Evolution of P Elements in Natural Populations of Drosophila willistoni and D. sturtevantiSequence data from this article have been deposited with the GenBank Data Library under accession nos. AY578739, AY578740, AY578741, AY578742, AY578743, AY578744, AY578745, AY578746, AY578747, AY578748, AY578749, AY578750, AY578751, AY578752, AY578753, AY578754, AY578755, AY578756, AY578757, AY578758, AY578759, AY578760, AY578761, AY578762, AY578763, AY578764, AY578765, AY578766, AY578767, AY578768, AY578769, AY578770, AY578771, AY578772, AY578773, AY578774, AY578775, AY578776, AY578777, AY578778, AY578779, AY578780, AY578781, AY578782, AY578783, AY578784.

To determine how population structure of the host species affects the spread of transposable elements and to assess the strength of selection acting on different structural regions, we sequenced P elements from strains of Drosophila willistoni and Drosophila sturtevanti sampled from across the distributions of these species. Elements from D. sturtevanti exhibited considerable sequence variation, and similarity among them was correlated to geographic distance between collection sites. By contrast, all D. willistoni elements sampled were essentially identical (pi < 0.2%) and exhibited patterns typical of a recent population expansion. While the canonical P elements sampled from D. sturtevanti appear to be long-time residents in that species, a rapid expansion of a very young canonical P-element lineage is suggested in D. willistoni, overcoming barriers such as large geographical distances and moderate levels of population subdivision. Between-species comparisons reveal selective constraints on P-element evolution, as indicated by significantly different substitution rates in noncoding, silent, and replacement sites. Most remarkably, in addition to replacement sites, selection pressure appears to be strong in the first and third introns and in the 3' and 5' flanking regions.