A screen for fast evolving genes from Drosophila

Abstract

In an attempt to quantify the rates of protein sequence divergence in Drosophila, we have devised a screen to differentiate between slow and fast evolving genes. We find that over one-third of randomly drawn cDNAs from a Drosophila melanogaster library do not cross-hybridize with Drosophila virilis DNA, indicating that they evolve with a very high rate. To determine the evolutionary characteristics of such protein sequences, we sequenced their homologs from a more closely related species (Drosophila yakuba). The amino acid substitution rates among these cDNAs are among the fastest known and several are only about 2-fold lower than the corresponding values for silent substitutions. An analysis of within-species polymorphisms for one of these sequences reveals an exceptionally high number of polymorphic amino acid positions, indicating that the protein is not under strong negative selection. We conclude that the Drosophila genome harbors a substantial proportion of genes with a very high divergence rate.

Figure 1

Polymorphic sites of 1G5 in different populations of D. melanogaster and D. simulans. Dots represent identical nucleotides with respect to the top sequences. The region surveyed includes bases 58–922 of clone 1G5 (total length of coding region is 1,081 bp and includes a small intron of 61 bp). The “fixed/polymorphic” line indicates whether a substitution is fixed (f) or polymorphic (p), and the “replacement/silent” line indicates replacement (r) and silent (s) substitutions. At position 605 is a 6-bp indel polymorphism and at position 835 a fixed indel difference of 9 bp which are disregarded for the calculation shown in Table 4. Positions 637 and 697 show two replacement polymorphisms each.