The evolution of novelty in conserved genes; evidence of positive selection in the Drosophila fruitless gene is localised to alternatively spliced exons

Abstract

There has been much debate concerning whether cis-regulatory or coding changes are more likely to produce evolutionary innovation or adaptation in gene function, but an additional complication is that some genes can dramatically diverge through alternative splicing, increasing the diversity of gene function within a locus. The fruitless gene is a major transcription factor with a wide range of pleiotropic functions, including a fundamental conserved role in sexual differentiation, species-specific morphology and an important influence on male sexual behaviour. Here, we examine the structure of fruitless in multiple species of Drosophila, and determine the patterns of selective constraint acting across the coding region. We found that the pattern of selection, estimated from the ratio of non-synonymous to synonymous substitutions, varied considerably across the gene, with most regions of the gene evolutionarily conserved but with several regions showing evidence of divergence as a result of positive selection. The regions that showed evidence of positive selection were found to be localised to relatively consistent regions across multiple speciation events, and are associated with alternative splicing. Alternative splicing may thus provide a route to gene diversification in key regulatory loci.

Figure 1

The structure and splicing pattern of the fruitless gene in D. melanogaster. P1 promoter mRNA transcripts are sex-specifically spliced at the 5′-end, resulting in the inclusion of the S exon and the addition of 101 amino acids (yellow) to male-specific isoforms (Fru^M) and the inclusion of a premature stop codon in females (UAA). Alternative splicing at the 3′-end of transcripts produced from the sex-specific P1 promoter and non-sex-specific P2-4 promoters results in the inclusion of alternative DNA-binding domains A (purple), B (orange), C (green) or D (brown). All isoforms contain the BTB domain (blue) and connector region (grey). Common exons C1-5 are included in fru^A/B/C isoforms, whereas the fru^D isoform includes exons C1–C4. Untranslated regions (UTRs) are shown in white and translation start codons are indicted (ATG).

Figure 2

Values of d_N/d_S (ω) between D. melanogaster and D. simulans, D. sechellia, D. erecta and D. yakuba across the coding region of fruitless. Values for each point represent the average d_N/d_S value for either a 102 bp window for D. erecta and D. yakuba or a 408-bp window for D. sechellia and D. simulans.

Figure 3

Values of d_N/d_S (ω) between D. melanogaster and D. takahashi, D. biarmipes, D. eugracilis, D. fisusphila and D. elegans across the coding region of fruitless. Values for each point represent the average d_N/d_S value in a 102-bp window.

Figure 4

Values of d_N and d_S for melanogaster group species from pairwise comparisons with D. melanogaster.