Which population is most genetically distant from Africans?

A comment below:

Razib, I don’t know much about genetics but is it true that these people of Melanesia are among the least related people (even more so than Europeans) to sub-saharan Africans genetically??

This is a common question. The typical scientifically curious intelligent person is generally aware that on the order of 100,000 years ago there was a movement of anatomically modern humans from Africa. They know that Africans have the most genetic variation of any human population, and that in fact Africa has more genetic variation than the rest of the world combined. It would stand to reason then that the further you are from Africa, the more genetically distant you are. Simply because of recent admixture of Sub-Saharan African ancestry in much of the Middle East there is some truth to this, but I think it misses the “big picture.”

To the best of my knowledge the current consensus on the origin and expansion of modern humans goes like so:


1) Anatomically modern humans emerge in Africa first ~200,000 years ago. This population is a sister lineage to the various Eurasian hominins, Neandertals, X-woman, etc.

2) Between 50,000 and 200,000 years ago a subset of the African population left Africa.

3) Sometime between the exit-from-Africa event and the present the anatomically modern humans replaced all other lineages (with some assimilation) and diversified.

My confidence in any specific aspect of the “orthodox census” is very high, though joint probability of the details is more modest. #3 for example had to be modified a bit recently because of the possible existence of Neandertal admixture in Eurasians. So back to my question, assuming this model, which population is most genetically distant from Africans? The answer is really none. Here are some figures from Xing et al., which gets at why the answer is “none of the above”:

AFRICAVSNONAFRICA

Here’s the text for the figure:

Figure 3. Population relationships between the 40 populations. A) Neighbor-joining tree. Populations are color-coded based on their continental origins. The hypothetical ancestral population is shown. Bootstrap support values for most branches are larger than 95% (the bootstrap consensus tree is shown in Supp. Figure S1). B) Principal components analysis. First two principal components (PCs) are shown. Each individual is represented by one dot and the color label corresponding to their regional origin. The percentage of variance explained by each PC is shown on the axis. C) Individual grouping inferred by ADMIXTURE. Results from K = 4 and K = 12 are shown. Each individual’s genome is represented by a vertical bar composed of colored sections, where each section represents the proportion of an individual’s ancestry derived from one of the K ancestral populations. Individuals are arrayed horizontally and grouped by population as indicated.

The tree makes it clear: all non-Africans form their own independent branch from Africans. In the PCA you see that along the biggest component of variation in the genetic data the non-African groups are about the same distance from Africans. And in the ADMIXTURE analysis when you assume four ancestral populations, the Africans and non-Africans separate out cleanly excluding groups which a high likelihood of European or Arab admixture. Remember the part about how Africans have more genetic diversity than all non-Africans combined? That’s also part of the puzzle. In some ways all non-Africans can be thought of as a subset of the genetic variation of Africans. Those humans who reside outside of Africa are simply a diversified branch of Africans. From what I can tell the data is converging on the likelihood that there was only one migration out of Africa which resulted in the branches of non-African humanity. That means that those of us of non-African ancestry are all equally distant from the African root.

Source: Discover Magazine – Gene Expression