evolution - Human genetic diversity in Africa in comparison with the rest of the world

Background

The claim ...

Most of the genetic diversity in humans is in Africa

... is quite common. On Biology.SE, it is easy to find posts that make this claim. Consider for example:

Question

• Is the claim true?


• What fraction of the total genetic diversity is present in Africa?

I understand that the term genetic diversity is often used in a vague sense. Please make sure to explain what statistics has been considered in the study you would refer to when giving estimates of what fraction of the genetic diversity is found in Africa. Note that I am not asking "why is it true?" but only "is it true"?

Answer

Here is a tree based on mitochondrial DNA variations in human populations.

van Oven M, Kayser M. Hum Mutat. 2009 Feb;30(2):E386-94. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation.

Looking at genetic distance between populations via mitochondria DNA, all nonafricans are descended from a founder in one mtDNA group (L3). All the other L groups are African populations: L0 is the San people, L1 is Mbenga pygmies, L5 is Mbuti pygmies, and the others are other African groups.

If one considers each L haplogroup to represent genetic variation then 5/6 (83%) of human genetic variation is from African populations.

From a different source looking at genetics differently A map of human genome variation from population scale sequencing Nature. 2010 Oct 28; 467(7319): 1061–1073

Populations with African ancestry contributed the largest number of variants and contained the highest fraction of novel variants, reflecting the greater diversity in African populations. For example, 63% of novel SNPs in the low coverage project and 76% in the exon project were discovered in the African populations, compared to 20% and 33% in the European ancestry populations for the exon and low coverage projects respectively.