The strangeness of the human genome

Here is a little experiment:

Calculate the first principal component of variation between Papuans, and Karitiana from Brazil. These are some of the populations most distant to Africa that one can find genetic data for. (One Papuan,HGDP00544, is substantially different from the rest, and is shifted towards East Asians, so he was removed, all analyses on 613,630 SNPs with all no-calls removed).

Project 18 Mbuti Pygmies+San (henceforth Palaeoafricans) and 21 Yoruba from the HGDP-CEPH onto this component.

What do we expect? According to the standard Out-of-Africa model, you expect that Palaeoafricans and Yoruba will not differ from each other along the axis in which Amerindians differ from Papuans. If you take into account the Denisovan admixture in Australo-Melanesians, you might expect Africans (who lack this admixture) to be more Amerindian-like (since Amerindians also lack that archaic component). But, you certainly don't expect in either scenario Palaeoafricans to differ from Yoruba.

What the data say. Here are the data points along PC1:

green = Papuans

magenta = Karitiana

Here is a blowup of the middle part, showing the African populations:

red = Palaeoafrican

blue = Yoruba

A t-test supports (p less than .000001) the obvious visual conclusion that Palaeoafricans differ from Yoruba in the same way that Papuans differ from Karitiana. This is quite remarkable: why would Yoruba differ from San/Pygmies in the same way that Amazonians differ from Australo-Melanesians?

The difference is not that great: the Paleoafrican/Yoruba means are -.022 and -.020 and the Papuan/Karitiana ones are -0.167 and 0.206 respectively. Hence, the difference between Palaeoafricans and Yoruba is only 0.54% or so in this projection. But it is there, and it points to events in human prehistory not covered by the "standard model".

Discussion

I have long argued that Africa should not be viewed only as a source, but also as a destination of population movemenets. If Africa was only a source, then there would be absolutely no reason for two different African groups to differ from each other in the same way that two of the most distant (from Africa) groups do. No one can reasonably argue, I think that Africans had the opportunity of any amount of gene flow with either Papuans or Amerindians.

I conjecture that the signal detected here is a legacy of a prehistoric episode of migration of Eurasians into Africa, which affected Yoruba more than it did Palaeoafricans. This population of Eurasians was slightly more similar to Karitiana than to Papuans. We will try to trace its origins next.

Using She instead of Karitiana

I repeat the previous experiment, but I use She, a far eastern ethnic group of China instead of the Karitiana.Here are the PC1 co-ordinates in this projection:

Yoruba: 0.111, Palaeoafrican: 0.108, Papuan: -0.155, She: 0.248

Hence, Yoruba are shifted by 0.74% on the Papuan-She axis relative to Palaeoafricans.

Using Tuscans instead of She

Using Tuscans the PC1 co-ordinates are:

Yoruba: 0.169, Palaeoafrican: 0.164, Papuan: -0.144, Tuscan: 0.289

Hence, Yoruba are shifted by 1.15% on the Papuan-Tuscan axis relative to Palaeoafricans.

Using Onge instead of Tuscans

Finally, I substituted Onge from the Indian Ocean for Tuscans. This analysis is based on 112,041 SNPs, so it's not directly comparable with the previous ones. Nonetheless:

Yoruba: 0.075, Palaeoafrican: 0.07, Papuan: -0.15, Onge: 0.267

Hence, Yoruba are shifted by 1.2% on the Papuan-Onge axis relative to Palaeoafricans.

Conclusion

In a previous post on McEvoy et al. (2011) I speculated about a possible West Eurasian back-migration into Africa. The results presented here are compatible with that theory, but they are also compatible with a second Out-of-Africa movement; the latter, however, if it happened, did not only affect West Eurasians, but also East Asians and even Amerindians, at least relative to Papuans who may have been more isolated than the rest.

On balance, I prefer a scenario with back-migration:

1. It is difficult to envision a second Out-of-Africa that reached Brazil in its spread but avoided Papua, moreover there are no diagnostic uniparental markers of such an event
2. It is simpler to think of a movement of Y-haplogroup DE-bearing men a short distance from "somewhere between the Indian Ocean (where the Andamanese live), and East Africa." which would introduce Eurasian-like genes into Sub-Saharan Africa.

UPDATE (May 16): See the interesting discussion on the problem of potential ascertainment bias in the comments. In short: the signal seems to persist in the She and Tuscan comparisons, but not in the Karitiana one. Perhaps this means that whatever event took place postdates the migration of Amerindians into the New World?