Fewer S‐alleles are maintained in plant populations with sporophytic as opposed to gametophytic self‐incompatibility

Plants use self‐incompatibility to reject pollen bearing alleles in common at the S‐locus. These systems are classified as gametophytic (GSI) if recognition involves haploid pollen or sporophytic (SSI) if recognition involves diploid paternal genotypes. Dominance in SSI systems reduces the number of S‐alleles, but it has not been clear which system should maintain greater diversity when all else is equal. We simulated finite populations to compare the equilibrium number of S‐alleles in populations with either GSI or a co‐dominant SSI system. When population size was constant, SSI systems maintained more S‐alleles than GSI systems. When populations fluctuated in response to an S‐Allee effect, fewer S‐alleles were observed in SSI systems when S‐allele diversity was low, and SSI populations were vulnerable to extinction over a broader range of parameters. Turnover rates at the S‐locus were also faster in SSI populations experiencing strong S‐Allee effects. Given the variable expectations concerning S‐allele diversity in these systems, we reviewed published estimates of S‐allele diversity. GSI populations have significantly more S‐alleles on average than SSI populations (GSI = 25.70 and SSI = 16.80). Dominance likely contributes to this pattern, although the demographic consequences of the S‐Allee effect may be important in populations with fewer than 10 S‐alleles.     

Inferences on the number and frequency of S-pollen gene (SFB) specificities in the polyploid Prunus spinosa

In flowering plants, self-incompatibility is a genetic mechanism that prevents self-fertilization. In gametophytic self-incompatibility (GSI), pollen specificity is encoded by the haploid genotype of the pollen tube. In GSI, specificities are maintained by frequency-dependent selection, and for diploid species, at equilibrium, equal specificity frequencies (isoplethy) are expected. This prediction has been tested in diploid, but never in polyploid self-incompatible species. For the latter, there is no theoretical expectation regarding isoplethy. Here, we report the first empirical study on specificity frequencies in a natural population of a polyploid self-incompatible species, Prunus spinosa. A total of 32 SFB (the pollen S gene) putative specificities are observed in a large sample from a natural population. Although P. spinosa is polyploid, the number of specificities found is similar to that reported for other diploid Rosaceae species. Unequal specificity frequencies are observed.     

Estimating the number,frequency, and dominance of S-alleles in a natural population of Arabidopsis lyrata(Brassicaceae) with sporophytic control of self-incompatibility

In homomorphic plant self-incompatibility (SI) systems, large numbers of alleles may be maintained at a single Mendelian locus. Most estimators of the number of alleles present in natural populations are designed for gametophytic self-incompatibility systems (GSI) in which the recognition phenotype of the pollen is determined by its own haploid genotype. In sporophytic systems (SSI), the recognition phenotype of the pollen is determined by the diploid genotype of its parent, and dominance differs among alleles. We describe research aimed at estimates of S-allele numbers in a natural population of Arabidopsis lyrata (Brassicaceae), whose SSI system has recently been described. Using a combination of pollination studies and PCR-based identification of alleles at a locus equivalent to the Brassica SRK gene, we identified and sequenced 11 putative alleles in a sample of 20 individuals from different maternal seed sets. The pollination results indicate that we have not amplified all alleles that must be present. Extensive partial incompatibility, nonreciprocal compatibility differences, and evidence of weakened expression of SI in some genotypes, prevent us from determining the exact number of missing alleles based only on cross-pollination data. Although we show that none of the theoretical models currently proposed is completely appropriate for estimating the number of alleles in this system, we estimate that there are between 13 and 16 different S-alleles in our sample, probably between 16 and 25 alleles in the population, and discuss the relative frequency of alleles in relation to dominance.     

THE EFFECTS OF SELECTION IN THE GAMETOPHYTE STAGE ON MUTATIONAL LOAD

We have studied a multilocus selection model of a plant population in which mutations to deleterious alleles occur that may affect not only the diploid sporophyte stage, but also the haploid pollen stage before zygote formation. We investigated the reduction in inbreeding depression (as measured in the sporophyte) caused by the lowering of mutant allele frequencies due to selection in the pollen. This is important for a full understanding of the role of inbreeding depression in the maintenance of outcrossing in seed plants. We also studied the theoretically expected relationship between the pollen fitnesses of different pollen donor genotypes and the fitnesses of the diploid progeny that they sire. This relationship can be compared with the results of experiments in which pollen was subjected to selection, and improved progeny quality was observed. We found that on the mutational load model there is, as expected intuitively, a positive covariance between the pollen and zygote fitnesses, but that it is likely to be small. Subjecting pollen to an episode of strong selection is usually expected to increase sporophyte fitness only slightly.     

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.     

Competitive interaction between two functional S-haplotypes confer self-compatibility on tetraploid Chinese cherry (Prunus pseudocerasus Lindl. CV. Nanjing Chuisi)

Self-incompatibility (SI) has been studied extensively at the molecular level in Solanaceae, Rosaceae and Scrophulariaceae, all of which exhibit gametophytic self-incompatibility (GSI). In the present study, four PpsS-haplotypes (Prunus pseudocerasus S-haplotypes) comprising at least two genes, i.e., PpsS-RNase (P. pseudocerasus S-RNase) and PpsSFB (P. pseudocerasus S-haplotype-specific F-box) have been successfully isolated in tetraploid P. pseudocerasus Lindl. CV. Nanjing Chuisi ("NC") which exhibited self-compatibility (SC), and its S-genotype was determined as S-1/S-3'/S-5/S-7. These PpsS-RNases, which were expressed exclusively in style, shared the typical structural features with S-RNases from other Prunus species exhibiting GSI. All PpsSFBs showed similar structure characteristics of SFBs from other Prunus species, and matched with the necessary conditions for pollen S-determinant. No mutations leading to dysfunction of S-haplotype were found in their full-length c-DNA sequences, except for PpsS-3'-haplotype which was not amplified by PCR. These four S-haplotypes complied with tetrasomic inheritance. Diploid pollen grains with S-genotypes S-7/S-1, S-7/S-5 and S-1/S-5 can grow the full length of the style after self-pollination, while pollen grains with S-3'/S-7, S-3'/S-1 and S-3'/S-5 cannot. These results suggest that PpsS-haplotypes-1, -5 and -7 are functional, and that competitive interaction between two of them confer self-compatibility on cultivar "NC". Furthermore, in terms of recognition specificity, diploid pollen grains carrying PpsS-3'-haplotype are equal to monoploid pollen grains carrying the other functional S-haplotype.     

Colchicine-induced changes in the self-incompatibility behaviour ofNicotiana

Colchicine treatment ofNicotiana seeds produced both genetic and nongenetic changes in the self-incompatibility reaction of the treated plants. Treatment with 0.25% colchicine produced a high number of tetraploid plants. Polyploidy brought about self-compatibility in all but one genotype ofS heterozygous constitution, which are normally self-incompatible in the diploid state. This genetic phenomenon, reported to be due to competitive interaction between two differentS alleles in the diploid pollen, was found to vary greatly in degree of expression not only between diferent genotypes but also between different plants of the same genotype. Treatment with a much lower strength of colchicine (0.1%) produced virtually no polyploids, but over 25% of the diploid seedlings showed selfcompatibility. This self-compatibility was very erratic, certain flowers in a continuous series of pollinations showing self-compatibility, while others showed self-incompatibility. Alterations of the self-incompatibility reaction, other than that due to competitive interaction, are ascribed here to changes in certain non-genetic, particulate or non-particulate cytoplasmic constituents. The inconsistency between flower pollinations is due to irregular inter-cellular distribution of the particulate elements. The non-particulate element(s) affected by the treatment is believed to be a constituent of the induction or repression system involved in the regulation ofS gene activity in the shoot or root.     

Gametophytic self-incompatibility: understanding the cellular mechanisms involved in “self” pollen tube inhibition

Self-incompatibility (SI) prevents the production of “self” seed and inbreeding by providing a recognition and rejection system for “self,” or genetically identical, pollen. Studies of gametophytic SI (GSI) species at a molecular level have identified two completely different S-genes and SI mechanisms. One GSI mechanism, which is found in the Solanaceae, Rosaceae and Scrophulariaceae, has S-RNase as the pistil S-component and an F-box protein as the pollen S-component. However, non-S-locus factors are also required. In an incompatible situation, the S-RNases degrade pollen RNA, thereby preventing pollen tube growth. Here, in the light of recent evidence, we examine alternative models for how compatible pollen escapes this cytotoxic activity. The other GSI mechanism, so far found only in the Papaveraceae, has a small secreted peptide, the S-protein, as its pistil S-component. The pollen S-component remains elusive, but it is thought to be a transmembrane receptor, as interaction of the S-protein with incompatible pollen triggers a signaling network, resulting in rapid actin depolymerization and pollen tube inhibition and programmed cell death (PCD). Here, we present an overview of what is currently known about the mechanisms involved in regulating pollen tube inhibition in these two GSI systems.     

FIXATION PROBABILITIES OF SELFING RATE MODIFIERS IN SIMULATIONS WITH SEVERAL DELETERIOUS ALLELES WITH LINKAGE

The fixation rates of selfing rate modifiers were found by stochastic simulation in an infinite site model, including effects of several deleterious alleles with variable effects, which were randomly distributed in the genome without assuming any pollen discounting. Previous results on the evolution of selfing obtained by more precise methods were in this study further validated, and it was concluded that the effect of genetic associations on the evolution of mating systems is small except in the case of full pollen discounting. Furthermore, attention was given to the uneven distribution of the genetic load in the population, and the accompanying large among-genome variation in fixation rates. This among-genome variation will be of significance for the evolution of mating systems.     

Dynamics of neutral and selected alleles when the offspring distribution is skewed

We analyze the dynamics of two alternative alleles in a simple model of a population that allows for large family sizes in the distribution of offspring number. This population model was first introduced by Eldon and Wakeley, who described the backward-time genealogical relationships among sampled individuals, assuming neutrality. We study the corresponding forward-time dynamics of allele frequencies, with or without selection. We derive a continuum approximation, analogous to Kimura's diffusion approximation, and we describe three distinct regimes of behavior that correspond to distinct regimes in the coalescent processes of Eldon and Wakeley. We demonstrate that the effect of selection is strongly amplified in the Eldon-Wakeley model, compared to the Wright-Fisher model with the same variance effective population size. Remarkably, an advantageous allele can even be guaranteed to fix in the Eldon-Wakeley model, despite the presence of genetic drift. We compute the selection coefficient required for such behavior in populations of Pacific oysters, based on estimates of their family sizes. Our analysis underscores that populations with the same effective population size may nevertheless experience radically different forms of genetic drift, depending on the reproductive mechanism, with significant consequences for the resulting allele dynamics.     

Phenotypic variation,sexual reproduction and evolutionary population dynamics

I studied the effects of introducing phenotypic variation into a well-known single species model for a population with discrete, non-overlapping generations. The phenotypes differed in their dynamic behaviour. The analysis was made under the assumption that the population was in an evolutionary stable state. Differences in the timing of the competitive impacts of the phenotypes on each other had a strong simplifying effect on the dynamics. This result could also be applied to competition between species. The effect of sexual reproduction on the dynamics of the population was analysed by assuming the simplest genetic model of one locus with two alleles. Sexual reproduction made the system much more stable in the (mathematical) sense that the number of attractors was reduced and their basins of attraction enlarged. In a dominant system sex tended to increase the frequency of the recessive allele, and in an overdominant system it induced gene frequencies of 1/2. Whether the attractors in the dominant system tended to be simpler or more complex than the attractors in the asexual system depended on the phenotype of the recessive homozygote. The overdominant sexual system tended to have simpler dynamics than the corresponding asexual population. A 2-locus model was used to study whether sexuals can invade an asexual population and vice versa. One locus coded for sexual and asexual reproduction, while the other coded for the dynamics. Enhanced stability through sexual reproduction seemed to be the reason why there was a clear asymmetry favouring sex in this evolutionary context.     

A general model to explore complex dominance patterns in plant sporophytic self-incompatibility systems

We developed a general model of sporophytic self-incompatibility under negative frequency-dependent selection allowing complex patterns of dominance among alleles. We used this model deterministically to investigate the effects on equilibrium allelic frequencies of the number of dominance classes, the number of alleles per dominance class, the asymmetry in dominance expression between pollen and pistil, and whether selection acts on male fitness only or both on male and on female fitnesses. We show that the so-called "recessive effect" occurs under a wide variety of situations. We found emerging properties of finite population models with several alleles per dominance class such as that higher numbers of alleles are maintained in more dominant classes and that the number of dominance classes can evolve. We also investigated the occurrence of homozygous genotypes and found that substantial proportions of those can occur for the most recessive alleles. We used the model for two species with complex dominance patterns to test whether allelic frequencies in natural populations are in agreement with the distribution predicted by our model. We suggest that the model can be used to test explicitly for additional, allele-specific, selective forces.     

Inheritance and dominance of self-incompatibility alleles in polyploid Arabidopsis lyrata

Natural populations of diploid Arabidopsis lyrata exhibit the sporophytic type of self-incompatibility system characteristic of Brassicaceae, in which complicated dominance interactions among alleles in the diploid parent determine self-recognition phenotypes of both pollen and stigma. The purpose of this study was to investigate how polyploidy affects this already complex system. One tetraploid population (Arabidopsis lyrata ssp kawasakiana from Japan) showed complete self-compatibility and produced viable selfed progeny for at least three generations subsequent to field collection. In contrast, individuals from a second tetraploid population (A. lyrata ssp petraea from Austria) were strongly self-incompatible (SI). Segregation of SI genotypes in this population followed Mendelian patterns based on a tetrasomic model of inheritance, with two to four alleles per individual, independent segregation of alleles, and little evidence of dosage effects of alleles found in multiple copies. Similar to results from diploids, anomalous compatibility patterns involving particular combinations of individuals occurred at a low frequency in the tetraploids, suggesting altered dominance in certain genetic backgrounds that could be due to the influence of a modifier locus. Overall, dominance relationships among S-alleles in self-incompatible tetraploid families were remarkably similar to those in related diploids, suggesting that this very important and complicated locus has not undergone extensive modification subsequent to polyploidization.     

On migration load of seeds and pollen grains in a local population

We have extended Wright's model of migration load to hermaphrodite plants showing variation at a single locus with two alleles. The model incorporates independent migration of seeds and pollen grains, the selection at both the haploid gametophyte and the diploid sporophyte stages, and a mixed mating system. The analytical relations between migration load and migration rate of seeds and pollen grains are explicitly formulated. The results show that under certain conditions, seed flow can have a more effect on migration load than pollen flow. Pollen selection at the gametophyte stage cannot substantially affect the migration load at the sporophyte stage. Selection at the diploid sporophyte stage is critical in determining the migration load of pollen grains. The relative migration loads of pollen versus seeds can be approximately estimated in predominantly outcrossing populations by the ratio of pollen flow to twice the seed flow, when the selection coefficient (s(T)) is greater than, or approximately equal to, the migration rate (m).     

Effects of population size and metapopulation dynamics on a mating-system polymorphism

The evolutionary dynamics of neutral alleles under the Wright-Fisher model are well understood. Similarly, the effect of population turnover on neutral genetic diversity in a metapopulation has attracted recent attention in theoretical studies. Here we present the results of computer simulations of a simple model that considers the effects of finite population size and metapopulation dynamics on a mating-system polymorphism involving selfing and outcrossing morphs. The details of the model are based on empirical data from dimorphic populations of the annual plant Eichhornia paniculata, but the results are also of relevance to species with density-dependent selfing rates in general. In our model, the prior selfing rate is determined by two alleles segregating at a single diploid locus. After prior selfing occurs, some remaining ovules are selfed through competing self-fertilisation in finite populations as a result of random mating among gametes. Fitness differences between the mating-system morphs were determined by inbreeding depression and pollen discounting in a context-dependent manner. Simulation results showed evidence of frequency dependence in the action of pollen discounting and inbreeding depression in finite populations. In particular, as a result of selfing in outcrossers through random mating among gametes, selfers experienced a "fixation bias" through drift, even when the mating-system locus was selectively neutral. In a metapopulation, high colony turnover generally favoured the fixation of the outcrossing morph, because inbreeding depression reduced opportunities for colony establishment by selfers through seed dispersal. Our results thus demonstrate that population size and metapopulation processes can lead to evolutionary dynamics involving pollen and seed dispersal that are not predicted for large populations with stable demography.     

Dissimilarity of individual microsatellite profiles under different mutation models: Empirical approach

Microsatellites (simple sequence repeats, SSRs) still remain popular molecular markers for studying neutral genetic variation. Two alternative models outline how new microsatellite alleles evolve. Infinite alleles model (IAM) assumes that all possible alleles are equally likely to result from a mutation, while stepwise mutation model (SMM) describes microsatellite evolution as stepwise adding or subtracting single repeat units. Genetic relationships between individuals can be analyzed in higher precision when assuming the SMM scenario with allele size differences as a proxy of genetic distance. If population structure is not predetermined in advance, an empirical data analysis usually includes (a) estimating proximity between individual SSR profiles with a selected dissimilarity measure and (b) determining putative genetic structure of a given set of individuals using methods of clustering and/or ordination for the obtained dissimilarity matrix. We developed new dissimilarity indices between SSR profiles of haploid, diploid, or polyploid organisms assuming different mutation models and compared the performance of these indices for determining genetic structure with population data and with simulations. More specifically, we compared SMM with a constant or variable mutation rate at different SSR loci to IAM using data from natural populations of a freshwater bryozoan Cristatella mucedo (diploid), wheat leaf rust Puccinia triticina (dikaryon), and wheat powdery mildew Blumeria graminis (monokaryon). We show that inferences about population genetic structure are sensitive to the assumed mutation model. With simulations, we found that Bruvo's distance performs generally poorly, while the new metrics are capturing the differences in the genetic structure of the populations.     

Population structure, mating system, and sex-determining allele diversity of the parasitoid wasp Habrobracon hebetor

Besides haplo-diploid sex determination, where females develop from fertilized diploid eggs and males from unfertilized haploid eggs, some Hymenoptera have a secondary system called complementary sex determination (CSD). This depends on genotypes of a 'sex locus' with numerous sex-determining alleles. Diploid heterozygotes develop as females, but diploid homozygotes become sterile or nonviable diploid males. Thus, when females share sex-determining alleles with their mates and produce low fitness diploid males, CSD creates a genetic load. The parasitoid wasp Habrobracon hebetor has CSD and displays mating behaviours that lessen CSD load, including mating at aggregations of males and inbreeding avoidance by females. To examine the influence of population structure and the mating system on CSD load, we conducted genetic analyses of an H. hebetor population in Wisconsin. Given the frequency of diploid males, we estimated that the population harboured 10-16 sex-determining alleles. Overall, marker allele frequencies did not differ between subpopulations, but frequencies changed dramatically between years. This reduced estimates of effective size of subpopulations to only N3 approximately 20-50, which probably reflected annual fluctuations of abundance of H. hebetor. We also determined that the mating system is effectively monogamous. Models relating sex-determining allele diversity and the mating system to female productivity showed that inbreeding avoidance always decreased CSD loads, but multiple mating only reduced loads in populations with fewer than five sex-determining alleles. Populations with N3 less than 100 should have fewer sex-determining alleles than we found, but high diversity could be maintained by a combination of frequency-dependent selection and gene flow between populations.     

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.     

Progress towards elucidating the mechanisms of self-incompatibility in the grasses: further insights from studies in Lolium

BACKGROUND AND SCOPE: Self-incompatibility (SI) in flowering plants ensures the maintenance of genetic diversity by ensuring outbreeding. Different genetic and mechanistic systems of SI among flowering plants suggest either multiple origins of SI or considerable evolutionary diversification. In the grasses, SI is based on two loci, S and Z, which are both polyallelic: an incompatible reaction occurs only if both S and Z alleles are matched in individual pollen with alleles of the pistil on which they alight. Such incompatibility is referred to as gametophytic SI (GSI). The mechanics of grass GSI is poorly understood relative to the well-characterized S-RNase-based single-locus GSI systems (Solanaceae, Rosaceae, Plantaginaceae), or the Papaver recognition system that triggers a calcium-dependent signalling network culminating in programmed cell death. There is every reason to suggest that the grass SI system represents yet another mechanism of SI. S and Z loci have been mapped using isozymes to linkage groups C1 and C2 of the Triticeae consensus maps in Secale, Phalaris and Lolium. Recently, in Lolium perenne, in order to finely map and identify S and Z, more closely spaced markers have been developed based on cDNA and repeat DNA sequences, in part from genomic regions syntenic between the grasses. Several genes tightly linked to the S and Z loci were identified, but so far no convincing candidate has emerged. RESEARCH AND PROGRESS: From subtracted Lolium immature stigma cDNA libraries derived from S and Z genotyped individuals enriched for SI potential component genes, kinase enzyme domains, a calmodulin-dependent kinase and a peptide with several calcium (Ca(2+)) binding domains were identified. Preliminary findings suggest that Ca(2+) signalling and phosphorylation may be involved in Lolium GSI. This is supported by the inhibition of Lolium SI by Ca(2+) channel blockers lanthanum (La(3+)) and verapamil, and by findings of increased phosphorylation activity during an SI response.     

Separable models for age-structured population genetics

This paper is concerned with the applications of nonlinear age-dependent dynamics to population genetics. Age-structured models are formulated for a single autosomal locus with an arbitrary number of alleles. The following cases are considered: a) haploid populations with selection and mutation; b) monoecious diploid populations with or without mutation reproducing by self-fertilization or by two types of random mating. The diploid models do not deal with selection. For these cases the genic and genotypic frequencies evolve towards time-persistent forms, whether the total population size tends towards exponential growth or not.