Selection of sporophytic and gametophytic self‐incompatibility in the absence of a superlocus

Self‐incompatibility (SI) is a complex trait that enforces outcrossing in plant populations. SI generally involves tight linkage of genes coding for the proteins that underlie self‐pollen detection and pollen identity specification. Here, we develop two‐locus genetic models to address the question of whether sporophytic SI (SSI) and gametophytic SI (GSI) can invade populations of self‐compatible plants when there is no linkage or weak linkage of the underlying pollen detection and identity genes (i.e., no S‐locus supergene). The models assume that SI evolves as a result of exaptation of genes formerly involved in functions other than SI. Model analysis reveals that SSI and GSI can invade populations even when the underlying genes are loosely linked, provided that inbreeding depression and selfing rate are sufficiently high. Reducing recombination between these genes makes conditions for invasion more lenient. These results can help account for multiple, independent evolution of SI systems as seems to have occurred in the angiosperms.     

Loss of gametophytic self-incompatibility with evolution of inbreeding depression

Gametophytic self-incompatibility (SI) in plants is a widespread mechanism preventing self-fertilization and the ensuing inbreeding depression, but it often evolves to self-compatibility. We analyze genetic mechanisms for the breakdown of gametophytic SI, incorporating a dynamic model for the evolution of inbreeding depression allowing for partial purging of nearly recessive lethal mutations by selfing, and accounting for pollen limitation and sheltered load linked to the S-locus. We consider two mechanisms for the breakdown of gametophytic SI: a nonfunctional S-allele and an unlinked modifier locus that inactivates the S-locus. We show that, under a wide range of conditions, self-compatible alleles can invade a self-incompatible population. Conditions for invasion are always less stringent for a nonfunctional S-allele than for a modifier locus. The spread of self-compatible genotypes is favored by extremely high or low selfing rates, a small number of S-alleles, and pollen limitation. Observed parameter values suggest that the maintenance of gametophytic SI is caused by a combination of high inbreeding depression in self-incompatible populations coupled with intermediate selfing rates of the self-compatible genotypes and sheltered load linked to the S-locus.     

Breakdown of gametophytic self-incompatibility in subdivided populations

In many hermaphroditic flowering plants, self-fertilization is prevented by self-incompatibility (SI), often controlled by a single locus, the S-locus. In single isolated populations, the maintenance of SI depends chiefly on inbreeding depression and the number of SI alleles at the S-locus. In subdivided populations, however, population subdivision has complicated effects on both the number of SI alleles and the level of inbreeding depression, rendering the maintenance of SI difficult to predict. Here, we explore the conditions for the invasion of a self-compatible mutant in a structured population. We find that the maintenance of SI is strongly compromised when a population becomes subdivided. We show that this effect is mainly caused by the decrease in the local diversity of SI alleles rather than by a change in the dynamics of inbreeding depression. Strikingly, we also find that the diversity of SI alleles at the whole population level is a poor predictor of the maintenance of SI. We discuss the implications of our results for the interpretation of empirical data on the loss of SI in natural populations.     

GENETIC ARCHITECTURE OF INBREEDING DEPRESSION AND THE MAINTENANCE OF GAMETOPHYTIC SELF‐INCOMPATIBILITY

Gametophytic self‐incompatibility (GSI) is a widespread genetic system, which enables hermaphroditic plants to avoid self‐fertilization and mating with close relatives. Inbreeding depression is thought to be the major force maintaining SI; however, inbreeding depression is a dynamical variable that depends in particular on the mating system. In this article we use multilocus, individual‐based simulations to examine the coevolution of SI and inbreeding depression within finite populations. We focus on the conditions for the maintenance of SI when self‐compatible (SC) mutants are introduced in the population by recurrent mutation, and compare simulation results with predictions from an analytical model treating inbreeding depression as a fixed parameter (thereby neglecting effects of purging within the SC subpopulation). In agreement with previous models, we observe that the maintenance of SI is associated with high inbreeding depression and is facilitated by high rates of self‐pollination. Purging of deleterious mutations by SC mutants has little effect on the spread of those mutants as long as most deleterious alleles have weak fitness effects: in this case, the genetic architecture of inbreeding depression has little effect on the maintenance of SI. By contrast, purging may greatly enhance the spread of SC mutants when deleterious alleles have strong fitness effects.     

Linear dominance relationship among four class-II S haplotypes in pollen is determined by the expression of SP11 in Brassica self-incompatibility

Self-incompatibility (SI) prevents self-fertilization by rejecting pollen from plants with the same S phenotype. The Brassica SI system is controlled sporophytically by multiple alleles at the single locus, S, and dominance relationships among S haplotypes are observed in both stigma and pollen. We have identified previously five different class-II S haplotypes in Brassica campestris. Here, we performed test-crosses between S heterozygotes and their respective parental S homozygotes for four of these class-II S haplotypes, and observed a linear dominance relationship on the pollen side. To determine how this relationship is controlled, we performed RNA gel blot analyses for six S heterozygotes and their respective parental S homozygotes using the corresponding SP11 clone as a probe. In all six S heterozygotes, SP11 derived from a dominant haplotype was predominantly expressed, and SP11 derived from a recessive haplotype was repressed. Thus, the linear dominance relationship of the SI phenotype on the pollen side is regulated by the expression of SP11.     

On the origin of self-incompatibility haplotypes: transition through self-compatible intermediates

Self-incompatibility (SI) in flowering plants entails the inhibition of fertilization by pollen that express specificities in common with the pistil. In species of the Solanaceae, Rosaceae, and Scrophulariaceae, the inhibiting factor is an extracellular ribonuclease (S-RNase) secreted by stylar tissue. A distinct but as yet unknown gene (provisionally called pollen-S) appears to determine the specific S-RNase from which a pollen tube accepts inhibition. The S-RNase gene and pollen-S segregate with the classically defined S-locus. The origin of a new specificity appears to require, at minimum, mutations in both genes. We explore the conditions under which new specificities may arise from an intermediate state of loss of self-recognition. Our evolutionary analysis of mutations that affect either pistil or pollen specificity indicates that natural selection favors mutations in pollen-S that reduce the set of pistils from which the pollen accepts inhibition and disfavors mutations in the S-RNase gene that cause the nonreciprocal acceptance of pollen specificities. We describe the range of parameters (rate of receipt of self-pollen and relative viability of inbred offspring) that permits the generation of a succession of new specificities. This evolutionary pathway begins with the partial breakdown of SI upon the appearance of a mutation in pollen-S that frees pollen from inhibition by any S-RNase presently in the population and ends with the restoration of SI by a mutation in the S-RNase gene that enables pistils to reject the new pollen type.     

Phenylketonuria in Spain: RFLP haplotypes and linked mutations

In order to investigate the molecular basis of phenylketonuria (PKU) in Spain, we analyzed the restriction fragment length polymorphism (RFLP) haplotypes and common mutations in the phenylalanine hydroxylase (PAH) gene in 32 unrelated Spanish PKU families. The distribution of RFLP haplotypes differs from that of northern Europe. Mutant haplotypes 2 and 3 were completely absent in our sample. Approximately 65% of the mutant alleles are confined to three RFLP haplotypes, namely haplotypes 1, 6 and 9, also frequently found in other Mediterranean populations. We screened for previously described PKU mutations using the polymerase chain reaction and allele-specific oligonucleotides, and found IVS10,165T, E280K and P281L as the major mutations, representing 41% of the PKU alleles. Other mutations found were Y414C, and a new one, P244L. Mutations R408W and IVS12, prevalent in northern Europe, as well as others present in southern European populations (R252W, R261Q, L249F) were not detected in our sample. Our results reveal the genetic heterogeneity present in the Spanish PKU population, which shows similarities to others of Mediterranean origin.     

Inbreeding depression in small populations of self-incompatible plants.

Self-incompatibility (SI) is a widespread mechanism that prevents inbreeding in flowering plants. In many species, SI is controlled by a single locus (the S locus) where numerous alleles are maintained by negative frequency-dependent selection. Inbreeding depression, the decline in fitness of selfed individuals compared to outcrossed ones, is an essential factor in the evolution of SI systems. Conversely, breeding systems influence levels of inbreeding depression. Little is known about the joint effect of SI and drift on inbreeding depression. Here we studied, using a two-locus model, the effect of SI (frequency-dependent selection) on a locus subject to recurrent deleterious mutations causing inbreeding depression. Simulations were performed to assess the effect of population size and linkage between the two loci on the level of inbreeding depression and genetic load. We show that the sheltering of deleterious alleles linked to the S locus strengthens inbreeding depression in small populations. We discuss the implications of our results for the evolution of SI systems.     

Recent selection for self‐compatibility in a population of Leavenworthia alabamica

The evolution of self‐compatibility (SC) is the first step in the evolutionary transition in plants from outcrossing enforced by self‐incompatibility (SI) to self‐fertilization. In the Brassicaceae, SI is controlled by alleles of two tightly linked genes at the S‐locus. Despite permitting inbreeding, mutations at the S‐locus leading to SC may be selected if they provide reproductive assurance and/or gain a transmission advantage in a population when SC plants self‐ and outcross. Positive selection can leave a genomic signature in the regions physically linked to the focus of selection when selection has occurred recently. From an SC population of Leavenworthia alabamica with a known nonfunctional mutation at the S‐locus, we collected sequence data from a ～690 Kb region surrounding the S‐locus, as well as from regions not linked to the S‐locus. To test for recent positive selection acting at the S‐locus, we examined polymorphism and the site‐frequency spectra. Using forward simulations, we demonstrate that recent selection of the strength expected for SC at a locus formerly under balancing selection can generate patterns similar to those seen in our empirical data.     

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.     

An evolutionary framework for common diseases: the ancestral-susceptibility model

Unlike rare mendelian diseases, which are due to new mutations (i.e. derived alleles), several alleles that increase the risk to common diseases are ancestral. Moreover, population genetics studies suggest that some derived alleles that protect against common diseases became advantageous recently. These observations can be explained within an evolutionary framework in which ancestral alleles reflect ancient adaptations to the lifestyle of ancient human populations, whereas the derived alleles were deleterious. However, with the shift in environment and lifestyle, the ancestral alleles now increase the risk of common diseases in modern populations. In this article, we develop an explicit evolutionary model and use population genetics simulations to investigate the expected haplotype structure and type of disease-association signals of ancestral risk alleles.     

The Role of a Pollen-Expressed Cullin1 Protein in Gametophytic Self-Incompatibility in Solanum

We previously isolated a pollen factor, ui6.1, which encodes a Cullin1 protein (CUL1) that functions in unilateral interspecific incompatibility (UI) in Solanum. Here we show that CUL1 is also required for pollen function in self-incompatibility (SI). We used RNA interference (RNAi) to reduce CUL1 expression in pollen of Solanum arcanum, a wild SI tomato relative. Hemizygous T₀ plants showed little or no transmission of the transfer DNA (T-DNA) through pollen when crossed onto nontransgenic SI plants, indicating that CUL1-deficient pollen are selectively eliminated. When crossed onto a related self-compatible (SC) accession lacking active S-RNase, pollen transmission of the T-DNA followed Mendelian ratios. These results provide further evidence for functional overlap between SI and UI on the pollen side and suggest that CUL1 mutations will reinforce SI-to-SC transitions in natural populations only if preceded by loss of pistil S-RNase expression.     

VNTR alleles associated with the alpha-globin locus are haplotype and population related.

The human alpha-globin complex contains several polymorphic restriction-enzyme sites (i.e., RFLPs) linked to form haplotypes and is flanked by two hypervariable VNTR loci, the 5' hypervariable region (HVR) and the more highly polymorphic 3'HVR. Using a combination of RFLP analysis and PCR, we have characterized the 5'HVR and 3'HVR alleles associated with the alpha-globin haplotypes of 133 chromosomes, and we here show that specific alpha-globin haplotypes are each associated with discrete subsets of the alleles observed at these two VNTR loci. This statistically highly significant association is observed over a region spanning approximately 100 kb. With the exception of closely related haplotypes, different haplotypes do not share identically sized 3'HVR alleles. Earlier studies have shown that alpha-globin haplotype distributions differ between populations; our current findings also reveal extensive population substructure in the repertoire of alpha-globin VNTRs. If similar features are characteristic of other VNTR loci, this will have important implications for forensic and anthropological studies.     

Balancing selection in the wild: testing population genetics theory of self-incompatibility in the rare species Brassica insularis

Self-incompatibility (SI) systems are widespread mechanisms that prevent self-fertilization in angiosperms. They are generally encoded by one genome region containing several multiallelic genes, usually called the S-locus. They involve a recognition step between the pollen and the pistil component and pollen is rejected when it shares alleles with the pistil. The direct consequence is that rare alleles are favored, such that the S-alleles are subject to negative frequency-dependent selection. Several theoretical articles have predicted the specific patterns of polymorphism, compared to neutral loci, expected for such genes under balancing selection. For instance, many more alleles should be maintained and populations should be less differentiated than for neutral loci. However, empirical tests of these predictions in natural populations have remained scarce. Here, we compare the genetic structure at the S-locus and microsatellite markers for five natural populations of the rare species Brassica insularis. As in other Brassica species, B. insularis has a sporophytic SI system for which molecular markers are available. Our results match well the theoretical predictions and constitute the first general comparison of S-allele and neutral polymorphism.     

Estimating pollen flow using SSR markers and paternity exclusion: accounting for mistyping

Highly informative genetic markers, such as simple sequence repeats (SSRs), can be used to directly measure pollen flow by parentage analysis. However, mistyping (i.e. false inference of genotypes caused by the occurrence of null alleles, mutations, and detection errors) can lead to substantial biases in the estimates obtained. Using computer simulations, we evaluated a direct method for estimating pollen immigration using SSR markers and a paternity exclusion approach. This method accounts for mistyping and does not rely on assumptions about the distribution of male reproductive success. If ignored, even minor rates of mistyping (1.5%) resulted in overestimating pollen immigration by up to 150%. When we required at least two mismatching loci before excluding candidate fathers from paternity, the resulting pollen immigration estimates had small biases for rates of mistyping up to 4.5%. Requiring at least three mismatches for exclusion was needed to minimize the upward biases of pollen immigration caused by rates of mistyping up to 10.5%. The minimum number of highly variable SSR loci needed to minimize cryptic gene flow and obtain reliable estimates of pollen immigration varied from five to seven for a sampling scheme applicable to most conifers (i.e. when paternal haplotypes can be unambiguously determined). Between five and nine highly variable SSR loci were needed for a more general sampling scheme that is applicable to all diploid seed plants. With moderately variable SSR markers, consistently accurate estimates of pollen immigration could be obtained only for rates of mistyping up to 4.5%. We developed the POLLEN FLOW (PFL) computer program which can be used to obtain unbiased and precise estimates of pollen immigration under a wide range of conditions, including population sizes as large as 600 parents and mistyping rates as high as 10.5%.     

The population genetics of X-autosome synthetic lethals and steriles

Epistatic interactions are widespread, and many of these interactions involve combinations of alleles at different loci that are deleterious when present in the same individual. The average genetic environment of sex-linked genes differs from that of autosomal genes, suggesting that the population genetics of interacting X-linked and autosomal alleles may be complex. Using both analytical theory and computer simulations, we analyzed the evolutionary trajectories and mutation-selection balance conditions for X-autosome synthetic lethals and steriles. Allele frequencies follow a set of fundamental trajectories, and incompatible alleles are able to segregate at much higher frequencies than single-locus expectations. Equilibria exist, and they can involve fixation of either autosomal or X-linked alleles. The exact equilibrium depends on whether synthetic alleles are dominant or recessive and whether fitness effects are seen in males, females, or both sexes. When single-locus fitness effects and synthetic incompatibilities are both present, population dynamics depend on the dominance of alleles and historical contingency (i.e., whether X-linked or autosomal mutations occur first). Recessive synthetic lethality can result in high-frequency X-linked alleles, and dominant synthetic lethality can result in high-frequency autosomal alleles. Many X-autosome incompatibilities in natural populations may be cryptic, appearing to be single-locus effects because one locus is fixed. We also discuss the implications of these findings with respect to standing genetic variation and the origins of Haldane's rule.     

Effects of pollen availability and the mutation bias on the fixation of mutations disabling the male specificity of self‐incompatibility

The evolution of self‐compatibility (SC) by the loss of self‐incompatibility (SI) is regarded as one of the most frequent transitions in flowering plants. SI systems are generally characterized by specific interactions between the male and female specificity genes encoded at the S‐locus. Recent empirical studies have revealed that the evolution of SC is often driven by male SC‐conferring mutations at the S‐locus rather than by female mutations. In this study, using a forward simulation model, we compared the fixation probabilities of male vs. female SC‐conferring mutations at the S‐locus. We explicitly considered the effects of pollen availability in the population and bias in the occurrence of SC‐conferring mutations on the male and female specificity genes. We found that male SC‐conferring mutations were indeed more likely to be fixed than were female SC‐conferring mutations in a wide range of parameters. This pattern was particularly strong when pollen availability was relatively high. Under such a condition, even if the occurrence of mutations was biased strongly towards the female specificity gene, male SC‐conferring mutations were much more often fixed. Our study demonstrates that fixation probabilities of those two types of mutation vary strongly depending on ecological and genetic conditions, although both types result in the same evolutionary consequence—the loss of SI.     

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.