Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila

Abstract

The polyhomeotic (ph) locus in Drosophila melanogaster consists of the two tandemly duplicated genes ph-d (distal) and ph-p (proximal). They code for transcriptional repressors belonging to the Polycomb group proteins, which regulate homeotic genes and hundreds of other loci. Although the duplication of ph occurred at least 25 million to 30 million years ago, both copies are very similar to each other at both the DNA and the protein levels, probably because of the action of frequent gene conversion. Despite this homogenizing force, differential regulation of both transcriptional units suggests that the functions of the duplicates have begun to diverge. Here, we provide evidence that this functional divergence is driven by positive selection. Based on resequencing of an approximately 30-kb region around the ph locus in an African sample of D. melanogaster X chromosomes, we identified a selective sweep, estimated its age and the strength of selection, and mapped the target of selection to a narrow interval of the ph-p gene. This noncoding region contains a large intron with several regulatory elements that are absent in the ph-d duplicate. Our results suggest that neofunctionalization has been achieved in the Drosophila ph genes through the action of strong positive selection and the inactivation of gene conversion in part of the gene.

Fig. 1.

Illustration of the ph-d–CG3835 region. (Upper) Modified from ref. , the entire wapl region is shown. The wapl fragment is indicated by a star. It harbors no variation in the European sample and was detected in a previous genome scan (34). The numbers on the x axis are the absolute genomic position (in Mb), and those on the y axis are nucleotide variability in the African sample (the solid line corresponds to θ and the dashed line corresponds to π). The arrow indicates the position of the target of selection predicted by Beisswanger et al. (17). (Lower) The region investigated in detail in this study. Exons are illustrated by thick black lines and introns by thin black lines. The direction of transcription is indicated by dotted arrows below each gene. Sequenced fragments are denoted by gray lines and numbers. Gray arrow heads indicate the position of the three SNPs shared between both ph copies. These SNPs are located within a region of 135 bp.

Fig. 2.

Site frequency spectra. The folded frequency spectrum of 27 loci randomly chosen from ref. . (Inset) Shown are the spectra of the ph-p intron and the 5′ UTR (a), the first half of the ph-p–CG3835 intergenic region (b), and the second half of that region (c). The gray lines indicate the equilibrium frequencies.