A moderate resolution single nucleotide polymorphism (SNP) map of the genom
e of Drosophila melanogaster that is designed for use in quantitative genet
ic mapping is described. Seventeen approximately 500 nucleotide gene sequen
ces spaced at 10 to 20 centimorgan intervals were combined with 49 shorter
sequence tag sites (STSs) at 5 to 10 centimorgan intervals to generate a ma
p that should not leave any gaps greater than one half of a chromosome arm
when any two wild type lines are compared. Of 20 markers with sufficient po
lymorphism to construct haplotype cladograms, 13 showed evidence for two di
vergent classes of haplotype. The possible mechanisms for and implications
of the unexpected finding that two thirds of all short gene sequences in D.
melanogaster may be dimorphic are discussed, including the suggestion that
admixture between two separate lineages may have been a major event in the
history of the species. (C) 2000 Wiley-Liss, Inc.