The genomic rate of adaptive evolution.

The role of positive darwinian selection in evolution at the molecular level has been keenly debated for many years, with little resolution. However, a recent increase in DNA sequence data and the development of new methods of analysis have finally made this question tractable. Here, I review the current state-of-play of the field. Initial estimates in Drosophila suggest that $50% of all amino acid substitutions, and a substantial fraction of substitutions in non-coding DNA, have been fixed as a consequence of adaptive evolution. Estimates in microorganisms are even higher. By contrast, there is little evidence of widespread adaptive evolution in our own species. Introduction In this post-genomic era, it is easy to forget just how big many genomes are and, as a consequence, how many DNAsequence differences separate even closely related species. For example, if we consider ourselves, our closest relative, the chimpanzee, is only 1% divergent from us, but this amounts to $34 million single nucleotide differences. Even if we concentrate our attention on the protein-coding complement of the genome, there are still $60 000 amino acid differences between us and chimpanzees. So what proportion of these differences have been fixed because they were beneficial and enabled us and chimpanzees to adapt to our respective environments, and how many were simply fixed by random genetic drift? For over 30 years, evolutionary biologists have debated this question as one part of the neutralist-selectionist debate in relation to all organisms, including humans. However, the question has remained unresolved, largely through a lack of data. But now, with the publication of many genome sequences and the increasingly large amounts of DNA sequence diversity data, we are beginning to answer this question. Here, I examine the methods that have been used to quantify the rate of adaptive evolution. I then describe the work that has been done on this question before briefly discussing some of the questions that the results raise