High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups

We recently proposed that patterns of evolution of non-LTRretrotransposable elements can be used to study patterns of spontaneousmutation. Transposition of non-LTR retrotransposable elements commonlyresults in creation of 5' truncated, "dead-on-arrival" copies. Theseinactive copies are effectively pseudogenes and, according to the neutraltheory, their molecular evolution ought to reflect rates and patterns ofspontaneous mutation. Maximum parsimony can be used to separate theevolution of active lineages of a non-LTR element from the fate of the"dead-on-arrival" insertions and to directly assess the relativefrequencies of different types of spontaneous mutations. We applied thisapproach using a non-LTR element, Helena, in the Drosophila virilis groupand have demonstrated a surprisingly high incidence of large deletions andthe virtual absence of insertions. Based on these results, we suggestedthat Drosophila in general may exhibit a high rate of spontaneous largedeletions and have hypothesized that such a high rate of DNA loss may helpto explain the puzzling dearth of bona fide pseudogenes in Drosophila. Wealso speculated that variation in the rate of spontaneous deletion maycontribute to the divergence of genome size in different taxa by affectingthe amount of superfluous "junk" DNA such as, for example, pseudogenes orlong introns. In this paper, we extend our analysis to the D. melanogastersubgroup, which last shared a common ancestor with the D. virilis groupapproximately 40 MYA. In a different region of the same transposableelement, Helena, we demonstrate that inactive copies accumulate deletionsin species of the D. melanogaster subgroup at a rate very similar to thatof the D. virilis group. These results strongly suggest that the high rateof DNA loss is a general feature of Drosophila and not a peculiar propertyof a particular stretch of DNA in a particular species group.