Patterns of nucleotide substitution in Drosophila and mammalian genomes

To estimate patterns of molecular evolution of unconstrained DNA sequences, we used maximum parsimony to separate phylogenetic trees of a non-long ter minal repeat retrotransposable element into either internal branches, repre senting mainly the constrained evolution of active lineages, or into termin al branches, representing mainly nonfunctional "dead-on-arrival" copies tha t are unconstrained by selection and evolve as pseudogenes. The pattern of nucleotide substitutions in unconstrained sequences is expected to be congr uent with the pattern of point mutation. We examined the retrotransposon He lena in the Drosophila virilis species group (subgenus Drosophila) and the Drosophila melanogaster species subgroup (subgenus Sophophora). The pattern s of point mutation are indistinguishable, suggesting considerable stabilit y over evolutionary time (40-60 million years). The relative frequencies of different point mutations are unequal, but the "transition bias" results l argely from an approximate to 2-fold excess of G.C to A.T substitutions. Sp ontaneous mutation is biased toward A.T base pairs, with an expected mutati onal equilibrium of approximate to 65% A + T (quite similar to that of long introns), These data also enable the first detailed comparison of patterns of point mutations in Drosophila and mammals. Although the patterns are di fferent, all of the statistical significance comes from a much greater rate of G.C to A.T substitution in mammals, probably because of methylated cyto sine "hotspots," When the G.C to AT substitutions are discounted, the remai ning differences are considerably reduced and not statistically significant .