When the DNA sequences of Homo sapiens and Pan troglodytes were sequenced, the difference between the sequences of coding genes was smaller than expected based on the phenotypic differences between both species. If not the coding genes, then what is responsible for these dissimilarities?

(Source: godlessgeeks.com)

In the words of the authors of a new study that took a look at this question:

Although humans and chimpanzees have accumulated significant differences in a number of phenotypic traits since diverging from a common ancestor about six to eight million years ago, their genomes are more than 98.5% identical at protein-coding loci. Since this modest degree of nucleotide divergence does not seem sufficient to explain the extensive phenotypic differences that exist between the two species, it has been hypothesized that the genetic basis of the differences lies at the level of gene regulation and is associated with the extensive insertion and deletion (INDEL) variation between the two species. 

So, it might not be the genes, but the genomic ‘gaps’ between them. Junk DNA, or stretches of the genome without any known function, does not code for any protein, and turns out to be quite different between human beings and chimpanzees. A lot of the difference between the two evolutionary cousins is due to the insertion or deletion of retrotransposons, genetic elements that amplify themselves and constitute about half the genome in both species.

These gaps between the genes in both genomes can affect the extent to which genes are 'turned on or off'. The research team has found that the gaps in both genomes are significantly correlated with differences in gene expression. This suggests that the difference between chimpanzees and human beings might not be mostly due to changes in genes, but rather in changes of gene regulation.

The researchers conclude:

The results presented herein are consistent with the hypothesis that large INDELs, particularly those associated with retrotransposons, have played a significant role in human-chimpanzee regulatory evolution.

Not so different after all?

(Source: Scientific American, What makes us human?)