From an open paper in Nature Human Genetics:
Regional DNA methylation differences between humans and chimpanzees are associated with genetic changes, transcriptional divergence and disease genes
[Introduction] Humans (Homo sapiens) and chimpanzees (Pan troglodytes) have approximately 1.2% difference in genomic sequence and yet show many phenotypic differences. In addition to the changes in protein repertoire, structure and function, the differences in gene expression patterns are considered to have an important role in phenotypic diversification. Indeed, comparative studies have identified transcriptional differences between humans and chimpanzees. Such differences can arise not only from genetic changes, such as gene duplication, translocation and nucleotide changes in regulatory elements but also from changes in epigenetic modifications in the regulatory regions. Although genetic differences between humans and chimpanzees have been extensively studied, epigenetic differences are less well characterized.
Actually, such differences have been largely ignored, in favour of “98—or even—99% similarity, the genes PROVE it.” But do they? …
In conclusion, our study revealed regional DNA methylation differences between humans and chimpanzees and showed that many of them arise from small genetic changes. We also showed that some of these differences are correlated with expression differences. Further studies will provide insights into the genetic and epigenetic mechanism of phenotypic divergence during hominid evolution.
Epigenetic studies provide some insights into ways in which similar genes can result in very different outcomes. Of course, they will significantly complicate the study of genetics and of evolution in consequence.
Hard times for genetic fundamentalists, one guesses. Not to worry, just watch: Soon, nobody but nobody will have ever been a genetic fundamentalist. Har har.