Large number of replacement polymorphisms in rapidly evolving genes of Drosophila: Implications for genome-wide surveys of DNA polymorphism

We present a survey of nucleotide polymorphism of three novel, rapidly evol ving genes in populations of Drosophila melanogaster and D. simulans. Level s of silent polymorphism are comparable to other loci, but the number of re placement polymorphisms is higher than that in most other genes surveyed in D. melanogaster and D. simulans. Tests of neutrality fail to reject neutra l evolution with one exception. This concerns a gene located in a region of high recombination rate in D. simulans and in a region of low recombinatio n rate in D. melanogaster, due to an inversion, in the latter case it shows a very low number of polymorphisms, presumably due to selective sweeps in the region. Patterns of nucleotide polymorphism suggest that most substitut ions are neutral or nearly neutral and that weak (positive and purifying) s election plays a significant role in the evolution of these genes. At all t hree loci, purifying selection of slightly deleterious replacement mutation s appears to be more efficient in D. simulans than in D. melanogaster, pres umably due to different effective population sizes. Our analysis suggests t hat current knowledge about genome-wide patterns of nucleotide polymorphism is far from complete with respect to the types and range of nucleotide sub stitutions and that further analysis of differences between local populatio ns will be required to understand the forces more completely. We note that rapidly diverging and nearly neutrally evolving genes cannot be expected on ly in the genome of Drosophila, but are likely to occur in large numbers al so in other organisms and that their function and evolution are little unde rstood so far.