Following my previous post on similarities between San people in southern South Africa, and Europeans, I read a paper about the San (Khoisan) and their "antiquity". It reports them as an ancient population that retained a large effective population while that of other groups fell (i.e. other Africans, Europeans, Asians, and the Out of Africa migrants).
The paper published in Nature in 2014 by Kim et al., (Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history). The image below shows how Ne (effective population) evolves over time (oldest to the right), for San, African Yoruba, Europeans, and Asians. As you can see all groups (actually, the ancestors leading to each of these populations) have similar population sizes till 100,000 years ago when a dramatic drop in population sizes occurs. I don't understand how they obtained Ne values for hominin populations 2 to 4 million years ago, this was the days of Australopiths and probably Homo habilis.
This drop in effective population size is attributed to climate changes within Africa. The paper includes a series of maps as Fig. 12 in its Supplementary Material to explain the process. They can be seen below:
Modern humans originated in Africa (a), blue circle in South Africa seems to imply an origin there, though the paper does not specify the location. Then these people spread north (b), the orange oval marks the new territories. Then came the climate change (c) around 150 or 100 kya. Drought in western and central Africa hit the humans there in central, western, and eastern Africa, but spared the San people in the southern part of Africa. This coincided with a fragmented population (structured) with isolated groups that did not interact with each other (see the different dots and colors on the map, marking these groups). Populations declined central and western Africa, and when the ancestors of Non-Africans (green arrows) (d) migrated Out of Africa (OOA), they carried this lower Ne, and it dwindled even more due to bottlenecks and founder effects as they advanced into Eurasia. The San, however, kept their population intact.
The authors reconstruction of this period is summarized as follows: "After the earliest split, between the ancestral Khoisan and non-Khoisan populations ~100–150 kyr ago, the ancestral Khoisan population maintained their high genetic diversity, while the effective population size of the non-Khoisan continued to decline for 30~120 kyr ago and lost more than half of its diversity. The ‘Out of Africa’ migration ~40–60 kyr ago accounts for the observed population split between African and non-African populations, and the subsequent smaller effective population size of non-Africans compared with non-Khoisan Africans."
Comments
However, and interestingly, as pointed out in my previous post, the San and Europeans share several unique allele variants that are ancestral (found also in Neanderthals and Denisovans) whcih confer lighter pigmented skin than that found among the remaining Africans and also South Asians and Australo-Melanesians, who carry a later (derived) mutation for darker pigmentation.
How does this similarity between a specific OOA group and San people tie in with the evolution and migration sproposed by Kim et al.?
Not well. We would have to imagine a group that split from the San, moved north, lived in isolation in Central Africa, then survived the climate crisis there, moved north, left Africa, surviving the founder effect, bottlenecks and genetic drift, established themselves in Europe and somehow managed to keep their skin-color alleles intact. While all the other groups in Africa mutated and adopted a dark skin set of alleles. Too complex to be the explanation.
The San (Khoisan or bushmen) have always intrigued me since the 1980s movie "The Gods Must Be Crazy", I was taken aback by their pale skin and oriental factions. So different from the usual African features. People living in the deserts of Namibia with a hunter-gatherer culture in the 20th century! I have never found a paper explaining their similarity with East Asians. I will explore this strange trait in a coming post.
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