Species and recombination effects on DNA variability in the tomato genus

Population genetics theory predicts that strong selection for rare, benefic ial mutations or against frequent, deleterious mutations reduces polymorphi sm at linked neutral (or weakly selected) sites. The reduction of genetic v ariation is expected to be more severe when recombination rates are lower. In outbreeding species, low recombination rates are usually confined to cer tain chromosomal regions, such as centromeres and telomeres. In contrast, i n predominantly selfing species, the rarity of double heterozygotes leads t o a reduced effective recombination rate in the whole genome. We investigat ed the effects of restricted recombination on DNA polymorphism in these two cases, analyzing five Lycopersicon species with contrasting mating systems : L. chilense, L. hirsutum, L. peruvianum, L. chmielewskii, and L. pimpinel lifolium, of which only the first three species have self-incompatibility a lleles. In each species, we determined DNA sequence variation of five singl e-copy genes located in chromosomal regions with either high or low recombi nation rate. We found that the mating system has a highly significant effec t on the level of polymorphism, whereas recombination has only a weak influ ence. The effect of recombination on levels of polymorphism in Lycopersicon is much weaker than in other well-studied species, including Drosophila. T o explain these observations, we discuss a number of hypotheses, invoking s election, recombination, and demographic factors associated with the mating system. We also provide evidence that L. peruvianum, showing a level of po lymorphism (almost 3%) that is comparable to the level of divergence in the whole genus, is the ancestral species from which the other species of the genus Lycopersicon have originated relatively recently.