Nonfixed duplication containing the Adh gene and a truncated form of the Adhr gene in the Drosophila funebris species group: Different modes of evolution of Adh relative to Adhr in Drosophila

The sequence of the genomic region that contains the Adh and Adhr genes of Drosophila funebris was used to demonstrate that both genes are present in species of the funebris group. The sequence of this genomic region reveals a 2.9-kb tandem duplication which encompasses 1.6 kb of the 5' flanking reg ion, the entire Adh gene, and two thirds of the first exon of the Adhr gene in D. funebris. This duplication is not fixed in this species since some s trains do not carry the duplication. The Adh duplication has also been foun d in another species of the funebris group, Drosophila macrospina macrospin a. The sequence analysis of the 5'-flanking region of the Adh gene indicate s a single promoter and shows stretches of high similarity with cis-acting elements responsible for the expression of Adh in Drosophila melanogaster. In confirmation of this indication, the larval and adult transcripts have t he same length, which corresponds to the transcription from the promoter pr oximal to the coding region. The codon bias of the Adh gene of D. funebris is among the lowest reported for any Adh gene in the Drosophilidae species and is very similar to that of the Adhr gene. The Adhr gene evolves slightl y faster than Adh at synonymous positions. At nonsynonymous positions, the Adh gene evolves 2.5 times faster than Adhr in the species pair D. funebris -Drosophila immigrans, while in other interspecific comparisons the average is about 1.25. However, in comparisons between some species within the mel anogaster and obscura groups, Adh evolves at half the rate of Adhr. The phy logenetic trees constructed with the coding region of the Adh gene cluster D. funebris and D. immigrans and clearly separate them from the clade in wh ich virilis, repleta, and Hawaiian species are grouped. Using the evolution ary synonymous rate estimated for Hawaiian species, the divergence time of D. funebris from the virilis-repleta-Hawaiian clade was estimated as 34.3 M yr, and the divergence time of D. funebris and D. immigrans was estimated a s 23.5 Myr.