A paper published in Nature on Dec. 3, 2014, deals with the genome of Africans . I found it interesting because, against the usual mainstream belief on African diversity, it reports that: "overall differentiation among African populations was modest [...] This suggests that a large proportion of differentiation observed among African populations could be due to Eurasian admixture, rather than adaptation to selective forces (Supplementary Note 6). Genes known to be under selection were notably enriched among the most differentiated loci after masking of Eurasian ancestry". 
So the differences are due to Eurasian admixture! and those that were not of Eurasian origin, differed because they were being selected for positively. Clearly not the kind of scenario expected if the myth of a "molecular clock" was true.
The interesting part is that regarding SNP diversity: " A substantial proportion of unshared (11%–23%) and novel (16%–24%) variants were observed, with the highest proportion among Ethiopian populations" . Note that they are Ethiopians not Sub Saharan Africans which are always mentioned as being the most diverse!
This higher diversity among "Ethiopian populations, possibly suggest[s] Eurasian gene flow", furthermore, analysis "supported evidence for substantial Eurasian and HG ancestry in SSA" (Sub Saharan Africans). The Eurasian admixture in Africans was substantial: "ranging from 0% to 50%".
An interesting discovery was that of the cause of diversity:
"On examining locus-specific Europe–Africa differentiation, enrichment of loci known to be under positive selection was observed among the most differentiated sites (P = 1.4 × 10−31). Furthermore, there was statistically significant enrichment for gene variants among these, indicating that this differentiation is unlikely to have arisen purely from random drift (P = 0.0002). Additionally, we found no evidence for background selection as the primary driver of differentiation among these loci (Supplementary Note 7)." 
In other words natural selection is acting to promote diversity and it is not due to "natural drift". No regularly ticking mutation clock here, what is acting is a clock ticking at higher and variable speed, prodded by Evolutionary adaptation to a changing environment.
 Deepti Gurdasani, et al., (2014). The African Genome Variation Project shapes medical genetics in Africa. Nature (2014) doi:10.1038/nature13997
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