S-allele diversity in a natural population of Physalis crassifolia (Solanaceae) (ground cherry) assessed by RT-PCR

Growth rate and life history shape plant resistance to herbivores

PREMISE

Plant defenses are shaped by many factors, including herbivory, lifespan, and mating system. Predictions about plant defense and resistance are often based on resource allocation trade-offs with plant growth and reproduction. Additionally, two types of plant resistance, constitutive and induced resistance, are predicted to be evolutionary alternatives or redundant strategies. Given the variety of plant trait combinations and non-mutually exclusive predictions, examining resistance strategies in related species with different combinations of growth and reproductive traits is important to tease apart roles of plant traits and evolutionary history on plant resistance.

METHODS

Phylogenetic comparative methods were used to examine the potentially interacting influences of life history (annual/perennial), mating system (self-compatible/self-incompatible), and species growth rates on constitutive resistance and inducibility (additional resistance following damage) across Physalis species (Solanaceae).

RESULTS

Resistance was evolutionarily labile, and there was no correlation between constitutive resistance and inducibility. Annual species with fast growth rates displayed higher constitutive resistance, but growth rate did not affect constitutive resistance in perennials. In contrast, inducibility was negatively associated with species growth rate regardless of life history or mating system.

CONCLUSIONS

The different effects of plant life history and growth rate on constitutive resistance and inducibility indicate that defensive evolution is unconstrained by a trade-off between resistance types. The interactions among plant life history, growth, and herbivore resistance show that plant defense is shaped not only by herbivore environment, but also by plant traits that reflect a plant's evolutionary history and local selective pressures.

Colonization, Baker's law, and the evolution of gynodioecy in Hawaii: implications from a study of Lycium carolinianum

PREMISE

As Baker's law suggests, the successful colonization of oceanic islands is often associated with uniparental reproduction (self-fertility), but the high incidence of dimorphism (dioecy, gynodioecy) on islands complicates this idea. Lycium carolinianum is widespread, occurring on the North American mainland and the Hawaiian Islands. We examined Baker's ideas for mainland and island populations of L. carolinianum and examined inbreeding depression as a possible contributor to the evolution of gynodioecy on Maui.

METHODS

Controlled crosses were conducted in two mainland populations and two populations in Hawaii. Treatments included self and cross pollination, unmanipulated controls, and autogamy/agamospermy. Alleles from the self-incompatibility S-RNase gene were isolated and compared between mainland and island populations. Given self-compatibility in Hawaii, we germinated seeds from self- and cross- treatments and estimated inbreeding depression using seven traits and a measure of cumulative fitness.

RESULTS

Mainland populations of Lycium carolinianum are predominately self-incompatible with some polymorphism for self-fertility, whereas Hawaiian populations are self-compatible. Concordantly, S-RNase allelic diversity is reduced in Hawaii compared to the mainland. Hawaiian populations also exhibit significant inbreeding depression.

CONCLUSIONS

Self-compatibility in Hawaii and individual variation in self-fertility in mainland populations suggests that a colonization filter promoting uniparental reproduction may be acting in this system. Comparison of S-RNase variation suggests a collapse of allelic diversity and heterozygosity at the S-RNase locus in Hawaii, which likely contributed to mate limitation upon arrival to the Pacific. Inbreeding depression coupled with autonomous self-fertilization may have led to the evolution of gynodioecy on Maui.

Learning from rejection: the evolutionary biology of single-locus incompatibility

The self-incompatibility (S-) locus of flowering plants is among the most polymorphic known. PCR methods can now be used to estimate both the number of alleles in natural populations and their sequence diversity. The number of alleles provides an estimate of recent effective population size, thus the S-locus provides a tool for examining how species characteristics affect population size. Sequence relationships among alleles provide another estimate of population size extending millions of years into the past. Relationships between S-alleles and related genes provide a means of dating the age of origin of incompatibility systems and determining which, if any, angiosperm families share incompatibility by homology.

Functional gametophytic self-incompatibility in a peripheral population of Solanum peruvianum (Solanaceae)

The transition from self-incompatibility to self-compatibility is a common transition in angiosperms often reported in populations at the edge of species range limits. Geographically distinct populations of wild tomato species (Solanum section Lycopersicon (Solanaceae)) have been described as polymorphic for mating system with both self-incompatible and self-compatible populations. Using controlled pollinations and sequencing of the S-RNase mating system gene, we test the compatibility status of a population of S. peruvianum located near its southern range limit. Pollinations among plants of known genotypes revealed strong self-incompatibility; fruit set following compatible pollinations was significantly higher than following incompatible pollinations for all tested individuals. Sequencing of the S-RNase gene in parents and progeny arrays was also as predicted under self-incompatibility. Molecular variation at the S-RNase locus revealed a diverse set of alleles, and heterozygosity in over 500 genotyped individuals. We used controlled crosses to test the specificity of sequences recovered in this study; in all cases, results were consistent with a unique allelic specificity for each tested sequence, including two alleles sharing 92% amino-acid similarity. Site-specific patterns of selection at the S-RNase gene indicate positive selection in regions of the gene associated with allelic specificity determination and purifying selection in previously characterized conserved regions. Further, there is broad convergence between the present and previous studies in specific amino-acid positions inferred to be evolving under positive selection.

The genetic location of the self-incompatibility locus in white clover (Trifolium repens L.)

White clover (Trifolium repens L.) is a forage legume of considerable economic importance in temperate agricultural systems. It has a strong self-incompatibility system. The molecular basis of self-incompatibility in T. repens is unknown, but it is under the control of a single locus, which is expressed gametophytically. To locate the self-incompatibility locus (S locus) in T. repens, we carried out cross-pollination experiments in an F(1) mapping population and constructed a genetic linkage map using amplified fragment length polymorphism and simple sequence repeat markers. As the first step in a map-based cloning strategy, we locate for the first time the S locus in T. repens on a genetic linkage map, on the homoeologous linkage group pair 1 (E), which is broadly syntenic to Medicago truncatula L. chromosome 1. On the basis of this syntenic relationship, the possibility that the S locus may or may not possess an S-RNase gene is discussed.

Molecular and genetic characterization of novel S-RNases from a natural population of Nicotiana alata

Self-incompatibility in the Solanaceae is mediated by S-RNase alleles expressed in the style, which confer specificity for pollen recognition. Nicotiana alata has been successfully used as an experimental model to elucidate cellular and molecular aspects of S-RNase-based self-incompatibility in Solanaceae. However, S-RNase alleles of this species have not been surveyed from natural populations and consequently the S-haplotype diversity is poorly known. Here the molecular and functional characterization of seven S-RNase candidate sequences, identified from a natural population of N. alata, are reported. Six of these candidates, S ( 5 ), S ( 27 ), S ( 70 ), S ( 75 ), S ( 107 ), and S ( 210 ), showed plant-specific amplification in the natural population and style-specific expression, which increased gradually during bud maturation, consistent with the reported S-RNase expression. In contrast, the S ( 63 ) ribonuclease was present in all plants examined and was ubiquitously expressed in different organs and bud developmental stages. Genetic segregation analysis demonstrated that S ( 27 ), S ( 70 ), S ( 75 ), S ( 107 ), and S ( 210 ) alleles were fully functional novel S-RNases, while S ( 5 ) and S ( 63 ) resulted to be non-S-RNases, although with a clearly distinct pattern of expression. These results reveal the importance of performing functional analysis in studies of S-RNase allelic diversity. Comparative phylogenetic analysis of six species of Solanaceae showed that N. alata S-RNases were included in eight transgeneric S-lineages. Phylogenetic pattern obtained from the inclusion of the novel S-RNase alleles confirms that N. alata represents a broad sample of the allelic variation at the S-locus of the Solanaceae.

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.

Studies of self-incompatibility in wild tomatoes: I. S-allele diversity in Solanum chilense (Dun.) Reiche [corrected] (Solanaceae)

We characterized the molecular allelic variation of RNases at the self-incompatibility (SI) locus of Solanum chilense Dun. We recovered 30 S-RNase allele sequences from 34 plants representing a broad geographic sample. This yielded a species-wide estimate of 35 (95% likelihood interval 31-40) S-alleles. We performed crosses to confirm the association with SI function of 10 of the putative S-RNase allele sequences. Results in all cases were consistent with the expectation that these sequences represent functional alleles under single-locus gametophytic SI. We used the allele sequences to conduct an analysis of selection, as measured by the excess of nonsynonymous changes per site, and found evidence for adaptive changes both within the traditionally defined hypervariable regions and downstream, near the 3'-end of the molecule.

Distribution of S-alleles in island populations of flowering cherry, Prunus lannesiana var. speciosa

We surveyed the distribution of S-alleles in natural island populations of Prunus lannesiana var. speciosa sampled from seven sites on the Izu Peninsula and six Izu islands, Japan. The S-genotypes of sampled individuals were determined by Southern analysis of RFLPs generated by restriction enzyme digestion of genomic DNA, using cDNA of the S-RNase gene as a probe. All individuals were heterozygous, as expected under gametophytic self-incompatibility (GSI). Sixty-three S-alleles were observed in the species, but 12 private to the Izu Peninsula population seemed to be derived from related species, giving a total of 75. The estimated number of S-alleles in each population ranged from 26 to 62, and was inversely correlated with the respective population's distance from the Izu Peninsula, the closest point in the mainland to the islands. This geographical cline in the estimated numbers of S-alleles suggests that gene flow to and from the distant island populations was less frequent, and that the studied species has migrated from the mainland to the Izu islands. The genetic relationship at the S-locus among populations also gave an "isolation by distance" pattern. The genetic differentiation at the S-locus among the populations was very low (F(ST) = 0.014, p < 0.001). The number of S-alleles in the species did not seem to depend on genetic differences associated with population subdivisions. This might be due to the greater effective migration rates of S-alleles, as expected under balancing selection in GSI.

Gametophytic self-incompatibility in Lycium parishii (Solanaceae): allelic diversity, genealogical structure, and patterns of molecular evolution at the S-RNase locus

We characterized allelic diversity at the locus controlling self-incompatibility (SI) for a population of Lycium parishii (Solanaceae) from Organ Pipe National Monument, Arizona. Twenty-four partial sequences of S-RNase alleles were recovered from 25 individuals. Estimates of allelic diversity range from 23 to 27 alleles and, consistent with expectations for SI, individuals are heterozygous. We compare S-RNase diversity, patterns of molecular evolution, and the genealogical structure of alleles from L. parishii to a previously studied population of its congener L. andersonii. Gametophytic SI is well characterized for Solanaceae and although balancing selection is hypothesized to be responsible for high levels of allelic divergence, the pattern of selection varies depending on the portion of the gene considered. Site-specific models investigating patterns of selection for L. parishii and L. andersonii indicate that positive selection occurs in those regions of the S-RNase gene hypothesized as important to the recognition response, whereas positive selection was not detected for any position within regions previously characterized as conserved. A 10-species genealogy including S-RNases from a pair of congeners from each of five genera in Solanaceae reveals extensive transgeneric evolution of L. parishii S-RNases. Further, within Lycium, the Dn/Ds ratios for pairs of closely related alleles for intraspecific versus interspecific comparisons were not significantly different, suggesting that the S-RNase diversity recovered in these two species was present prior to the speciation event separating them. Despite this, two S-RNases from L. parishii are identical to two previously reported alleles for L. andersonii, suggesting gene flow between these species.

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.

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.

Allelic diversity of S-RNase at the self-incompatibility locus in natural flowering cherry populations (Prunus lannesiana var. speciosa)

In the Rosaceae family, which includes Prunus, gametophytic self-incompatibility (GSI) is controlled by a single multiallelic locus (S-locus), and the S-locus product expressed in the pistils is a glycoprotein with ribonuclease activity (S-RNase). Two populations of flowering cherry (Prunus lannesiana var. speciosa), located on Hachijo Island in Japan's Izu Islands, were sampled, and S-allele diversity was surveyed based on the sequence polymorphism of S-RNase. A total of seven S-alleles were cloned and sequenced. The S-RNases of flowering cherry showed high homology to those of Prunus cultivars (P. avium and P. dulcis). In the phylogenetic tree, the S-RNases of flowering cherry and other Prunus cultivars formed a distinct group, but they did not form species-specific subgroups. The nucleotide substitution pattern in S-RNases of flowering cherry showed no excess of nonsynonymous substitutions relative to synonymous substitutions. However, the S-RNases of flowering cherry had a higher Ka/Ks ratio than those of other Prunus cultivars, and a subtle heterogeneity in the nucleotide substitution rates was observed among the Prunus species. The S-genotype of each individual was determined by Southern blotting of restriction enzyme-digested genomic DNA, using cDNA for S-RNase as a probe. A total of 22 S-alleles were identified. All individuals examined were heterozygous, as expected under GSI. The allele frequencies were, contrary to the expectation under GSI, significantly unequal. The two populations studied showed a high degree of overlap, with 18 shared alleles. However, the allele frequencies differed considerably between the two populations.

Effects of inbreeding on the genetic diversity of populations

The study of variability within species is important to all biologists who use genetic markers. Since the discovery of molecular variability among normal individuals, data have been collected from a wide range of organisms, and it is important to understand the major factors affecting diversity levels and patterns. Comparisons of inbreeding and outcrossing populations can contribute to this understanding, and therefore studying plant populations is important, because related species often have different breeding systems. DNA sequence data are now starting to become available from suitable plant and animal populations, to measure and compare variability levels and test predictions.

The population genetics of sporophytic self-incompatibility in Senecio squalidus L. (Asteraceae) I: S allele diversity in a natural population

Twenty-six individuals of the sporophytic self-incompatible (SSI) weed, Senecio squalidus were crossed in a full diallel to determine the number and frequency of S alleles in an Oxford population. Incompatibility phenotypes were determined by fruit-set results and the mating patterns observed fitted a SSI model that allowed us to identify six S alleles. Standard population S allele number estimators were modified to deal with S allele data from a species with SSI. These modified estimators predicted a total number of approximately six S alleles for the entire Oxford population of S. squalidus. This estimate of S allele number is low compared to other estimates of S allele diversity in species with SSI. Low S allele diversity in S. squalidus is expected to have arisen as a consequence of a disturbed population history since its introduction and subsequent colonisation of the British Isles. Other features of the SSI system in S. squalidus were also investigated: (a) the strength of self-incompatibility response; (b) the nature of S allele dominance interactions; and (c) the relative frequencies of S phenotypes. These are discussed in view of the low S allele diversity estimates and the known population history of S. squalidus.

S-allele diversity in Sorbus aucuparia and Crataegus monogyna (Rosaceae: Maloideae)

RT-PCR was used to obtain the first estimates from natural populations of allelic diversity at the RNase-based gametophytic self-incompatibility locus in the Rosaceae. A total of 20 alleles were retrieved from 20 Sorbus aucuparia individuals, whereas 17 alleles were found in 13 Crataegus monogyna samples. Estimates of population-level allele numbers fall within the range observed in the Solanaceae, the only other family with RNase-based incompatibility for which estimates are available. The nucleotide diversity of S-allele sequences was found to be much lower in the two Rosaceae species as compared with the Solanaceae. This was not due to a lower sequence divergence among most closely related alleles. Rather, it is the depth of the entire genealogy that differs markedly in the two families, with Rosaceae S-alleles exhibiting more recent apparent coalescence. We also investigated patterns of selection at the molecular level by comparing nucleotide diversity at synonymous and nonsynonymous sites. Stabilizing selection was inferred for the 5' region of the molecule, while evidence of diversifying selection was present elsewhere.

Recombination, balancing selection and phylogenies in MHC and self-incompatibility genes

Using a coalescent model of multiallelic balancing selection with recombination, the genealogical process as a function of recombinational distance from a site under selection is investigated. We find that the shape of the phylogenetic tree is independent of the distance to the site under selection. Only the timescale changes from the value predicted by Takahata's allelic genealogy at the site under selection, converging with increasing recombination to the timescale of the neutral coalescent. However, if nucleotide sequences are simulated over a recombining region containing a site under balancing selection, a phylogenetic tree constructed while ignoring such recombination is strongly affected. This is true even for small rates of recombination. Published studies of multiallelic balancing selection, i.e., the major histocompatibility complex (MHC) of vertebrates, gametophytic and sporophytic self-incompatibility of plants, and incompatibility of fungi, all observe allelic genealogies with unexpected shapes. We conclude that small absolute levels of recombination are compatible with these observed distortions of the shape of the allelic genealogy, suggesting a possible cause of these observations. Furthermore, we illustrate that the variance in the coalescent with recombination process makes it difficult to locate sites under selection and to estimate the selection coefficient from levels of variability.

Consequences of population structure on genes under balancing selection

This paper describes a new approach to modeling population structure for genes under strong balancing selection of the type seen in plant self-incompatibility systems and the major histocompatibility complex (MHC) system of vertebrates. Simple analytic solutions for the number of alleles maintained at equilibrium and the expected proportion of alleles shared between demes at various levels are derived and checked against simulation results. The theory accurately captures the dynamics of allele number in a subdivided population and identifies important values of m (migration rate) at which allele number and distribution change qualitatively. Starting from a panmictic population, as migration among demes decreases a qualitative change in dynamics is seen at approximately m(crit) approximately equal to the square root of(s/4piNT) where NT is the total population size and s is a measure of the strength of selection. At this point, demes can no longer maintain their panmictic allele number, due to increasing isolation from the total population. Another qualitative change occurs at a migration rate on the same order of magnitude as the mutation rate, mu. At this point, the demes are highly differentiated for allele complement, and the total number of alleles in the population is increased. Because in general u << m<(crit) at intermediate migration rates slightly fewer alleles may be maintained in the total population than are maintained at panmixia. Within this range, total allele number may not be the best indicator of whether a population is effectively panmictic, and some caution should be used when interpreting samples from such populations. The theory presented here can help to analyze data from genes under balancing selection in subdivided populations.

Roles of lineage sorting and phylogenetic relationship in the genetic diversity at the self-incompatibility locus of Solanaceae

Allelic polymorphism at the S locus that determines the gametophytic self-incompatibility (GSI) system in the pistil predates speciation. Understanding the evolution of a GSI system therefore requires knowledge of how lineage sorting and interspecific phylogenetic relationship affect S allele polymorphism. In searching for patterns of lineage sorting among species of various phylogenetic relationships, 22 S-alleles from 34 genets randomly taken at three Tennessee sites from a newly known GSI species Physalis longifolia were sequenced. Analyses of these data along with the previous sequences of three solanaceous species indicate that much of the combined allelic genealogy may be explained by lineage sorting and phylogenetic relationship. Using the mean terminal branch lengths of trans-specific alleles on the allelic genealogy to infer phylogenetic relationship among species, P. longifolia was found to be more closely related to P. cinerascens than to P. crassifolia. Nonetheless, the distribution of terminal branch lengths of P. longifolia was more similar to that of P. crassifolia than to that of P. cinerascens, suggesting phylogenetic relationship may have little effect on species-specific polymorphism. Similar habitat and growth characters, yet contrasting S-polymorphism, between P. longifolia and P. cinerascens also reject previous hypotheses that habitat and growth characters are the major factors responsible for interspecific differences in S-polymorphism. A likely scenario is that species-specific S-polymorphism is based on lineage sorting whose effect is further modified by species age and historical changes in population parameters.

Evidence that intragenic recombination contributes to allelic diversity of the S-RNase gene at the self-incompatibility (S) locus in Petunia inflata

For Solanaceae type self-incompatibility, discrimination between self and nonself pollen by the pistil is controlled by the highly polymorphic S-RNase gene. To date, the mechanism generating the allelic diversity of this gene is largely unknown. Natural populations offer a good opportunity to address this question because they likely contain different alleles that share recent common progenitors. We identified 19 S haplotypes from a natural population of Petunia inflata in Argentina, used reverse transcriptase-polymerase chain reaction to obtain cDNAs for 15 alleles of the S-RNase gene, and sequenced all the cDNAs. Phylogenetic studies revealed that five of these alleles and two previously identified alleles form a major clade, and that the 5' region of S(19) allele was derived from an ancestor allele closely related to S(2), whereas its 3' region was derived from an ancestor allele closely related to S(8). A similar evolutionary relationship was found among S(3), S(12), and S(15) alleles. These findings suggest that intragenic recombination contributed to the generation of the allelic diversity of the S-RNase gene. Two additional findings emerged from the sequence comparisons. First, the nucleotide sequence of the S(1) allele identified in this work is completely identical to that of the previously identified S(1) allele of a different origin. Second, in the two hypervariable regions HVa and HVb, thought to be involved in determining S allele specificity, S(6) and S(9) alleles differ only by four nucleotides, all in HVb, resulting in two amino acid differences. The implications of these findings are discussed.

Cellular and molecular mechanisms of sexual incompatibility in plants and fungi

Plants and fungi show an astonishing diversity of mechanisms to promote outbreeding, the most widespread of which is sexual incompatibility. Sexual incompatibility involves molecular recognition between mating partners. In fungi and algae, highly polymorphic mating-type loci mediate mating through complementary interactions between molecules encoded or regulated by different mating-type haplotypes, whereas in flowering plants polymorphic self-incompatibility loci regulate mate recognition through oppositional interactions between molecules encoded by the same self-incompatibility haplotypes. This subtle mechanistic difference is a consequence of the different life cycles of fungi, algae, and flowering plants. Recent molecular and biochemical studies have provided fascinating insights into the mechanisms of mate recognition and are beginning to shed light on evolution and population genetics of these extraordinarily polymorphic genetic systems of incompatibility.

Self-incompatibility alleles from Physalis: implications for historical inference from balanced genetic polymorphisms

Balanced genetic polymorphism has been proposed as a source from which to infer population history complementary to that of neutral genetic polymorphism, because genetic polymorphism maintained by balancing selection permits inferences about population size over much longer spans of time. However, empirical data for both S genes and major histocompatibility complex genes do not fit expectations of coalescent theory. Species-specific gene genealogies have longer terminal branches than expected, indicating an apparent slowdown in the origination of new alleles. Here, we present evidence that divergent S alleles were selectively maintained in Physalis cinerascens during a reduction in population size, generating longer terminal branches in the S gene genealogy relative to the congener Physalis crassifolia. Retention of divergent alleles during reduction in the number of alleles violates assumptions of the coalescent model used to estimate effective population size. Recent theoretical and empirical results are consistent with the proposition that nonrandom sorting is a general property of balanced genetic polymorphisms, suggesting that studies of balanced polymorphism that infer the absence of population bottlenecks may overestimate effective population size.

Allelic genealogies in sporophytic self-incompatibility systems in plants

Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed.

The number of self-incompatibility alleles in a finite, subdivided population

The actual and effective number of gametophytic self-incompatibility alleles maintained at mutation-drift-selection equilibrium in a finite population subdivided as in the island model is investigated by stochastic simulations. The existing theory founded by Wright predicts that for a given population size the number of alleles maintained increases monotonically with decreasing migration as is the case for neutral alleles. The simulation results here show that this is not true. At migration rates above Nm = 0.01-0.1, the actual and effective number of alleles is lower than for an undivided population with the same number of individuals, and, contrary to Wright's theoretical expectation, the number of alleles is not much higher than for an undivided population unless Nm < 0.001. The same pattern is observed in a model where the alleles display symmetrical overdominant selection. This broadens the applicability of the results to include proposed models for the major histocompatibility (MHC) loci. For a subdivided population over a large range of migration rates, it appears that the number of self-incompatibility alleles (or MHC-alleles) observed can provide a rough estimate of the total number of individuals in the population but it underestimates the neutral effective size of the subdivided population.