Nucleotide variation in the tinman and bagpipe homeobox genes of Drosophila melanogaster

The tinman (tin) and bagpipe (bap) genes are members of the NK homeobox gene family of Drosophila, so that tin occupies a higher position than bap in the regulatory hierarchy. Little is known about the level and pattern of genetic polymorphism in homeobox genes. We have analyzed nucleotide polymorphism in 27 strains of Drosophila melanogaster and one each of D. simulans and D. sechellia, within two closely linked regions encompassing a partial sequence of tin and the complete sequence of bap. The two genes exhibit different levels and patterns of nucleotide diversity. Two sets of sharply divergent sequence types are detected for tin. The haplotype structure of bap is more complex: about half of the sequences are identical (or virtually so), while the rest are fairly heterogeneous. The level of silent nucleotide variability is 0.0063 for tin but significantly higher, 0.0141, for bap, a level of polymorphism comparable to the most polymorphic structural genes of D. melanogaster. Recombination rate and gene conversion are also higher for bap than for tin. There is strong linkage disequilibrium, with the highest values in the introns of both genes and exon II of bap. The patterns of polymorphism in tin and bap are not compatible with an equilibrium model of selective neutrality. We suggest that negative selection and demographic history are the major factors shaping the pattern of nucleotide polymorphism in the tin and bap genes; moreover, there are clear indications of positive selection in the bap gene.