A new article in Nature Genetics brings together two themes that I've blogged about before: human brains and King and Wilson. In fact, I've even already blogged about the article, but this post contains a more thorough treatment of the science.
The long and short of it is that some people think that differences in protein coding sequences can't explain the morphological differences between humans and chimps. Additionally, there are other phenotypes that differ between the species, including cognitive abilities and dietary preferences. There is evidence for adaptive evolution in protein coding genes expressed in neuronal tissues, so this isn't an all or none story. What researchers are trying to elucidate are the relative contributions of protein coding and regulatory changes in the divergence of the human and chimp phenotypes (and, in general, the divergence between any two taxa).
The paper I'm writing about here presents the results of an analysis of non-coding regions located upstream of a few thousand protein coding genes. The authors assume that these regions are responsible for regulating the expression of the genes they flank and refer to them as "promoters" (although their role as promoter sequences is not supported by experimental evidence). They compare rates of evolution of these promoter regions with nearby introns for the purpose of identifying promoters that are evolving at accelerated rates. These rapidly evolving sequences are likely to be under positive selection. In doing so, the authors assume that the genetic changes responsible for the differences between humans and chimps were under positive selection (feel free to discuss whether this assumption is valid in the comments).
Using macaque as an outgroup, the authors were able to identify rapidly evolving promoters in both the human and chimp genomes. There is an enrichment of rapidly evolving promoters near genes involved in neural development and function (and this enrichment is greater along the human lineage than the chimp lineage). Could selection on these promoters explain some of the cognitive differences between humans and chimps? Also, genes involved in glucose metabolism are enriched in the dataset, and humans and chimps have different dietary preferences.
The also also tried to incorporate gene expression data from various tissues into their analysis, but their results weren't all that informative. They found that genes with pancreas specific expression tended to have signatures of positive selection in their promoter regions, consistent with selection acting on metabolic traits. But many of the genes with evidence for adaptive evolution in their promoter regions have unknown functions, so the authors were limited in the amount of hand-waving they could do when discussing their results.
Haygood et al. 2007. Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nature Genet. 39: 1140-1144 doi:10.1038/ng2104
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I recently read an article on Cerebral Cortex (commmented on my LJ) on differences of expression patterns of thrombospondins between humans, chimps and macaques. As I was writing the post, I stumbled upon your post here... gaddammit, now I'll have to read those incredible articles and update it all =)