Two preprints/papers.
Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals:
Admixture has played a prominent role in shaping patterns of human genomic variation, including gene flow with now-extinct hominins like Neanderthals and Denisovans. Here, we describe a novel probabilistic method called IBDmix to identify introgressed hominin sequences, which, unlike existing approaches, does not use a modern reference population. We applied IBDmix to 2,504 individuals from geographically diverse populations to identify and analyze Neanderthal sequences segregating in modern humans. Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.
Basically, this paper concludes that Eurasian back-migration related to Europeans/West Asians seems to be around 30% of Sub-Saharan African ancestry. They carry about 30% of the Neanderthal ancestry of Eurasians.
Then, a preprint that uses a pretty sophisticated method, Ancient Admixture into Africa from the ancestors of non-Africans:
Genetic diversity across human populations has been shaped by demographic history, making it possible to infer past demographic events from extant genomes. However, demographic inference in the ancient past is difficult, particularly around the out-of-Africa event in the Late Middle Paleolithic, a period of profound importance to our species’ history. Here we present SMCSMC, a Bayesian method for inference of time-varying population sizes and directional migration rates under the coalescent-with-recombination model, to study ancient demographic events. We find evidence for substantial migration from the ancestors of present-day Eurasians into African groups between 40 and 70 thousand years ago, predating the divergence of Eastern and Western Eurasian lineages. This event accounts for previously unexplained genetic diversity in African populations and supports the existence of novel population substructure in the Late Middle Paleolithic. Our results indicate that our species’ demographic history around the out-of-Africa event is more complex than previously appreciated.
This paper estimates 35-40% back-migration from the ancestral proto-Eurasian population, with less (~20%) in African hunter-gatherers. This paper didn’t detect Neanderthal ancestry and argues that the back-migration predates the West vs East Eurasian split. It plausibly argues African effective population sizes are inflated by the admixture event.
The two results here clearly contradict the details.
The implication is that the difference between Khoisan and Bantu represents a shift in the direction of Eurasian human evolution?
Potentially relevant to this topic, this new paper should be extremely interesting whenever it comes out:
Ancient DNA and deep population structure in sub-Saharan African foragers
Multiple lines of genetic and archaeological evidence suggest major demographic changes in the terminal Late Pleistocene and early Holocene of sub-Saharan Africa. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured more ancient population structures. To probe deeper time, we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the last ~18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase data quality on 15 previously published ancient individuals, and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, likely reflecting Pleistocene interactions ~80-20 thousand years ago: deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of central African ancestry. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analysis but remain contested, suggesting increasing regionalisation at the end of the Pleistocene.
https://www.ebi.ac.uk/ena/browser/vi…291?show=reads