Hidden evolution: progress and limitations in detecting multifarious natural selection.
From illustrative examples of research on the best-studied group of species to date, Drosophila melanogaster and its closest relatives, we argue that selection is multifarious, but often hidden. Selective fixation of new, highly advantageous alleles is the most parsimonious explanation for a typical pattern of molecular variation observed in genomic regions characterized by very low recombination: drastically reduced DNA sequence variation within species and typical levels of sequence divergence among species. At the same time, the identity of the gene (or genes) influenced by selection is not just difficult to discern; it may be impossible. Studies of the genetic basis of reproductive isolation demonstrate that, although the D. melanogaster complex species appear virtually identical, dozens of currently unidentified genes contribute to hybrid sterility. We argue that these findings are best explained by selectively-driven functional divergence and demonstrate the multifarious nature of selection. Although multifarious selection certainly occurs, the exact characters responsible for differences in survival and reproductive success are unknown. We do not see these inherent limits as a cause for despair or a problem for evolutionary biology. Instead, we hope to raise awareness of these complexities of evolution by highlighting both the progress and the limitations of characterizing multifarious natural selection.