In my chapter THE RIDDLE OF THE 1.6% I present plenty of evidence that evolutionary changes to parts of the genome that regulate gene expression (rather than DNA sequence change inside those genes) has an important role to play in human evolution, particularly of the brain and cognition. And this fact - beautifully, and recently, established by Ralph Haygood and colleagues, explains why two species - humans and chimps - that differ so little at the level of DNA sequence can be so different over many parameters. Now this same team have taken another wide-angle look at the human genome and have established strong correlations between evolution of non-coding regulatory sequences of DNA and gene expression "indicating that neural development and function have adapted mainly through non-coding changes...whereas adaptation via coding changes (evolution inside genes) is dominated by immunity, olfaction and male reproduction."
Genes that are highly tissue-specific in terms of where they are expressed are more likely to undergo sequence evolution than genes more widely expressed in several tissues. The authors suggest that, since genes work in teams such that any one gene may affect various aspects of the phenotype of an organism (this is called pliotropy) this constrains sequence evolution in genes (potentially throwing a spanner into complex machinery) in favour of gene expression changes. They conclude: "Our findings underscore the probable importance of non-coding changes in the evolution of human traits, particularly cognitive traits."
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