In recent years, it has been discovered that many human beings not from sub-Saharan Africa trace a few percent of their DNA back to two mostly extinct species, the Neanderthals and the Denisovans.

But what about Africans? Do they have lost ancestors of their own?

A preprint:

New Results

Recovering signals of ghost archaic admixture in the genomes of present-day Africans Arun Durvasula, Sriram Sankararaman This article is a preprint and has not been peer-reviewed . Abstract Analyses of Neanderthal and Denisovan genomes have characterized multiple interbreeding events between archaic and modern human populations. While several studies have suggested the presence of deeply diverged lineages in present-day African populations, we lack methods to precisely characterize these introgression events without access to reference archaic genomes. We present a novel reference-free method that combines diverse population genetic summary statistics to identify segments of archaic ancestry in present-day individuals. Using this method, we find that ~7.97±0.6% of the genetic ancestry from the West African Yoruba population traces its origin to an unidentified, archaic population (FDR ≤20%). We find several loci that harbor archaic ancestry at elevated frequencies and that the archaic ancestry in the Yoruba is reduced near selectively constrained regions of the genome suggesting that archaic admixture has had a systematic impact on the fitness of modern human populations both within and outside of Africa.

John Hawks tweets:

If this @biorxivpreprint from Durvasula and Sankararaman is correct, it shows a remarkable level of deep hybridization in the ancestry of today’s African populations. Could some West African populations (in this case, Yoruba) really have 8% of their genomes from a deeply diverged, extinct population? The estimate is not hugely more than the 5% that Jeff Wall suggested back in 2006, based on different methods, so in one sense this is an incremental increase (and independent confirmation) of the level of introgression. In this new preprint, the methods don’t support any inferences about the nature of the “archaic” source population. We might like to know how deeply divergent it was: equal to Neandertals? More? Answers will take better datasets. This sentence I predict we will hear a lot more of in the near future: “there was a rich diversity of hominin species within Africa and that introgression was commonplace” To be clear, we are talking about species that continued to exist and mix with modern populations within the last 50,000 years.

Dienekes blogs:

I have long maintained that the higher genetic diversity of extant Sub-Saharan Africans is the result of admixture between “Afrasians” (a population that spawned Eurasians and much of the ancestry of Sub-Saharans and which had “low” (Eurasian-level) of genetic diversity) and multiple layers of “Palaeoafricans”. It would seem that one such layer has now been discovered. Where did the Afrasians live? Recent developments pushed back the presence of modern humans in both North Africa and the Middle East, making both regions highly competitive as the cradle of the Afrasians. The odds for Sub-Saharan Africa have greatly diminished also by the discovery of late non-sapiens H. naledi in South Africa (which was naively postulated as a cradle based on the presence there today of genetically diverse San Bushmen, but who are not descendants of even Late Pleistocene South Africans), as well as of the archaic component in the genomes of West Africans. These discoveries pile up on top of known archaic skulls of late provenance in both Central and West Africa. Remember though, that the archaic admixture in West Africans is “less archaic” (more closely related to H. sapiens) than the Neandertal/Denisovan ancestry which contributed to extant Eurasians. All Africans (modern or archaic) are a branch within the phylogeny of Eurasians, with Australoids (and now apparently East Asians too) having the deepest known strain of human ancestry inherited from the elusive Denisovans.

Here’s an earlier post by Dienekes:

Out of Africa: a theory in crisis January 26, 2018 The sensational discovery of modern humans in the Levant 177-194 thousand years ago should cause a rethink of the currently held Out-of-Africa orthodoxy. By Out-of-Africa, I mean here the origin of anatomically modern humans, as opposed to the earlier origin of the genus Homo or the later origin of behaviorally fully modern humans. Two main pieces of evidence supported the conventional OOA theory: 1. The observation that modern Eurasians possess a subset of the genetic variation of modern Africans.

2. The greater antiquity of AMH humans in the African rather than the Eurasian palaeoanthropological record. Both these observations are in crisis.

You can read the whole thing there.