There is some evidence (although not conclusive) that a duplication of a gene in Homo habilis led to an increase in their intelligence by increasing the number of connections between the neurons in their brains. In two reports published in Cell in May 2012, Evan Eichler, a geneticist at the University of Washington in Seattle and others investigated their earlier finding that humans have four copies of a gene called SRGAP2. They calculate that at least one of the copies appeared about 2.4 million years ago, at the time that Homo habilis first appeared. Franck Polleux, a neurobiologist at the Scripps Research Institute in La Jolla, California, found that when this gene is added to mice brains it increases the number of connections between their neurons and so, probably, their intelligence.
More information at Human brain shaped by duplicate genes : Nature News & Comment.