Haplotype dimorphism in a SNP collection from Drosophila melanogaster

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.