Cut locus variation in natural populations of Drosophila.

The amount of DNA sequence variability and the frequency distribution of different types of mutations in various genomic regions provide information about evolutionary processes occurring within and between closely related populations. Comparison of DNA variation at homologous genes in regions of “normal” crossing-over suggests that Drosophila simulans has twoto threefold higher nucleotide heterozygosity and a much lower incidence of large insertions than does the sibling species, D. melanogaster ( Aquadro 1992 ) . Nucleotide heterozygosity is very low for both species in genomic regions experiencing severely reduced recombination rates ( Begun and Aquadro 199 1; Berry et al. 199 1; Martin-Campos et al. 1992; Langley et al. 1993); a positive correlation between heterozygosity and recombination in D. melanogaster has been interpreted as evidence for hitchhiking effects of advantageous and/or deleterious alleles (Begun and Aquadro 1992; Charlesworth et al. 1993 ) . As part of a continuing effort to estimate average heterozygosity over many large genomic regions in D. simulans and D. melanogaster, we present in this report six-cutter restriction-map data from the cut locus region. Since cut appears to have “normal” rates of crossingover in D. melanogaster (see below), we expected the absolute and relative levels of variability to be similar to those observed at other loci in regions of normal recombination surveyed in both species. We also expected to observe a very low incidence of large insertions in D. simulans and a somewhat higher incidence of such insertions in D. melanogaster. The data from cut are contrary to these expectations. Population samples of D. simulans (n =34) and D. melanogaster ( n = 35 ) X chromosomes from California and six-cutter restriction-map analysis using BamHI, BglII, EcoRI, HindII, SalI, and XhoI were as described by Begun and Aquadro ( 199 1). The genomic region surveyed spans approximately 40 kb, from about coordinate position 75 to 115 of Jack ( 1985). The vast majority of DNA in the survey is from the first intron of cut, with the remaining DNA located in the small first exon and a small amount of 5 ‘ flanking region (fig. 1 of Liu et al. 199 1). The haplotypes observed in our survey