Advances in sequencing technology have brought opportunities to refine our searches for adaptive evolution and to address and identify new questions regarding how adaptive evolution has shaped genomic diversity. Recent theoretical developments incorporate demographic and complex selective histories into tests of non-neutral evolution, thereby significantly improving our power to detect selection. These analyses combined with large data sets promise to identify targets of selection for which there was no a priori expectation. Moreover, they contribute to elucidate the role selection has played in shaping diversity in transposable elements, conserved noncoding DNA, gene family size, and other multicopy features of genomes.
Bibliographical noteFunding Information:
We thank Stephen Wright for sharing the data and computer code used in Box 1 , David A Moeller for helpful comments on an earlier version of this article, and Juliette de Meaux for comments on the article and the opportunity to contribute to this issue. MIT is supported by French Agence National de la Recherche grant ANR-05-JCJC-0067-01 and PLT by US National Science Foundation grants DEB-0515466 and DBI-0701911.