evolution and is important to conservation and crop improvement. Studies of inbreeding depression purging have not been conducted in self-incompatible plants before. An experimental ('ancestral') treatment was first created from self-incompatible plants of Leavenworthia alabamica. Lines derived from this population were maintained by self-pollination for three generations in the attempt to create a 'purged' population with fewer recessive, deleterious mutations of large effect. Fitness components and the frequency of malformed phenotypes were monitored in progeny derived from selfing and outcrossing in the ancestral and purged treatments. Fitness component means and inbreeding depression were largely unchanged by three generations of forced self-pollination, and there was no reduction in the frequency of plants exhibiting malformed phenotypes. Our findings indicate that inbreeding depression in this species is largely a result of mutations of mild effect, consistent with the observation that self-incompatibility is maintained in most populations of L. alabamica, despite the presence of genetic variants with weaker self-incompatibility. Moreover, although population theory suggests that deleterious mutations of large effect should be sheltered from selection in the region of self-incompatibility locus, our results do not support this prediction.

Genetics of distyly and homostyly in a self-compatible Primula

The transition from outcrossing to selfing through the breakdown of distyly to homostyly has occurred repeatedly among families of flowering plants. Homostyles can originate by major gene changes at the S-locus linkage group, or by unlinked polygenic modifiers. Here, we investigate the inheritance of distyly and homostyly in Primula oreodoxa, a subalpine herb endemic to Sichuan, China. Controlled self- and cross-pollinations confirmed that P. oreodoxa unlike most heterostylous species is fully self-compatible. Segregation patterns indicated that the inheritance of distyly is governed by a single Mendelian locus with the short-styled morph carrying at least one dominant S-allele (S-) and long-styled plants homozygous recessive (ss). Crossing data were consistent with a model in which homostyly results from genetic changes at the distylous linkage group, with the homostylous allele (S^h) dominant to the long-styled allele (s), but recessive to the short-styled allele (S). Progeny tests of open-pollinated seed families revealed high rates of intermorph mating in the L-morph but considerable selfing and possibly intramorph mating in the S-morph and in homostyles. S-morph plants homozygous at the S-locus (SS) occurred in several populations but may experience viability selection. The crossing data from distylous and homostylous plants are consistent with either recombination at the S-locus governing distyly, or mutation at gene(s) controlling sex-organ height; both models predict the same patterns of segregation. Recent studies on the molecular genetics of distyly in Primula demonstrating the hemizygous nature of genes at the S-locus make it more likely that homostyles have resulted from mutation rather than recombination.

Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection

Deleterious mutations are expected to evolve under negative selection and are usually purged from the population. However, deleterious alleles segregate in the human population and some disease-associated variants are maintained at considerable frequencies. Here, we test the hypothesis that balancing selection may counteract purifying selection in neighboring regions and thus maintain deleterious variants at higher frequency than expected from their detrimental fitness effect. We first show in realistic simulations that balancing selection reduces the density of polymorphic sites surrounding a locus under balancing selection, but at the same time markedly increases the population frequency of the remaining variants, including even substantially deleterious alleles. To test the predictions of our simulations empirically, we then use whole-exome sequencing data from 6,500 human individuals and focus on the most established example for balancing selection in the human genome, the major histocompatibility complex (MHC). Our analysis shows an elevated frequency of putatively deleterious coding variants in nonhuman leukocyte antigen (non-HLA) genes localized in the MHC region. The mean frequency of these variants declined with physical distance from the classical HLA genes, indicating dependency on genetic linkage. These results reveal an indirect cost of the genetic diversity maintained by balancing selection, which has hitherto been perceived as mostly advantageous, and have implications both for the evolution of recombination and also for the epidemiology of various MHC-associated diseases.

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.

Centromere-associated meiotic drive and female fitness variation in Mimulus

Female meiotic drive, in which chromosomal variants preferentially segregate to the egg pole during asymmetric female meiosis, is a theoretically pervasive but still mysterious form of selfish evolution. Like other selfish genetic elements, driving chromosomes may be maintained as balanced polymorphisms by pleiotropic or linked fitness costs. A centromere-associated driver (D) with a ∼58:42 female-specific transmission advantage occurs at intermediate frequency (32-40%) in the Iron Mountain population of the yellow monkeyflower, Mimulus guttatus. Previously determined male fertility costs are sufficient to prevent the fixation of D, but predict a higher equilibrium frequency. To better understand the dynamics and effects of D, we developed a new population genetic model and measured genotype-specific lifetime female fitness in the wild. In three of four years, and across all years, D imposed significant recessive seedset costs, most likely due to hitchhiking by deleterious mutations. With both male and female costs as measured, and 58:42 drive, our model predicts an equilibrium frequency of D (38%) very close to the observed value. Thus, D represents a rare selfish genetic element whose local population genetic dynamics have been fully parameterized, and the observation of equilibrium sets the stage for investigations of coevolution with suppressors.

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.

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.

Evolutionary genetics of an S-like polymorphism in Papaveraceae with putative function in self-incompatibility

BACKGROUND

Papaver rhoeas possesses a gametophytic self-incompatibility (SI) system not homologous to any other SI mechanism characterized at the molecular level. Four previously published full length stigmatic S-alleles from the genus Papaver exhibited remarkable sequence divergence, but these studies failed to amplify additional S-alleles despite crossing evidence for more than 60 S-alleles in Papaver rhoeas alone.

METHODOLOGY/PRINCIPAL FINDINGS

Using RT-PCR we identified 87 unique putative stigmatic S-allele sequences from the Papaveraceae Argemone munita, Papaver mcconnellii, P. nudicuale, Platystemon californicus and Romneya coulteri. Hand pollinations among two full-sib families of both A. munita and P. californicus indicate a strong correlation between the putative S-genotype and observed incompatibility phenotype. However, we also found more than two S-like sequences in some individuals of A. munita and P. californicus, with two products co-segregating in both full-sib families of P. californicus. Pairwise sequence divergence estimates within and among taxa show Papaver stigmatic S-alleles to be the most variable with lower divergence among putative S-alleles from other Papaveraceae. Genealogical analysis indicates little shared ancestral polymorphism among S-like sequences from different genera. Lack of shared ancestral polymorphism could be due to long divergence times among genera studied, reduced levels of balancing selection if some or all S-like sequences do not function in incompatibility, population bottlenecks, or different levels of recombination among taxa. Preliminary estimates of positive selection find many sites under selective constraint with a few undergoing positive selection, suggesting that self-recognition may depend on amino acid substitutions at only a few sites.

CONCLUSIONS/SIGNIFICANCE

Because of the strong correlation between genotype and SI phenotype, sequences reported here represent either functional stylar S-alleles, tightly linked paralogs of the S-locus or a combination of both. The considerable complexity revealed in this study shows we have much to learn about the evolutionary dynamics of self-incompatibility systems.

A novel sperm-delivered toxin causes late-stage embryo lethality and transmission ratio distortion in C. elegans

The evolutionary fate of an allele ordinarily depends on its contribution to host fitness. Occasionally, however, genetic elements arise that are able to gain a transmission advantage while simultaneously imposing a fitness cost on their hosts. We previously discovered one such element in C. elegans that gains a transmission advantage through a combination of paternal-effect killing and zygotic self-rescue. Here we demonstrate that this element is composed of a sperm-delivered toxin, peel-1, and an embryo-expressed antidote, zeel-1. peel-1 and zeel-1 are located adjacent to one another in the genome and co-occur in an insertion/deletion polymorphism. peel-1 encodes a novel four-pass transmembrane protein that is expressed in sperm and delivered to the embryo via specialized, sperm-specific vesicles. In the absence of zeel-1, sperm-delivered PEEL-1 causes lethal defects in muscle and epidermal tissue at the 2-fold stage of embryogenesis. zeel-1 is expressed transiently in the embryo and encodes a novel six-pass transmembrane domain fused to a domain with sequence similarity to zyg-11, a substrate-recognition subunit of an E3 ubiquitin ligase. zeel-1 appears to have arisen recently, during an expansion of the zyg-11 family, and the transmembrane domain of zeel-1 is required and partially sufficient for antidote activity. Although PEEL-1 and ZEEL-1 normally function in embryos, these proteins can act at other stages as well. When expressed ectopically in adults, PEEL-1 kills a variety of cell types, and ectopic expression of ZEEL-1 rescues these effects. Our results demonstrate that the tight physical linkage between two novel transmembrane proteins has facilitated their co-evolution into an element capable of promoting its own transmission to the detriment of organisms carrying it.

Origin and diversification dynamics of self-incompatibility haplotypes

Self-incompatibility (SI) is a genetic system found in some hermaphrodite plants. Recognition of pollen by pistils expressing cognate specificities at two linked genes leads to rejection of self pollen and pollen from close relatives, i.e., to avoidance of self-fertilization and inbred matings, and thus increased outcrossing. These genes generally have many alleles, yet the conditions allowing the evolution of new alleles remain mysterious. Evolutionary changes are clearly necessary in both genes, since any mutation affecting only one of them would result in a nonfunctional self-compatible haplotype. Here, we study diversification at the S-locus (i.e., a stable increase in the total number of SI haplotypes in the population, through the incorporation of new SI haplotypes), both deterministically (by investigating analytically the fate of mutations in an infinite population) and by simulations of finite populations. We show that the conditions allowing diversification are far less stringent in finite populations with recurrent mutations of the pollen and pistil genes, suggesting that diversification is possible in a panmictic population. We find that new SI haplotypes emerge fastest in populations with few SI haplotypes, and we discuss some implications for empirical data on S-alleles. However, allele numbers in our simulations never reach values as high as observed in plants whose SI systems have been studied, and we suggest extensions of our models that may reconcile the theory and data.

Sporophytic self-incompatibility in Senecio squalidus (Asteraceae): S allele dominance interactions and modifiers of cross-compatibility and selfing rates

Understanding genetic mechanisms of self-incompatibility (SI) and how they evolve is central to understanding the mating behaviour of most outbreeding angiosperms. Sporophytic SI (SSI) is controlled by a single multi-allelic locus, S, which is expressed in the diploid (sporophyte) plant to determine the SI phenotype of its haploid (gametophyte) pollen. This allows complex patterns of independent S allele dominance interactions in male (pollen) and female (pistil) reproductive tissues. Senecio squalidus is a useful model for studying the genetic regulation and evolution of SSI because of its population history as an alien invasive species in the UK. S. squalidus maintains a small number of S alleles (7-11) with a high frequency of dominance interactions. Some S. squalidus individuals also show partial selfing and/or greater levels of cross-compatibility than expected under SSI. We previously speculated that these might be adaptations to invasiveness. Here we describe a detailed characterization of the regulation of SSI in S. squalidus. Controlled crosses were used to determine the S allele dominance hierarchy of six S alleles and effects of modifiers on cross-compatibility and partial selfing. Complex dominance interactions among S alleles were found with at least three levels of dominance and tissue-specific codominance. Evidence for S gene modifiers that increase selfing and/or cross-compatibility was also found. These empirical findings are discussed in the context of theoretical predictions for maintenance of S allele dominance interactions, and the role of modifier loci in the evolution of SI.

Trans-species polymorphism, HLA-disease associations and the evolution of the MHC

Currently, the paradigm is that major histocompatibility complex (MHC) polymorphism is maintained by balancing selection on the immune genes. However, other evolutionary forces besides selection also play a role in the population genetics of this multigene family. van Oosterhout proposed a new theory of MHC evolution called associative balancing complex (ABC) evolution.1 This theory incorporates the effects of the evolutionary forces in the entire MHC region (peri-MHC), and it proposes that recessive deleterious mutations can accumulate in the peri-MHC in a process similar to Muller's ratchet.2 These mutations are not easily purged because epistasis and high gene diversity in the MHC reduce the efficacy of natural selection. Because natural selection is less efficient, it could also make the MHC prone to the onslaught of genomic parasites such as retroviruses and transposable elements (TEs). The accumulated genetic load has important consequences for the evolution of this immune gene family, and it can reinforce linkage disequilibria and help to maintain the MHC polymorphism. ABC evolution offers new insights into some of the most puzzling aspects of the MHC, including the occurrence of identical MHC sequences in diverged species (i.e., trans-species polymorphism). It may also explain why the large numbers of disease-associated mutations are not removed by natural selection, and why the genes that protect vertebrates against infectious diseases are associated to such a wide variety of genetic disorders.

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.

The effect of sheltered load on reproduction in Solanum carolinense, a species with variable self-incompatibility

In previous studies, we have investigated the strength of self-incompatibility (SI) in Solanum carolinense, a highly successful weed with a fully functional SI system that inhabits early successional and other disturbed habitats. We have found that the SI response in S. carolinense is a plastic trait-its strength being affected by the age of the flowers, and the presence of developing fruits and that there are genetic differences among families in their self-fertility. However, in species with a fully functional SI response, selfing would not be that common. As a result, deleterious recessives scattered though the genome of horsenettle are only occasionally exposed to selection. It has been suggested that deleterious recessives accumulate near S-alleles in strong SI species because the S-locus is located in a non-recombining region of the genome and because strong S-alleles are never in the homozygous state, thus sheltering some of the genetic load near the S-locus from selection. We performed a series of laboratory and greenhouse experiments to determine the extent to which sheltered load adds to the overall magnitude of inbreeding depression in horsenettle. Specifically, we amplified and sequenced the S-alleles from 16 genets collected from a large population in Pennsylvania and performed a series of controlled self-pollinations. We then grew the selfed progeny in the greenhouse; recorded various measures of growth and reproductive output; and amplified and sequenced their S-allele(s). We found that the heterozygous progeny of self-pollinations produce more flowers and have a greater ability to set both self and cross seed than S-homozygous progeny. We also found evidence of variation in the magnitude of load among S-alleles. These results suggest that sheltered load might slow the fixation of weak (partially compatible) S-alleles in this population, thus adding to the maintenance of a mixed mating system rather than leading to the fixation of the selfing alleles.

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.

A tale of two continents: Baker's rule and the maintenance of self-incompatibility in Lycium (Solanaceae)

Over 50 years ago, Baker (1955, 1967) suggested that self-compatible species were more likely than self-incompatible species to establish new populations on oceanic islands. His logic was straightforward and rested on the assumption that colonization was infrequent; thus, mate limitation favored the establishment of self-fertilizing individuals. In support of Baker's rule, many authors have documented high frequencies of self-compatibility on islands, and recent work has solidified the generality of Baker's ideas. The genus Lycium (Solanaceae) has ca. 80 species distributed worldwide, and phylogenetic studies suggest that Lycium originated in South America and dispersed to the Old World a single time. Previous analyses of the S-RNase gene, which controls the stylar component of self-incompatibility, have shown that gametophytically controlled self-incompatibility is ancestral within the genus, making Lycium a good model for investigating Baker's assertions concerning reproductive assurance following oceanic dispersal. Lycium is also useful for investigations of reproductive evolution, given that species vary both in sexual expression and the presence of self-incompatibility. A model for the evolution of gender dimorphism suggests that polyploidy breaks down self-incompatibility, leading to the evolution of gender dimorphism, which arises as an alternative outcrossing mechanism. There is a perfect association of dimorphic gender expression, polyploidy, and self-compatibility (vs. cosexuality, diploidy, and self-incompatibility) among North American Lycium. Although the association between ploidy level and gender expression also holds for African Lycium, to date no studies of mating systems have been initiated in Old World species. Here, using controlled pollinations, we document strong self-incompatibility in two cosexual, diploid species of African Lycium. Further, we sequence the S-RNase gene in 15 individuals from five cosexual, diploid species of African Lycium and recover 24 putative alleles. Genealogical analyses indicate reduced trans-generic diversity of S-RNases in the Old World compared to the New World. We suggest that genetic diversity at this locus was reduced as a result of a founder event, but, despite the bottleneck, self-incompatibility was maintained in the Old World. Maximum-likelihood analyses of codon substitution patterns indicate that positive Darwinian selection has been relatively strong in the Old World, suggesting the rediversification of S-RNases following a bottleneck. The present data thus provide a dramatic exception to Baker's rule, in addition to supporting a key assumption of the Miller and Venable (2000) model, namely that self-incompatibility is associated with diploidy and cosexuality.

Hitch-hiking to a locus under balancing selection: high sequence diversity and low population subdivision at the S-locus genomic region inArabidopsis halleri

Hitch-hiking to a site under balancing selection is expected to produce a local increase in nucleotide polymorphism and a decrease in population differentiation compared with the background genomic level, but empirical evidence supporting these predictions is scarce. We surveyed molecular diversity at four genes flanking the region controlling self-incompatibility (the S-locus) in samples from six populations of the herbaceous plantArabidopsis halleri, and compared their polymorphism with sequences from five control genes unlinked to the S-locus. As a preliminary verification, the S-locus flanking genes were shown to co-segregate withSRK, the gene involved in the self-incompatibility reaction at the pistil level. In agreement with theory, our results demonstrated a significant peak of nucleotide diversity around the S-locus as well as a significant decrease in population genetic structure in the S-locus region compared with both control genes and a set of seven unlinked microsatellite markers. This is consistent with the theoretical expectation that balancing selection is increasing the effective migration rate in subdivided populations. Although only four S-locus flanking genes were investigated, our results suggest that these two signatures of the hitch-hiking effect are localized in a very narrow genomic region.

Effects of recombination on hitchhiking diversity in the Brassica self-incompatibility locus complex

In self-incompatibility, a number of S haplotypes are maintained by frequency-dependent selection, which results in trans-specific S haplotypes. The region of several kilobases (approximately 40-60 kb) from SP6 to SP2, including self-incompatibility-related genes and some adjacent genes in Brassica rapa, has high nucleotide diversity due to the hitchhiking effect, and therefore we call this region the "S-locus complex." Recombination in the S-locus complex is considered to be suppressed. We sequenced regions of >50 kb of the S-locus complex of three S haplotypes in B. rapa and found higher nucleotide diversity in intergenic regions than in coding regions. Two highly similar regions of >10 kb were found between BrS-8 and BrS-46. Phylogenetic analysis using trans-specific S haplotypes (called interspecific pairs) of B. rapa and B. oleracea suggested that recombination reduced the nucleotide diversity in these two regions and that the genes not involved in self-incompatibility in the S-locus complex and the kinase domain, but not the S domain, of SRK have also experienced recombination. Recombination may reduce hitchhiking diversity in the S-locus complex, whereas the region from the S domain to SP11 would disfavor recombination.

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.

Correlated evolution of self-incompatibility and clonal reproduction in Solanum (Solanaceae)

It has been suggested that clonality provides reproductive assurance in cross-fertilizing species subject to pollen limitation, relieving one of the main selective pressures favoring the evolution of self-fertilization. According to this hypothesis, cross-fertilizing species subject to pollen limitation should often be clonal. Here, we investigated the association between clonality and a genetic mechanism enforcing outcrossing, self-incompatibility, in Solanum (Solanaceae). We collected self-incompatibility and clonality information on 87 species, and looked for an association between these two traits. To account for the contribution of shared evolutionary history to this association, we incorporated phylogenetic information from chloroplast (NADH dehydrogenase subunit F) sequence data. We found that self-incompatibility is strongly associated with clonal reproduction: all self-incompatible species reproduce clonally, while the absence of clonality is widespread among self-compatible taxa. The observed correlation persists after taking into account shared phylogenetic history, assumptions about the evolutionary history of self-incompatibility, uncertainty associated with phylogeny estimation, and associations with life history (annual/perennial). Our results are consistent with the hypothesis that clonality provides reproductive assurance, and suggest that the consequences of clonal growth in the evolution of plant reproductive strategies may be more significant than previously thought.

Comparative analysis of the within-population genetic structure in wild cherry (Prunus avium L.) at the self-incompatibility locus and nuclear microsatellites

Gametophytic self-incompatibility (SI) systems in plants exhibit high polymorphism at the SI controlling S-locus because individuals with rare alleles have a higher probability to successfully pollinate other plants than individuals with more frequent alleles. This process, referred to as frequency-dependent selection, is expected to shape number, frequency distribution, and spatial distribution of self-incompatibility alleles in natural populations. We investigated the genetic diversity and the spatial genetic structure within a Prunus avium population at two contrasting gene loci: nuclear microsatellites and the S-locus. The S-locus revealed a higher diversity (15 alleles) than the eight microsatellites (4-12 alleles). Although the frequency distribution of S-alleles differed significantly from the expected equal distribution, the S-locus showed a higher evenness than the microsatellites (Shannon's evenness index for the S-locus: E = 0.91; for the microsatellites: E = 0.48-0.83). Also, highly significant deviations from neutrality were found for the S-locus whereas only minor deviations were found for two of eight microsatellites. A comparison of the frequency distribution of S-alleles in three age-cohorts revealed no significant differences, suggesting that different levels of selection acting on the S-locus or on S-linked sites might also affect the distribution and dynamics of S-alleles. Autocorrelation analysis revealed a weak but significant spatial genetic structure for the multilocus average of the microsatellites and for the S-locus, but could not ascertain differences in the extent of spatial genetic structure between these locus types. An indirect estimate of gene dispersal, which was obtained to explain this spatial genetic pattern, indicated high levels of gene dispersal within our population (sigma(g) = 106 m). This high gene dispersal, which may be partly due to the self-incompatibility system itself, aids the effective gene flow of the microsatellites, thereby decreasing the contrast between the neutral microsatellites and the S-locus.

Modes and rates of selfing and associated inbreeding depression in the self-incompatible plant Senecio squalidus (Asteraceae): a successful colonizing species in the British Isles

The strength of the self-incompatibility (SI) response in Senecio squalidus was measured across its British range. Geographic variation in SI was investigated and the extent and inheritance of pseudo-self-compatibility (PSC) and inbreeding depression were determined. Mean self-fruit-set per capitulum was calculated for individuals and sample populations. The heritability of PSC and the magnitude of inbreeding depression were assessed by comparing selfing rates and fitness trait values between SI and PSC parent-progeny lines. SI was found to be strongly expressed in S. squalidus throughout its British range, with only 3.1% of the individuals sampled showing PSC. This PSC had relatively low heritability with stronger expression of SI in selfed progeny relative to PSC parents. Inbreeding depression was shown to be great in S. squalidus, with mean life history stage values ranging from 0.18 to 0.25. The strength of SI in S. squalidus appears not to have weakened in response to its rapid colonization of Britain. The avoidance of inbreeding depression is likely to be the primary factor maintaining strong SI in this successful colonizing species.

Contributions of domesticated plant studies to our understanding of plant evolution

BACKGROUND

Plant evolutionary theory has been greatly enriched by studies on crop species. Over the last century, important information has been generated on many aspects of population biology, speciation and polyploid genetics.

SCOPE

Searches for quantitative trait loci (QTL) in crop species have uncovered numerous blocks of genes that have dramatic effects on adaptation, particularly during the domestication process. Many of these QTL have epistatic and pleiotropic effects making rapid evolutionary change possible. Most of the pioneering work on the molecular basis of self-incompatibility has been conducted on crop species, along with the sequencing of the phytopathogenic resistance genes (R genes) responsible for the 'gene-to-gene' relations of coevolution observed in host-pathogen relationships. Some of the better examples of co-adaptation and early acting inbreeding depression have also been elucidated in crops. Crop-wild progenitor interactions have provided rich opportunities to study the evolution of novel adaptations subsequent to hybridization. Most crop/wild F1 hybrids have reduced fitness, but in some instances the crop relatives have acquired genes that make them more efficient weeds through crop mimicry. Studies on autopolyploid alfalfa and potato have uncovered the means by which polyploid gametes are formed and have led to hypotheses about how multiallelic interactions are associated with fitness and self-fertility. Research on the cole crops and wheat has discovered that newly formed polyploids can undergo dramatic genome rearrangements that could lead to rapid evolutionary change.

CONCLUSIONS

Many more important evolutionary discoveries are on the horizon, now that the whole genome sequence is available of the two major subspecies of rice Oryza sativa ssp. japonica and O. sativa ssp. indica. The rice sequence data can be used to study the origin of genes and gene families, track rates of sequence divergence over time, and provide hints about how genes evolve and generate products with novel biological properties. The rice sequence data has already been mined to show that transposable elements often carry fragments of cellular genes. This type of genome shuffling could play a role in creating novel, reorganized genes with new adaptive properties.

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.

Steps in the evolution of heteromorphic sex chromosomes

We review some recently published results on sex chromosomes in a diversity of species. We focus on several fish and some plants whose sex chromosomes appear to be 'young', as only parts of the chromosome are nonrecombining, while the rest is pseudoautosomal. However, the age of these systems is not yet very clear. Even without knowing what proportions of their genes are genetically degenerate, these cases are of great interest, as they may offer opportunities to study in detail how sex chromosomes evolve. In particular, we review evidence that recombination suppression occurs progressively in evolutionarily independent cases, suggesting that selection drives loss of recombination over increasingly large regions. We discuss how selection during the period when a chromosome is adapting to its role as a Y chromosome might drive such a process.

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.