The genetic complexity of recent migration into southern Africa

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Erika Check Hayden in this week’s Nature reports on a current preprint by Joseph Pickrell and coworkers from David Reich’s lab: “African genes tracked back”

By measuring the extent of the fragmentation, the researchers could estimate how many generations ago the chromosome had been introduced into Khoe-San genomes. They saw signs reflecting two waves of migration: one about 3,000 years ago, of non-Africans entering east Africa, and a second one 9001,800 years ago, as east Africans migrated to southern Africa and brought non-African genes along with them (see Out of Africa and back in).
Because of this two-step migration, some Khoe-San groups who were thought to have been genetically quite isolated actually carry 15% non-African DNA, report the studys authors, led by David Reich and postdoctoral fellow Joseph Pickrell.

The preprint is available on the arXiv: “Ancient west Eurasian ancestry in southern and eastern Africa”. Here is the abstract:

The history of southern Africa involved interactions between indigenous hunter-gatherers and a range of populations that moved into the region. Here we use genome-wide genetic data to show that there are at least two admixture events in the history of Khoisan populations (southern African hunter-gatherers and pastoralists who speak non-Bantu languages with click consonants). One involved populations related to Niger-Congo-speaking African populations, and the other introduced ancestry most closely related to west Eurasian (European or Middle Eastern) populations. We date this latter admixture event to approximately 900-1,800 years ago, and show that it had the largest demographic impact in Khoisan populations that speak Khoe-Kwadi languages. A similar signal of west Eurasian ancestry is present throughout eastern Africa. In particular, we also find evidence for two admixture events in the history of Kenyan, Tanzanian, and Ethiopian populations, the earlier of which involved populations related to west Eurasians and which we date to approximately 2,700 - 3,300 years ago. We reconstruct the allele frequencies of the putative west Eurasian population in eastern Africa, and show that this population is a good proxy for the west Eurasian ancestry in southern Africa. The most parsimonious explanation for these findings is that west Eurasian ancestry entered southern Africa indirectly through eastern Africa.

I want to point out a corollary of this research, which has the potential to change a lot of our consideration of modern human origins.

Some history: The 1990s and early 2000s saw a long series of finding putatively “ancient” gene lineages outside of Africa, proposed as possible evidence of archaic hominin contribution to those populations, or a longer chronology to the emergence of African genes into those populations. In many cases, the gene lineage was later found in Africa at very low frequency, as a result of denser sampling of African populations. This greatly fueled the concept that non-African populations have only a “subset” of African population variation.

John Relethford had pointed out in a series of papers (e.g., Relethford:1995) that most of the observations on variation inside and outside of sub-Saharan Africa did not really demonstrate a recent large-scale migration out of Africa. This is because it was possible to construct a matrix of long-term, low-level gene flow among populations that gave the same outcome. Different ancient population sizes also could contribute to the pattern, reducing the level of genetic drift in Africa relative to non-Africans (e.g., Relethford:Harpending:1995).

If there was long-term gene flow into Africa, either episodically or continually, then we would expect ancient gene lineages outside of Africa would often – maybe always – exist inside Africa as well. If we neglect such gene flow, we might apparently never have evidence of ancient gene survival outside Africa that couldn’t be explained by a very selective recent migration of genes out of Africa.

Only if a gene lineage remained very rare outside Africa would there be a good chance for the combined effects of migration and drift to keep it out of the large African population. Or if selection made the gene lineage an extreme disadvantage in African environments.

The Neandertal and Denisovan genomes allow a much more informative comparison about the question of early versus later gene flow. But they have raised other questions. Many derived alleles are shared between sub-Saharan Africans and these ancient genomes. Certainly the vast majority of these shared alleles are due to incomplete lineage sorting from ancestral African populations. But some fraction reflects Late Pleistocene and Holocene gene flow into Africa from Eurasia (and via Madagascar). And some fraction reflects gene flow from Neandertal populations into Africa. Determining how much can be attributed to these different time periods will be possible by using techniques like that applied by Pickrell and colleagues here.

More important, no African population today is a “pristine” descendant of LSA Africans. The global population has been highly connected by gene flow throughout the Holocene, as a function of population growth and long-distance movement. This paper demonstrates at least two periods of important gene flow, but this is almost certainly an simplified version of the complex reality.

Models that don’t incorporate substantial recent gene flow are going to misrepresent modern human origins.