I was then reminded, that a full genome of Khoisan individual (KB1) was, in fact, published by Schuster et al. in 2010, and both the paper and the genome are freely available online.
Why is this interesting? Consider the following figure from Schuster et al. (2010):
Notice that the African hunter-gatherer (KB1) has 1,704 private SNPs compared to a Yoruba (NA19240) and Archbishop Desmond Tutu (ABT), and 2,038 SNPs compared to a European American (J. C. Venter), and a Chinese (YH).
This amount of private variation admits to two explanations:
- Higher effective population size in Khoisan
- Deep population structure followed by admixture
There is no mystery why this is the case: accumulated genetic variation is a consequence of the mutation rate (how aggressively variation is introduced), and the effective population size (which controls how severely variation is lost due to drift).
A substantial difference in effective population size means that almost certainly the indiscriminate use of a single 2.5x10-8 mutation rate for different human populations is unwise.
This is a serious limitation, as far as I can tell, of the PMSC method introduced by Li & Durbin, as it assumes a single mutation rate parameter which is then used to estimate past population sizes.
In any case, it would be interesting to see how far back the divergence of the Khoisan individual from other humans will be, even if the 2.5x10-8 rate is employed, how large the Khoisan effective population will be, and also what antiquity of population substructure followed by admixture within Africa will be sufficient to "save the phenomena."
Another interesting observation is that the genealogical autosomal mutation rate in humans (1.1x10-8) is actually lower than the estimated evolutionary rate from human-chimpanzee divergence (2.5x10-8)
Nothing in evolutionary biology can account for such a discrepancy, I think, unless there is extreme balancing selection maintaining variation across the entire genome.
- There is a serious flaw in the genealogical rate as estimated from 1000 Genomes trios, or
- We are about to find out that quite deep population structure and admixture played a role in the history of the genus Homo, deep in a sense of human-ape interbreeding after Homo-Pan speciation 7 million years ago, an idea that was proposed, for different reasons, a few years ago
For example, Li & Durbin propose that gene flow between Eurasians could have been effected during the Ice Age, as they retreated southwards; such a proposal is necessary to account for divergence between Europeans and East Asians of ~20ky, which is about half the earliest known colonization of Europe. Halving the mutation rate harmonizes the genetic divergence with archaeology, but would push the divergence of Eurasians from West Africans to the dawn of anatomical modernity, and African hunter-gatherer antiquity well beyond it.
I predict that the next few years will reignite many old debates in anthropology.