Greg Cochran contradicted Steve Sailer in a comment at Steve’s blog. I asked him to elaborate, and here is his response:
Total genetic diversity is higher in Africa: most of that is neutral diversity that doesn’t do anything, just as it is in any other group. Is a given Swede closer to another Swede than to any sub-Saharan African, by a measure of genetic distance (one that does not consider the actual effects of those genetic differences)? Yes, always. If this true if we restrict the measure to noncoding parts of the genome? Yes. Is it true if we restrict the measure to coding part of the genome, the fraction that makes proteins? Still true. Is it true if looked at a measure of phenotypic difference, which would correspond to a genetic distance in which genetic differences were weighted by their effects? Even more true.

What’s the right way to define race? Not as a partially inbred extended family. It depends on the level of differences you are considering. At the finest level, any population (a group that mates within itself fairly freely and has for quite a while) that is different enough in some interesting observable quality from some other population could be considered a race. At a coarse level, large subdivisions of human that have been geographically isolated and had low levels of mixing until fairly recently: this corresponds moderately well to traditional groupings such as Caucasoids, Australoids, Amerindians, etc. Things have become a good deal more mixed (in some areas) since the development of decent sailing ships, especially after Columbus.

We now know there are interesting differences in ancestry/origins, and those may have some surprising implications. It looks as if Eurasians all have some Neanderthal ancestry while sub-Saharan Africans do not, or at least have a lot less. ( I’m sure we’ll find some in groups influenced by Arab gene flow, such as the Somalis and some peoples in coastal east Africa). That Neanderthal genetic contribution should have furnished some adaptively important alleles, in my opinion: but we don’t know that for sure yet. We might know fairly soon. There may have been other regional mixtures with other old-fashioned hominids: there are hints of this for Pygmies, Bushmen, and Australoids. To some extent, some of the existing racial groupings may be the shadows of past subspecies – although all populations seem to be mostly descended from a fairly recent African population.

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