Allelic diversity and gene genealogy at the self-incompatibility locus in the Solanaceae

Evidence for rare recombination at the gametophytic self-incompatibility locus

The gametophytic self-incompatibility locus has been thought to be a nonrecombining genomic region. Inferences have been made, however, about the functional importance of different parts of the S-locus, based on differences in the levels of variability along the gene, and this is valid only if recombination occurs. It is thus important to test whether recombination occurs within and near the S-locus. Several recent attempts to test this have reached conflicting conclusions. In this study, we examine a large data set on sequence variation at the S-locus in several species with gametophytic self-incompatibility systems, in the Solanaceae, Rosaceae and Scrophulariaceae. We use the longest sequences available to test for recombination based on linkage disequilibrium between polymorphic sites in the S-locus. The relationship between linkage disequilibrium and physical distance between the sites suggests rare intragenic exchange in the evolutionary history of four species of Solanaceae and two species of Rosaceae.

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.

The transition to gender dimorphism on an evolutionary background of self-incompatibility: an example from Lycium (Solanaceae)

Populations of three North American species of Lycium (Solanaceae) are morphologically gynodioecious and consist of male-sterile (i.e., female) and hermaphroditic plants. Marked individuals were consistent in sexual expression across years and male sterility was present throughout much of the species' ranges. Controlled pollinations reveal that L. californicum, L. exsertum, and L. fremontii are functionally dioecious. Fruit production in females ranged from 36 to 63%, whereas hermaphrodites functioned essentially as males. Though hermaphrodites were mostly male, investigation of pollen tube growth reveals that hermaphrodites of all dimorphic species were self-compatible. Self-fertilization and consequent inbreeding depression are commonly invoked as important selective forces promoting the invasion of male-sterile mutants into cosexual populations. A corollary prediction of these models is that gender dimorphism evolves from self-compatible ancestors. However, fruit production, seed production, and pollen tube number following outcross pollination were significantly higher than following self-pollination for three diploid, cosexual species that are closely related to the dimorphic species. The data presented here on incompatibility systems are consistent with the hypothesis that polyploidy disrupted the self-incompatibility system in the gynodioecious species leading to the evolution of gender dimorphism.

Ancient mitochondrial haplotypes and evidence for intragenic recombination in a gynodioecious plant

Because of their extremely low nucleotide mutation rates, plant mitochondrial genes are generally not expected to show variation within species. Remarkably, we found nine distinct cytochrome b sequence haplotypes in the gynodioecious alpine plant Silene acaulis, with two or more haplotypes coexisting locally in each of three sampled regions. Moreover, there is evidence for intragenic recombination in the history of the haplotype sample, implying at least transient heteroplasmy of mitochondrial DNA (mtDNA). Heteroplasmy might be achieved by one of two potential mechanisms, either continuous coexistence of subgenomic fragments in low stoichiometry, or occasional paternal leakage of mtDNA. On the basis of levels of synonymous nucleotide substitutions, the average divergence time between haplotypes is estimated to be at least 15 million years. Ancient coalescence of extant haplotypes is further indicated by the paucity of fixed differences in haplotypes obtained from related species, a pattern expected under trans-specific evolution. Our data are consistent with models of frequency-dependent selection on linked cytoplasmic male-sterility factors, the putative molecular basis of females in gynodioecious populations. However, associations between marker loci and the inferred male-sterility genes can be maintained only with very low rates of recombination. Heteroplasmy and recombination between divergent haplotypes imply unexplored consequences for the evolutionary dynamics of gynodioecy, a widespread plant breeding system.

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.

Plant molecular diversity and applications to genomics

Surveys of nucleotide diversity are beginning to show how genomes have been shaped by evolution. Nucleotide diversity is also being used to discover the function of genes through the mapping of quantitative trait loci (QTL) in structured populations, the positional cloning of strong QTL, and association mapping.

Molecular mechanisms underlying the breakdown of gametophytic self-incompatibility

The breakdown of self-incompatibility has occurred repeatedly throughout the evolution of flowering plants and has profound impacts on the genetic structure of populations. Recent advances in understanding of the molecular basis of self-incompatibility have provided insights into the mechanisms of its loss in natural populations, especially in the tomato family, the Solanaceae. In the Solanaceae, the gene that controls self-incompatibility in the style codes for a ribonuclease that causes the degradation of RNA in pollen tubes bearing an allele at the S-locus that matches either of the two alleles held by the maternal plant. The pollen component of the S-locus has yet to be identified. Loss of self-incompatibility can be attributed to three types of causes: duplication of the S-locus, mutations that cause loss of S-RNase activity, and mutations that do not cause loss of S-RNase activity. Duplication of the S-locus has been well studied in radiation-induced mutants but may be a relatively rare cause of the breakdown of self-incompatibility in nature. Point mutations within the S-locus that disrupt the production of S-RNase have been documented in natural populations. There are also a number of mutants in which S-RNase production is unimpaired, yet self-incompatibility is disrupted. The identity and function of these mutations is not well understood. Careful work on a handful of model organisms will enable population biologists to better understand the breakdown of self-incompatibility in nature.

Molecular variation at the self-incompatibility locus in natural populations of the genera Antirrhinum and Misopates

The self-incompatibility system of flowering plants is a classic example of extreme allelic polymorphism maintained by frequency-dependent selection. We used primers designed from three published Antirrhinum hispanicum S-allele sequences in PCR reactions with genomic DNA of plants sampled from natural populations of Antirrhinum and Misopates species. Not surprisingly, given the polymorphism of S-alleles, only a minority of individuals yielded PCR products of the expected size. These yielded 35 genomic sequences, of nine different sequence types of which eight are highly similar to the A. hispanicum S-allele sequences, and one to a very similar unpublished Antirrhinum S-like RNase sequence. The sequence types are well separated from the S-RNase sequences from Solanaceae and Rosaceae, and also from most known "S-like" RNase sequences (which encode proteins not involved in self-incompatibility). An association with incompatibility types has so far been established for only one of the putative S-alleles, but we describe evidence that the other sequences are also S-alleles. Variability in these sequences follows the pattern of conserved and hypervariable regions seen in other S-RNases, but no regions have higher replacement than silent diversity, unlike the results in some other species.

Recognition specificity of self-incompatibility maintained after the divergence of Brassica oleracea and Brassica rapa

The determinants of recognition specificity of self-incompatibility in Brassica are SRK in the stigma and SP11/SCR in the pollen, respectively. In the pair of S haplotypes BrS46 (S46 in B. rapa) and BoS7 (S7 in B. oleracea), which have highly similar SRK alleles, the SP11 alleles were found to be similar, with 96.1% identity in the deduced amino acid sequence. Two other pairs of S haplotypes, BrS47 and BoS12, and BrS8 and BoS32, having highly similar SRK and SP11 alleles between the two species were also found. The haplotypes in each pair are considered to have been derived from a single S haplotype in the ancestral species. The allotetraploid produced by interspecific hybridization between homozygotes of BrS46 and BoS15 showed incompatibility with a BoS7 homozygote and compatibility with other B. oleracea S haplotypes in reciprocal crossings. This result indicates that BrS46 and BoS7 have maintained the same recognition specificity after the divergence of the two species and that amino acid substitutions found in such cases in both SRK alleles and SP11 alleles do not alter the recognition specificity. DNA blot analysis of SRK, SP11, SLG and other S-locus genes showed different DNA fragment sizes between the interspecific pairs of S haplotypes. A much lower level of sequence similarity was observed outside the genes of SRK and SP11 between BrS46 and BoS7. These results suggest that the DNA sequences of the regions intervening between the S-locus genes were diversified after or at the time of speciation. This is the first report demonstrating the presence of common S haplotypes in different plant species and presenting definite evidence of the trans-specific evolution of self-incompatibility genes.

MHC class II beta sequence diversity in the deer mouse (Peromyscus maniculatus): implications for models of balancing selection

We studied population polymorphism at a major histocompatibility complex (MHC) class II beta gene in the deer mouse (Peromyscus maniculatus). We found that: (i) a single population of P. maniculatus has significantly higher levels of DNA and protein sequence diversity than worldwide samples from homologous genes in other taxa, including humans and mice; and (ii) the genealogy of allelic sequences in P. maniculatus deviates significantly from theoretical expectation under a model of symmetric balancing selection, in that alleles are relatively more divergent than expected. We suggest that the observation of high levels of pairwise allelic sequence divergence and deviation of the genealogy from theoretical expectation in P. maniculatus together provide support for a divergent allele advantage model for the maintenance of MHC polymorphism.

Fine scale mapping in the sex locus region of the honey bee (Apis mellifera)

Isolating an unknown gene with fine-scale mapping is possible in a "non-model" organism. Sex determination in honey bees consists of a single locus (sex locus) with several complementary alleles. Diploid females are heterozygous at the sex locus, whereas haploid males arise from unfertilized eggs and are hemizygous. The construction of specific inbred crosses facilitates fine scale mapping in the sex locus region of the honey bee. The high recombination rate in the honey bee reduces the physical distance between markers compared with model organisms and facilitates a novel gene isolation strategy based on step-wise creation of new markers within small physical distances. We show that distances less than 25 kb can be efficiently mapped with a mapping population of only 1000 individuals. The procedure described here will accelerate the mapping, analysis and isolation of honey bee genes.

Accelerated regulatory gene evolution in an adaptive radiation

The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations. We have isolated homologues to the Arabidopsis APETALA3 (ASAP3/TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL A/B BINDING PROTEIN9 (ASCAB9) photosynthetic structural gene from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. We have compared rates of regulatory and structural gene evolution in the Hawaiian species to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases in nonsynonymous relative to synonymous nucleotide substitution rates in the ASAP3/TM6 and ASAP1 regulatory genes in the rapidly evolving Hawaiian species. By contrast, no general increase is evident in neutral mutation rates for these loci in the Hawaiian species. An increase in nonsynonymous relative to synonymous nucleotide substitution rate is also evident in the ASCAB9 structural gene in the Hawaiian species, but not to the extent displayed in the regulatory loci. The significantly accelerated rates of regulatory gene evolution in the Hawaiian species may reflect the influence of allopolyploidy or of selection and adaptive divergence. The analyses suggest that accelerated rates of regulatory gene evolution may accompany rapid morphological diversification in adaptive radiations.

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.

Gene families from the Arabidopsis thaliana pollen coat proteome

The pollen extracellular matrix contains proteins mediating species specificity and components needed for efficient pollination. We identified all proteins >10 kilodaltons in the Arabidopsis pollen coating and showed that most of the corresponding genes reside in two genomic clusters. One cluster encodes six lipases, whereas the other contains six lipid-binding oleosin genes, including GRP17, a gene that promotes efficient pollination. Individual oleosins exhibit extensive divergence between ecotypes, but the entire cluster remains intact. Analysis of the syntenic region in Brassica oleracea revealed even greater divergence, but a similar clustering of the genes. Such allelic flexibility may promote speciation in plants.

The use of intraallelic variability for testing neutrality and estimating population growth rate

To better understand the forces affecting individual alleles, we introduce a method for finding the joint distribution of the frequency of a neutral allele and the extent of variability at closely linked marker loci (the intraallelic variability). We model three types of intraallelic variability: (a) the number of nonrecombinants at a linked biallelic marker locus, (b) the length of a conserved haplotype, and (c) the number of mutations at a linked marker locus. If the population growth rate is known, the joint distribution provides the basis for a test of neutrality by testing whether the observed level of intraallelic variability is consistent with the observed allele frequency. If the population growth rate is unknown but neutrality can be assumed, the joint distribution provides the likelihood of the growth rate and leads to a maximum-likelihood estimate. We apply the method to data from published data sets for four loci in humans. We conclude that the Delta32 allele at CCR5 and a disease-associated allele at MLH1 arose recently and have been subject to strong selection. Alleles at PAH appear to be neutral and we estimate the recent growth rate of the European population to be approximately 0.027 per generation with a support interval of (0.017-0.037). Four of the relatively common alleles at CFTR also appear to be neutral but DeltaF508 appears to be significantly advantageous to heterozygous carriers.

Identification and characterization of a polymorphic receptor kinase gene linked to the self-incompatibility locus of Arabidopsis lyrata

We study the segregation of variants of a putative self-incompatibility gene in Arabidopsis lyrata. This gene encodes a sequence that is homologous to the protein encoded by the SRK gene involved in self-incompatibility in Brassica species. We show by diallel pollinations of plants in several full-sib families that seven different sequences of the gene in A. lyrata are linked to different S-alleles, and segregation analysis in further sibships shows that four other sequences behave as allelic to these. The family data on incompatibility provide evidence for dominance classes among the S-alleles, as expected for a sporophytic SI system. We observe no division into pollen-dominant and pollen-recessive classes of alleles as has been found in Brassica, but our alleles fall into at least three dominance classes in both pollen and stigma expression. The diversity among sequences of the A. lyrata putative S-alleles is greater than among the published Brassica SRK sequences, and, unlike Brassica, the alleles do not cluster into groups with similar dominance.

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.

Evolution of balanced genetic polymorphism

Extreme genetic polymorphism maintained by balancing selection (so called because many alleles are maintained in a balance by a mechanism of rare allele advantage) is intimately associated with the important task of self/non-self-discrimination. Widely disparate self-recognition systems of plants, animals and fungi share several general features, including the maintenance of large numbers of alleles at relatively even frequency, and persistence of this variation over very long time periods. Because the evolutionary dynamics of balanced polymorphism are very different from those of neutral genetic variation, data on balanced polymorphism have been used as a novel source for inference of the history of populations. This review highlights the unique evolutionary properties of balanced genetic polymorphism, and the use of theoretical understanding in analysis and application of empirical data for inference of population history. However, a second goal of this review is to point out where current theory is incomplete. Recent observations suggest that entirely novel selective forces may act in concert with balancing selection, and these novel forces may be extremely potent in shaping genetic variation at self-recognition loci.

Polyploidy and the evolution of gender dimorphism in plants

Gender dimorphism and polyploidy are important evolutionary transitions that have evolved repeatedly in many plant families. We show that gender dimorphism in North American Lycium (Solanaceae) has evolved in polyploid, self-compatible taxa whose closest relatives are cosexual, self-incompatible diploids. This has occurred independently in South African Lycium. We present additional evidence for this pathway to gender dimorphism from 12 genera involving at least 20 independent evolutionary events. We propose that polyploidy is a trigger of unrecognized importance for the evolution of gender dimorphism, which operates by disrupting self-incompatibility and leading to inbreeding depression. Subsequently, male sterile mutants invade and increase because they are unable to inbreed.

DNA polymorphism, haplotype structure and balancing selection in the Leavenworthia PgiC locus

A study of DNA polymorphism and divergence was conducted for the cytosolic phosphoglucose isomerase (PGI:E.C.5.3.1.9) gene of five species of the mustard genus Leavenworthia: Leavenworthia stylosa, L. alabamica, L. crassa, L. uniflora, and L. torulosa. Sequences of an internal 2.3-kb PgiC gene region spanning exons 6-16 were obtained from 14 L. stylosa plants from two natural populations and from one to several plants for each of the other species. The level of nucleotide polymorphism in L. stylosa PgiC gene was quite high (pi = 0.051, theta = 0.052). Although recombination is estimated to be high in this locus, extensive haplotype structure was observed for the entire 2.3-kb region. The L. stylosa sequences fall into at least two groups, distinguished by the presence of several indels and nucleotide substitutions, and one of the three charge change nucleotide replacements within the region sequenced correlates with the haplotypes. The differences between the haplotypes are older than between the species, and the haplotypes are still segregating in at least two of five species studied. There is no evidence of recent or ancient population subdivision that could maintain distinct haplotypes. The age of the haplotypes and the results of Kelly's Z(nS) and Wall's B and Q tests with recombination suggest that the haplotypes are maintained due to balancing selection at or near this locus.

All males are not created equal: fertility differences depend on gamete recognition polymorphisms in sea urchins

Behaviors, morphologies, and genetic loci directly involved in reproduction have been increasingly shown to be polymorphic within populations. Explaining how such variants are maintained by selection is crucial to understanding the genetic basis of fertility differences, but direct tests of how alleles at reproductive loci affect fertility are rare. In the sea urchin genus Echinometra, the protein bindin mediates sperm attachment to eggs, evolves quickly, and is polymorphic within species. Eggs exposed to experimental sperm mixtures show strong discrimination on the basis of the males' bindin genotype. Different females produce eggs that nonrandomly select sperm from different males, showing that variable egg-sperm interactions determine fertility. Eggs select sperm with a bindin genotype similar to their own, suggesting strong linkage between female choice and male trait loci. These experiments demonstrate that alleles at a single locus can have a strong effect on fertilization and that reproductive loci may retain functional polymorphisms through epistatic interactions between male and female traits. They also suggest that positive selection at gamete recognition loci like bindin involves strong selection within species on mate choice interactions.

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.

The signature of balancing selection: fungal mating compatibility gene evolution

A key problem in evolutionary biology has been distinguishing the contributions of current and historical processes to the maintenance of genetic variation. Because alleles at self-recognition genes are under balancing selection, they exhibit extended residence times in populations and thus may provide unique insight into population demographic history. However, evidence for balancing selection and extended residence times has almost exclusively depended on identification of transspecific polymorphisms; polymorphisms retained in populations through speciation events. We present a broadly applicable approach for detecting balancing selection and apply it to the b1 mating type gene in the mushroom fungus Coprinus cinereus. The comparison of neutral molecular variation within and between allelic classes was used to directly estimate the strength of balancing selection. Different allelic classes are defined as encoding different mating compatibility types and are thus potentially subject to balancing selection. Variation within an allelic class, where all alleles have the same mating compatibility type, provided an internal standard of neutral evolution. Mating compatibility in this organism is determined by the complex A mating type locus, and b1 is one of several redundantly functioning genes. Consequently, we conducted numerical simulations of a model with two subloci and varying levels of recombination to show that balancing selection should operate at each sublocus. Empirical data show that strong balancing selection has indeed occurred at the b1 locus. The widespread geographic distribution of identical b1 alleles suggests that their association with differing A mating types is the result of recent recombination events.

KIN INTERACTIONS IN A COLONIAL HYDROZOAN (HYDRACTINIA SYMBIOLONGICARPUS): POPULATION STRUCTURE ON A MOBILE LANDSCAPE

Many sessile colonial organisms intensively compete with conspecifics for growing space. This competition can result in either cooperative fusion or aggressive rejection between colonies, and some species have evolved highly polymorphic genetic systems that mediate the outcome of these interactions. Here we demonstrate the potential for interactions among close kin as the basis for the evolutionary maintenance of a genetically polymorphic allorecognition system in the colonial hydroid Hydractinia symbiolongicarpus, which lives on gastropod shells occupied by hermit crabs. Fusion between hydroids in the laboratory is restricted mainly to encounters between full siblings, whereas other encounters result in aggressive rejection. Natural selection acting on the costs or benefits of fusion between colonies could be responsible for the present maintenance of such a highly specific behavioral response, but only if encounters between fusible colonies still occur in contemporary populations. The large size of these hydroid populations and the mobility of the crabs should limit the potential for interactions among closely related hydroids on the same shell. However, RAPD polymorphisms among a large sample of hydroids from a population off the coast of Massachusetts indicate that genetically similar colonies are often found together on the same shell. Some genetic distances between colonies on the same shell were low relative to genetic distances between colonies on different shells or genetic distances between known full siblings from laboratory matings. We conservatively estimate that 2-18% of co-occurring colonies may be full sibling pairs. These observations suggest that encounters between genetically similar hydroids are common, despite the mobile nature of their habitat, and these encounters may provide frequent opportunities for natural selection to influence the evolution of cooperative and agonistic behaviors and their polymorphic genetic basis.

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.

Nonsynonymous substitution in abalone sperm fertilization genes exceeds substitution in introns and mitochondrial DNA

Strong positive Darwinian selection acts on two sperm fertilization proteins, lysin and 18-kDa protein, from abalone (Haliotis). To understand the phylogenetic context for this dramatic molecular evolution, we obtained sequences of mitochondrial cytochrome c oxidase subunit I (mtCOI), and genomic sequences of lysin, 18-kDa, and a G protein subunit. Based on mtDNA differentiation, four north Pacific abalone species diverged within the past 2 million years (Myr), and remaining north Pacific species diverged over a period of 4-20 Myr. Between-species nonsynonymous differences in lysin and 18-kDa exons exceed nucleotide differences in introns by 3.5- to 24-fold. Remarkably, in some comparisons nonsynonymous substitutions in lysin and 18-kDa genes exceed synonymous substitutions in mtCOI. Lysin and 18-kDa intron/exon segments were sequenced from multiple red abalone individuals collected over a 1,200-km range. Only two nucleotide changes and two sites of slippage variation were detected in a total of >29,000 nucleotides surveyed. However, polymorphism in mtCOI and a G protein intron was found in this species. This finding suggests that positive selection swept one lysin allele and one 18-kDa allele to fixation. Similarities between mtCOI and lysin gene trees indicate that rapid adaptive evolution of lysin has occurred consistently through the history of the group. Comparisons with mtCOI molecular clock calibrations suggest that nonsynonymous substitutions accumulate 2-50 times faster in lysin and 18-kDa genes than in rapidly evolving mammalian genes.

Flowering plant self-incompatibility: the molecular population genetics of Brassica S-loci

Self-incompatibility systems in different angiosperm families are reviewed, and the evidence that incompatibility has arisen several times is outlined. New data on the sequence polymorphism of self-incompatibility loci from two different angiosperm families are compared with results from other highly polymorphic loci, particularly MHC loci. We discuss what molecular genetic analyses of these sequences can tell us about the nature and maintenance of the polymorphism at self-incompatibility loci. We suggest that there is evidence for recombination at the Brassica self-incompatibility loci, so that it may be possible to discern regions that are particularly functionally important in the recognition reaction, even though the long-term maintenance of polymorphisms in these amino acid residues has caused the evolution of many other sequence differences between alleles.

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.

Characterization of the flanking regions of the S-RNase genes of Japanese pear (Pyrus serotina) and apple (Malus x domestica)

Genomic sequences of the self-incompatibility genes, the S-RNase genes, from two rosaceous species, Japanese pear and apple, were characterized. Genomic Southern blot and sequencing of a 4.5-kb genomic clone showed that the S4-RNase gene of Japanese pear is surrounded by repetitive sequences as in the case of the S-RNase genes of solanaceous species. The flanking regions of the S2- and Sf-RNase genes of apple were also cloned and sequenced. The 5' flanking regions of the three alleles bore no similarity with those of the solanaceous S-RNase genes, although the position and sequence of the putative TATA box were conserved. The putative promoter regions of the Japanese pear S4- and apple Sf-RNase genes shared a stretch of about 200bp with 80% sequence identity. However, this sequence was not present in the S2-RNase gene of apple, and thus it may reflect a close relationship between the S4- and Sf-RNase genes rather than a cis-element important in regulating gene expression. Despite the uniform pattern of expression of the rosaceous S-RNase genes, sequence motifs conserved in the 5' flanking regions of the three alleles were not found, implying that the cis-element controlling pistil specific gene expression also locates at the intragenic region or upstream of the analyzed promoter region.

Molecular genetic basis of adaptive selection: examples from color vision in vertebrates

A central unanswered question in phototransduction is how photosensitive molecules, visual pigments, regulate their absorption spectra. In nature, there exist various types of visual pigments that are adapted to diverse photic environments. To elucidate the molecular mechanisms involved in the adaptive selection of these pigments, we have to identify amino acid changes of pigments that are potentially important in changing the wavelength of maximal absorption (lambda max) and then determine the effects of these mutations on the shift in lambda max. The desired mutants can be constructed using site-directed mutagenesis, expressed in tissue culture cells, and the functional effect of virtually any such mutant can be rigorously determined. The availability of these cell/molecular methods makes vision an ideal model system in studying adaptive mechanisms at the molecular level. The identification of potentially important amino acid changes using evolutionary biological means is an indispensable step in elucidating the molecular mechanisms that underlie the spectral tuning of visual pigments.

Variation at the b Mating Type Locus of Ustilago maydis

ABSTRACT Population level diversity at the Ustilago maydis b mating type locus was determined in samples from four Minnesota locations using a combination of plate mating techniques and a polymerase chain reaction (PCR)-based assay. The PCR method allows rapid identification of b types from samples of natural populations and utilizes the hypervariable regions of the b locus that determine mating type specificity. Results demonstrated high levels of b diversity within populations, with one population yielding 17 of the total 18 b types found in the study. Pairwise G(ST) values were in the range of 0.02 to 0.05, and common b mating types were found across broad geographic distances. These data demonstrated that very low levels of differentiation among U. maydis populations occur with respect to b locus variation. Consistent with frequency-dependent selection models, b types were represented at approximately equal frequencies within the entire Minnesota population. However, neutral evolutionary models for patterns of geographic distribution and variation at b cannot be entirely excluded. The importance to agricultural practices of understanding population genetic processes is discussed.

Insights into the evolutionary process from patterns of DNA sequence variability

Studies of DNA sequence diversity, particularly in Drosophila, reveal both the complexity of natural selection and the importance of the interaction of natural selection and variation in rates of recombination within genomes and between species in determining levels of sequence variability in different genes and different species. The impact of both adaptive and deleterious mutations are evident. Extension of these types of studies to other organisms has begun in earnest.

Neutral behavior of shared polymorphism

Several cases have been described in the literature where genetic polymorphism appears to be shared between a pair of species. Here we examine the distribution of times to random loss of shared polymorphism in the context of the neutral Wright-Fisher model. Order statistics are used to obtain the distribution of times to loss of a shared polymorphism based on Kimura's solution to the diffusion approximation of the Wright-Fisher model. In a single species, the expected absorption time for a neutral allele having an initial allele frequency of 1/2 is 2.77 N generations. If two species initially share a polymorphism, that shared polymorphism is lost as soon as either of two species undergoes fixation. The loss of a shared polymorphism thus occurs sooner than loss of polymorphism in a single species and has an expected time of 1.7 N generations. Molecular sequences of genes with shared polymorphism may be characterized by the count of the number of sites that segregate in both species for the same nucleotides (or amino acids). The distribution of the expected numbers of these shared polymorphic sites also is obtained. Shared polymorphism appears to be more likely at genetic loci that have an unusually large number of segregating alleles, and the neutral coalescent proves to be very useful in determining the probability of shared allelic lineages expected by chance. These results are related to examples of shared polymorphism in the literature.

Primary structures of two ribonucleases from ginseng calluses. New members of the PR-10 family of intracellular pathogenesis-related plant proteins

The amino acid sequences of two ribonucleases from a callus cell culture of Panax ginseng were determined. The two sequences differ at 26% of the amino acid positions. Homology was found with a large family of intracellular pathogenesis-related proteins, food allergens and tree pollen allergens from both dicotyledonous and monocotyledonous plant species. There is about 30% sequence difference with proteins from species belonging to the same plant order (Apiales: parsley and celery), 60% with those from four other dicotyledonous plant orders and about 70% from that of the monocotyledonous asparagus. More thorough evolutionary analyses of sequences lead to the conclusion that the general biological function of members of this protein family may be closely related to the ability to cleave intracellular RNA and that they have an important role in cell metabolism. As the three-dimensional structure of one of the members of this protein family has been determined recently [Gajhede et al., Nature Struct Biol 3 (1996) 1040-1045], it may be possible to assign active-site residues in the enzyme molecule and make hypotheses about its mode of action. Structural features in addition to the cellular site of biosynthesis indicate that this family of ribonucleases is very different from previously investigated ones.

Seeing selection in S allele sequences

New data on allelic sequence diversity in natural populations provide evidence for natural selection acting on the self-incompatibility loci of two plant species; there are interesting parallels with, and differences from, other polymorphic systems such as mammalian MHC loci.

Neutral theory of molecular evolution

DNA sequence data are generally interpreted as favouring Kimura's neutral theory but not without dissent and often with a great deal of controversy with respect to molecular clocks, DNA polymorphism, adaptive evolution, and gene genealogy. Although the theory serves as a guiding principle, many issues concerning mutation, recombination, and selection remain unsettled. Of particular importance is the need for more knowledge about the function and structure of molecules.