Abstract

The genomic DNA sequences of humans and chimpanzees differ by only 1.24%. Recently, however, substantial differences in gene-expression patterns between the two species have been revealed. In this article, we investigate the genomic distribution of such differences. Besides confirming previous findings about the evolution of sex chromosomes and duplications, we show that chromosomal rearrangements are associated with increased gene-expression differences in the brain and that rearrangements can have both direct and indirect effects on the expression of linked genes. In addition, our results are consistent with a role for some rearrangements in the original speciation events that separated the human and chimpanzee lineages.