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I've never understood why so many people think that 'races' in the human species should be qualitatively different from 'subspecies' in other animals.
I don't have any real opinion on whether human population structure is unusual or not. I'm just of the opinion that use of the term "race" for anything biological about humans at this point produces more confusion and less communication than any possible gain it brings.
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See my not-very-well-written paper, "The Race FAQ" at Just a moment...
Interesting material, especially that comparing human variation with other species. Much of that is new to me, since I don't know much about non-human genetics (having somehow neglected to take a course in genetics at any point in my schooling). One thing that make me scratch my head, though: it's becoming clear from autosomal SNP data (vast quantities of autosomal SNP data) that chimps really do have at least twice the diversity of humans -- but this rather significant difference doesn't show up at all in the tables. No doubt (as usual) more data will clarify the situation.
I think there are a few distinctions that you slide over too quickly, however, for a FAQ that's addressing the question of race in humans. You treat folk definitions, anthropological definitions and genetic definitions of human races as if they were interchangeable. They're not. In the U.S., folk definitions of races are such that any detectable amount of African ancestry makes a person "black". Since such a person may be genetically and morphologically more similar to the average European, this means that the folk category does not align well with any biological category. This may not matter much if you're interested only in whether humans can be described as having subspecies, but it matters a heck of a lot if you actually want to use race as a category in the real world.
Similarly, anthropological definitions are not the same as genetic ones. "Sub-saharan African" is not one of the traditional, widely used racial categories; "Negroid" is. The latter category includes Africans, Filipinos, Andaman Islanders, and Melanesians, groups that don't form any kind of meaningful genetic cluster. Using racial terminology again serves only to confuse things, for no obvious purpose.
There's a more subtle problem in the use of "clade" (and not just by you). Despite Nei and Roychudhury's language, you can't really form a phylogenetic tree for human populations, or for any interbreeding diploid populations; or rather, you can't form a unique, non-reticulating tree. Genes have phylogenetic trees; populations form webs. For many purposes a phylogenetic tree is a reasonable approximation, but when one uses it it's easy to forget that it
is only an approximation, and that the population you're talking about may be an average that doesn't correspond to any actual individuals. I point this out mostly because talking about Africans as a clade bugs me. It seems very likely that the Out of Africa migration(s) came from a source population in East Africa, much of which remained in Africa; their descendents are still there. If you're thinking in terms of phylogenetic trees, that branch together with the rest of the African population do not form a clade; rather, the East Africans form a clade with the rest of the world's populations. When you cluster people by gene frequency, however, you will find that the East Africans' descendents within Africa
do form a "clade" (a cluster, really) with other Africans, at least at most loci, thanks to continuing gene flow within Africa.