Whatever the significance of it, there is certainly evidence that our brains have not stood still since we left Africa. All populations have changed due to selection and drift. There are three lines of evidence we will look at:
1) Past and present variation in cranial capacity
3) Structural brain variation
Variation in Cranial Capacity
Despite the idea being (baselessly) ridiculed by Stephen J. Gould(1), it has been found that cranial capacity varies among populations in a generally latitudinal cline, with southerly populations having smaller skulls, and increasing in size as one moves northwards. (2,3) This variation has existed for thousands of years(4).
There has also been a worldwide decline in cranial capacity, which happened at different rates and to different degrees in different populations, over the last 10-20,000 years – but in general cranial capacity shrunk by over 100cm3. (4)
Craniometric studies on modern populations have also found differentiation on a number of cranial measures, much of which is neutral, but some having high fst values (such as cranial breadth), indicating selection(5).
In sum, not only did the average cranial capacity of populations diverge as they migrated throughout the world, but they later began, independently, to shrink. We also know that the differentiation in cranial capacity is likely due to selection, as was the global trend towards smaller brains. It is clear that our brains were being remodeled well after the Out of Africa event and the dispersal of populations.
Genomic studies on modern populations have found not just population differences in genes related to neuron development, but strong evidence of selection.
Wu and Zhang (2011) found high levels of population differentiation in genes involved in the nervous system. See the figure to the right – specifically, genes related to neuron development, positive regulation of neuron differentiation, hindbrain development and dorsotubal neural tube patterning all have as much, or much higher levels of population differentiation, than pigmentation. This strongly indicates selection on the nervous systems of various populations.
Also: Pickrell, Coop, Novembre, et. al., 2009. Signals of recent positive selection in a worldwide sample of Human Populations:
“The NRG–ERBB4 signaling pathway is well-studied and known to be involved in the development of a number of tissues, including heart, neural, and mammary tissue (Gassmann et al. 1995; Tidcombe et al. 2003). Variants in genes in this pathway have been associated with risk of schizophrenia and various psychiatric phenotypes (Stefansson et al. 2002; Hall et al. 2006; Mei and Xiong 2008). We suggest that an unidentified phenotype affected by this pathway has experienced strong recent selection in non-African populations”
Structural Brain Variation
There is some suggestive evidence of structural differences in the brain between populations. However, this is a trickier area, and may well be caused by environmental/cultural factors. Klekamp et al (1994) reported that Australian Aborigines have significantly larger visual cortices than Europeans. Differences have been found by Chee et al (2011) in a comparison of Chinese and Americans, and, in another study, between white and black Americans (source). It is however, known that brain structure can respond to environmental demands (source).
See Race, genes, and disparity for an in depth look at the issue of brain size and IQ