A nice excerpt from Razib Khan…
For whatever reason many salient physical traits which we use to classify populations don’t exhibit the pattern of the total genome, whereby all non-Africans are a branch of the tree of H. sapiens, which mostly consists of African lineages which are much more variegated. Likely new environmental selection pressures once populations left Africa play a role in this.
But there may also be other factors. Biological anthropologist Henry Harpending once explained to me that even if populations exchange genes regularly so as to become indistinguishable on their total genome content, there may be social selection for particular traits correlated with group membership. Harpending explained that on many neutral markers, such as mtDNA lineages, the Bushmen and their Bantu neighbors seem to be relatively undifferentiated. But when it came to physical appearance there was a sharp distinction. Why? Harpending suggested that perhaps there is a strong fitness advantage for someone of mixed ancestry to look more like the group they’re born into. For example, imagine a Bushman man takes a Bantu wife, some of his children favor the father, some the mother. In terms of total genome content all the offspring reflect the parental populations, but on the subset of genes which control traits salient in marking Bushmen-Bantu differences (e.g., epicanthic eye fold) there may be greater fitness to those who carry genotypes which reflect the group into which they’re born.*
Obviously genetics is fascinating to me, and probably you if you’re reading this weblog. When applied to humans it has a very strong emotional impact, consider the popularity of genealogical companies which utilize genetic methods. But it is important to remember that our own intuitive model of our species is to some extent pre-scientific, and mapping colloquial concepts and preconceptions onto scientific findings can result is less than perfect clarity. In this, the 1980s hullabaloo over mitochondrial Eve served as simply a foretaste of what was to come.
* As a toy example, imagine that the epicanthic eye fold is monogenic, controlled by a locus which comes in two flavors, E & e. Those with EE have the fold, those with ee do not, while those with Ee are somewhere in the middle. Imagine that the Bushmen have very high frequencies of EE, while their Bantu neighbors have lower frequencies of the E allele, but not trivial. Imagine if a Bantu woman is of the genotype Ee, while her Bushmen husband is EE. 50% of the offspring would exhibit the Bushmen epicanthic eye fold phenotype. In terms of total genome content these individuals would be no more Bushmen than their Ee siblings, but they would look more Bushmen to others of the tribe, and so might have more success finding a mate due to lower levels of social exclusion. Extrapolate this process generally and you can see how genes which control outwardly salient traits may exhibit more between group difference than the overall genome.