Self-incompatibility (SI) is a genetic system found in some hermaphrodite plants. Recognition of pollen by pistils expressing cognate specificities at two linked genes leads to rejection of self pollen and pollen from close relatives, i.e., to avoidance of selffertilization and inbred matings, and thus increased outcrossing. These genes generally have many alleles, yet the conditions allowing the evolution of new alleles remain mysterious. Evolutionary changes are clearly necessary in both genes, since any mutation affecting only one of them would result in a nonfunctional self-compatible haplotype. Here, we study diversification at the S-locus (i.e., a stable increase in the total number of SI haplotypes in the population, through the incorporation of new SI haplotypes), both deterministically (by investigating analytically the fate of mutations in an infinite population) and by simulations of finite populations. We show that the conditions allowing diversification are far less stringent in finite populations with recurrent mutations of the pollen and pistil genes, suggesting that diversification is possible in a panmictic population. We find that new SI haplotypes emerge fastest in populations with few SI haplotypes, and we discuss some implications for empirical data on S-alleles. However, allele numbers in our simulations never reach values as high as observed in plants whose SI systems have been studied, and we suggest extensions of our models that may reconcile the theory and data.G ENES involved in recognition systems, such as the major histocompatibility complex in vertebrates (Solberg et al. 2008), mating types either in fungi (Billiard et al. 2011) or protists (Phadke andZufall 2009), and self-incompatibility (SI) in plants (Lawrence 2000), typically show extraordinarily high levels of genetic diversity. SI is widespread in angiosperms [found in .100 families ] and is highly multiallelic [up to 200 SI haplotypes (Lawrence 2000)]. This system enables hermaphrodite plants to avoid selfing and mating with close relatives and is based on recognition and rejection of pollen by pistils if they express cognate SI specificities. In many species, SI specificity is controlled by a single genetic locus (the S-locus) composed of two linked genes, one expressed in pollen and the other in styles (Takayama and Isogai 2005). The maintenance of high diversity in gametophytic self-incompatibility (GSI) is easily explained by negative frequency-dependent selection, whereby individuals with a rare SI haplotype can fertilize more partners than individuals with a common SI haplotype. As a consequence, rare SI haplotypes are unlikely to be lost by drift, especially new SI haplotypes arising by mutation (Wright 1939). A major unsolved puzzle, though, is how new SI haplotypes appear, while it is a long-standing question (Lewis 1949;Fisher 1961). Some information exists about sequence changes affecting the specificity of the pollen or pistil protein, e.g., in the Solanum chacoense pistil gene (Matton et al. 1999) and ...

Base composition varies among and within eukaryote genomes. Although mutational bias and selection have initially been invoked, more recently GC-biased gene conversion (gBGC) has been proposed to play a central role in shaping nucleotide landscapes, especially in yeast, mammals, and birds. gBGC is a kind of meiotic drive in favor of G and C alleles, associated with recombination. Previous studies have also suggested that gBGC could be at work in grass genomes. However, these studies were carried on third codon positions that can undergo selection on codon usage. As most preferred codons end in G or C in grasses, gBGC and selection can be confounded. Here we investigated further the forces that might drive GC content evolution in the rice genus using both coding and noncoding sequences. We found that recombination rates correlate positively with equilibrium GC content and that selfing species (Oryza sativa and O. glaberrima) have significantly lower equilibrium GC content compared with more outcrossing species. As recombination is less efficient in selfing species, these results suggest that recombination drives GC content. We also detected a positive relationship between expression levels and GC content in third codon positions, suggesting that selection favors codons ending with G or C bases. However, the correlation between GC content and recombination cannot be explained by selection on codon usage alone as it was also observed in noncoding positions. Finally, analyses of polymorphism data ruled out the hypothesis that genomic variation in GC content is due to mutational processes. Our results suggest that both gBGC and selection on codon usage affect GC content in the Oryza genus and likely in other grass species.