The evolutionary analysis of "orphans" from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes

In genome projects of eukaryotic model organisms, a large number of novel g enes of unknown function and evolutionary history ("orphans") are being ide ntified. Since many orphans have no known homologs in distant species, it i s unclear whether they are restricted to certain taxa or evolve rapidly, ei ther because of a lack of constraints or positive Darwinian selection. Here we use three criteria for the selection of putatively rapidly evolving gen es from a single sequence of Drosophila melanogaster. Thirteen candidate ge nes were chosen from the Adh region on the second chromosome and I from the tip of the X chromosome. We succeeded in obtaining sequence from 6 of thes e in the closely related species D. simulans and D. yakuba. Only 1 of the 6 genes showed a large number of amino acid replacements and in-frame insert ions/deletions. A population survey of this gone suggests that its rapid ev olution is due to the fixation of many neutral or nearly neutral mutations. Two other genes showed "normal" levels of divergence between species. Four genes had insertions/deletions that destroy the putative reading frame wit hin exons, suggesting that these exons have been incorrectly annotated. The evolutionary analysis of orphan genes in closely related species is useful for the identification of both rapidly evolving and incorrectly annotated genes.