We analyzed the effects of mating system and recombination rate on single nucleotide polymorphisms using 14 single-copy nuclear loci from single populations of five species of wild tomatoes (Solanum section Lycopersicon). The taxa investigated comprise two self-compatible (SC) and three self-incompatible (SI) species. The observed reduction in nucleotide diversity in the SC populations compared to the SI populations is much stronger than expected under the neutral effects of the mating system on effective population size. Importantly, outgroup sequences available for 11 of the 14 loci yield strong positive correlations between silent nucleotide diversity and silent divergence, indicative of marked among-locus differences in mutation rates and/or selective constraints. Furthermore, using a physical estimate of local recombination rates, we find that silent nucleotide diversity (but not divergence) is positively correlated with recombination rate in two of the SI species. However, this correlation is not nearly as strong as in other well-characterized species (in particular, Drosophila). We propose that nucleotide diversity in Lycopersicon is dominated mainly by differences in neutral mutation rates and/or selective constraints among loci, demographic processes (such as population subdivision), and background selection. In addition, we hypothesize that the soil seed bank plays an important role in the maintenance of the large genetic diversity in the SI species (in particular L. peruvianum).W HETHER diversity levels in the genomes of animals and plants are shaped mainly by neutral processes or selection is a recurrent theme in population genetics. In many organisms, genes in regions of low recombination exhibit reduced levels of DNA polymorphism, while divergence among species remains relatively unaffected. These observations may be explained by genetic hitchhiking, involving advantageous mutations sweeping through a population (Maynard Smith and Haigh 1974) and/or by background selection eliminating unconditionally deleterious mutations (Charlesworth et al. 1993(Charlesworth et al. , 1995. Depending on the effective recombination rate in the regions subjected to either of the above processes and on the strength of natural selection, linked neutral variation is reduced under both selection scenarios, while interspecific divergence is not influenced.A positive correlation between DNA diversity and recombination rate has been found in many organisms, both animals (Aguadé et al. 1989;Stephan and Langley 1989;Begun and Aquadro 1992;Nachman 1997;Nachman et al. 1998) and plants (Dvorak et al. 1998;Kraft et al. 1998;Stephan and Langley 1998). Such patterns were usually attributed to the action of natural selection. However, neutral explanations for an observed positive correlation between recombination and diversity have also been proposed, when, in addition to intraspecific variation, divergence also scaled with recombination rate (e.g., Wang et al. 1997;Hellmann et al. 2003).Among plants, maize (Zea mays ssp. m...