This paper by Katherine Pollard and colleagues in the (execrable) Nature "online early" section examines a rapidly evolving region of the genome that, well, read it yourself:
We devised a ranking of regions in the human genome that show significant evolutionary acceleration. Here we report that the most dramatic of these 'human accelerated regions', HAR1, is part of a novel RNA gene (HAR1F) that is expressed specifically in Cajal-Retzius neurons in the developing human neocortex from 7 to 19 gestational weeks, a crucial period for cortical neuron specification and migration. HAR1F is co-expressed with reelin, a product of Cajal-Retzius neurons that is of fundamental importance in specifying the six-layer structure of the human cortex. HAR1 and the other human accelerated regions provide new candidates in the search for uniquely human biology.
1. This is not a protein-coding gene, but an RNA gene. It likely plays an important role in the regulation of other genes, specifically in the developing cortex.
2. This research team went looking through the noncoding areas of the genome for such fast-evolving areas. There are others, whose function remains to be seen but may be just as interesting as this one.
3. I am very impressed with the number of substitutions on the human lineage compared with other vertebrates. The region is highly conserved: only two bases are different between chimpanzees and chickens. In contrast, there have been 18 substitutions on the human lineage! It's like every other species is driving the same Plymouth Reliant, and humans are driving a Ferrari!
4. It remains possible that the human sequence has been shaped by a relaxation of a selective constraint that acts in other species, rather than positive selection. But it doesn't seem very likely, especially since the gene still has a critical developmental function.
5. Now, this is the fastest of the regions of rapid evolution in the non-protein-coding genome, according to the paper. But if there are any substantial number of these, the number of selected substitutions they involve could easily exceed the number of amino acid substitutions between the human and chimpanzee genomes (already more than 40,000).
6. That being said, it may be hard to figure this number out, since most regions will not have the unusual combination of high conservation among distant taxa and rapid change in humans. Most will have more or less equal substitution rates among taxa. But amino acid substitutions are starting to look like the low-hanging fruit of a very tall tree.
Here's a hint of what's to come, from the last paragraph of the paper:
Many of the other top candidates are associated with genes known to be involved in neurodevelopment, an area where there has been significant divergence since our last common ancestor with chimpanzee. Thus, this seems to be a promising approach to identifying candidate regions involved in neurodevelopmental aspects of our uniquely human biology.
This approach may well find many of the important neurodevelopmental genetic changes, since many of these will be uniquely human. But it will definitely underestimate the rate of selection on noncoding regions, so other methods will be necessary to look at other kinds of phenotypes.
(via Gene Expression)
Pollard KS and 15 others. 2006. An RNA gene expressed during cortical development evolved rapidly in humans. Nature (online early) DOI link