Continuing with my series of posts on the diversity and higher heterozygosity of contemporary Africans, which may be due to many factors: post-OOA admixture within Africa with diverse archaic hominins leading to a higher Ne. A higher mutation rate due to this higher Ne, and to adapting to the environmental challenges of Africa. Higher mutation rate driven by higher heterozygosity. All of which lead to a higher diversity in contemporary Africans (note that we have no ancient DNA sequences from H. sapiens in Africa as we do for Neanderthals in Eurasia, and H. sapiens in Eurasia, Oceania, and America.
There is also the question of Neanderthal admixture in Africans. I discussed this in a 2019 post and in a 2020 post but more papers have appeared on the subject as we will see below.
The generalized notion is that human beings admixed with Neanderthals, who lived in Eurasia, during the Out Of Africa migration. Since there were no Neanderthals in Africa, those humans who remained behind in Africa never mingled with the Neanderthals, and therefore have no genetic input from them. But, back in 2018 a paper reported a Neanderthal genes in East Africa, they were carried there by Eurasian humans who had admixed with the Neanderthals in Eurasia
In and Out of Africa. Copyright © 2026 by Austin Whittall
The map above shows the homeland of the OOA migrants, in the Horn of Africa (Ethiopia) and the red arrows mark the OOA migration across Eurasia and Oceania. In Europe and Western Asia they met the Neanderthals who lived there, mated, admixed, and some modern humans returned to Africa (blue arrows) carrying Neanderthal alleles with them.
The 2020 paper mentioned above suggests that "Back-Migration with Non-Africans and Pre-out-of-Africa Human-to-Neanderthal Gene Flow Contribute to Apparent Neanderthal Ancestry in Africans", two mechanisms, one, the backflow and second, an early gene flow from an early, failed OOA migration that introgressed human alleles in Neanderthals (100-250 ky ago), and which appear as shared between Neanderthals and humans when they are compared.
Below is an image from A. Ragsdale (2023), that shows these gene sharing events (early-OOA with Neanderthals, and Neanderthal-Later OOA admixture and backmigration of Eurasians to Africa).
Figure 1. A history of reciprocal introgression between humans and Neanderthals.
(A) Population structure among the ancestors of modern humans extended deep in the past, though common ancestry of all present-day humans is more recent than the expansion of early Homo sapiens out of Africa that resulted in human-to-Neanderthal admixture. Arrows indicate major migration and admixture events.. Fig. 1A in Ragsdale (2023)
The Neanderthal admixture was present in samples obtained from LWK = Luhya in Webuye, Kenya, East Africa. GWD = Gambian in Western Division, Mandinka, in West Africa. MSL = A Mende population from Sierra Leone in West Africa. YRI = Yoruba in Ibadan, Nigeria, in West Africa. ESN = Esan in Nigeria, West Africa. This is a pan-African presence.
This paper found that "of the Neanderthal sequence identified in African samples, more than 94% was shared with non-Africans..." only a small part was uniquely African, as you can see in the following image, Fig. 2 B in that paper captioned: "Venn diagram showing the amount of overlap in identified Neanderthal sequence in non-African and African populations." Europeans have ~80% more unique Neanderthal alleles than Africans, yet they have their own unique alleles not shared with Eurasians, they seem to have been lost in Eurasia, or, did they come from introgressions with other archaics in Africa, carrying these alleles?
Then they "also performed extensive simulations and found that the signal of Neanderthal ancestry in Africans was unlikely to be explained by false positives due to shared ancestry." They therefore attribute the signal to admixture. But where? In Africa or due to a backflow?
The paper states that they considered both options: "studied models where non-African individuals, who carry Neanderthal sequences inherited from hybridization, migrated back to Africa and models of human-to-Neanderthal gene flow due to an early pre-out-of-Africa (pre-OOA) dispersal of modern humans." Note that they don't consider the inside-of-Africa mixing but, instead, admixing in an Early out of Africa mixing (more on this below).
Regarding backflow they found that "These data are consistent with the hypothesis that back-migration contributes to the signal of Neanderthal ancestry in Africans. Furthermore, the data indicate that this back-migration came after the split of Europeans and East Asians, from a population related to the European lineage."
Early Out Of Africa
The paper then finds that there is "strong evidence that human sequence in the Neanderthal genome also contributes to the signal of the Neanderthal ancestry we detect in Africans." The first out of Africa event which supposidly took place betewwn 100 and 150, or even 250 ky ago introgressed human genes into Neanderthals, a gene flow from H. sapiens of this first wave into Neanderthals. Previous studies have noted the genetic contribution of a pre-out-of-Africa gene-flow event from humans into Neanderthals. So, when comparing Neanderthals with current modern humans, we find that we share some alleles (of course, they were originally human genes).
West Africa
Both the 2020 paper mentioned above, and anothe paper by Anders Bergström (2020) found ancient admixture of Neanderthal genes in West Africa. West Africa! which is on the opposite side of Africa from which the OOA event ocurred. How could there be Neanderthal genes so far from East Africa?
Bergström assumes it is a backflow from Eurasia, but also adds that they may be relict alleles from the period that predates the OOA event, and that preserved these genes in Africa, which were lost elsewhere:
"We found small amounts of Neanderthal ancestry in West African genomes, most likely reflecting Eurasian admixture. Despite their very low levels or absence of archaic ancestry, African populations share many Neanderthal and Denisovan variants that are absent from Eurasia, reflecting how a larger proportion of the ancestral human variation has been maintained in Africa....
Alleles private to Africa, however, include a higher proportion of ancestral alleles, and this proportion increases with allele frequency, reflecting old variants that have been lost outside of Africa. For the same reason, many high frequency private African variants are also found in available Neanderthal or Denisovan genomes."
If Africans carry variants of Neanderthal and Denisovan genes not found elsewhere it means that these introgressed into Africans, within Africa, maybe from isolated populations of these ancient humans found inside of Africa.
When it comes to splits within African populations, Bergström's paper assumed "a mutation rate of 1.25 × 10−8 per base pair per generation and a generation time of 29 years" and calculated the splits between populations but found that "all of these curves are clearly inconsistent with clean splits, suggesting a picture where genetic separations within Africa were gradual and shaped by ongoing gene flow over tens of thousands of years. For example, there is evidence of gene flow between the San and the Biaka until at least 50 kya, and between the Mbuti, the Biaka, and the Yoruba until the present day." This is in line with an "enrichment" of modern Africandiversity by agglutination of the past diversity preserved in isolated African populations, as mentioned in my recent posts.
Ancient structure influenced modern diversity: "For the deepest splits, there is some evidence of genetic separation dating back to before 300 or even 500 kya... The implication of this is that there lived populations already at this time that contributed more to some present-day human ancestries than to others... but also a small fraction of present-day ancestries retaining traces of structure that is older than this, potentially by hundreds of thousands of years." Here, I ask, are these ancient alleles result of recent post OOA introgression of ultra-archaic hominins in Africans? or the common ancestors of humans and Neanderthal-Denisovans?
The presence of Neanderthal alleles in Africans was quantified by Bergström as follows: "The West African Yoruba also display a Neanderthal admixture signal that is similar in shape but much less pronounced than that in non-Africans (Fig. 6D and fig. S9). Other African populations do not clearly display the same behavior. These results provide evidence for low amounts of Neanderthal ancestry in West Africa, consistent with previous results that were based on other approaches, and we estimate this at 0.18 ± 0.06% in the Yoruba using an f4-ratio (assuming that the Mbuti have none). The most likely source for this is West Eurasian admixture and, assuming a simple linear relationship to Neanderthal ancestry, our estimate implies 8.6 ± 3% Eurasian ancestry in the Yoruba."
Sub Saharian Africa (SSA)
The people living in Africa south of the Sahara also carry Neanderthal alleles, a study by Harris et al., 2024: " As a percentage of the genome, therefore, Neanderthal ancestry in the 180 SSA dataset ranges from 0% to ~1.5%, with the highest levels observed in the Amhara and Fulani."
They favor the sequence: early migration of anatomically Moderh Humans (AMH) out of Africa ~250 ky ago, admixing with Neanderthals in Eurasia, leaving a ~6% AMH genetic trace in Neanderthals. Then, the final OOA event with modern humans, who mated with Neanderthals (~40 to 55 kya), receiving these AMH haplotypes from the Neanderthal (NIRs). Then, " Third, at least two subsequent recent migrations of non-sub-Saharan African AMHs into sub-Saharan Africa brought introgressed Neanderthal haplotypes (NIRs) to sub-Saharan African AMH populations with whom they admixed."
Perhaps the best theory is the one that suggests that the Neanderthal signal was acquired inside Africa, as we will see below.
An introgression within Africa
Arun Durvasula and Sriram Sankararaman (2020) on the other hand suggest that the Neanderthal genes came from a direct "within Africa" admixing event:
"We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans... Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations."
They compared three different models in which part of the West African ancestry comes from, (A) people who split from their ancestors after modern humans and Neanderthals split; (B) people who derive from the ancestors of Neanderthals after they split from modern Humans, and (C) people who split from the ancestors of modern humans and Neanderthals before modern humans and Neanderthals split. They found that (C) was the best model:
"support for a contribution to the genetic ancestry of present-day West African populations from an archaic ghost population whose divergence from the ancestors of modern humans predates the split of Neanderthals and modern humans.
... We determined the posterior mean for the split time to be 625,000 years before the present (B.P.) [95% highest posterior density interval (HPD): 360,000 to 975,000], the admixture time to be 43,000 years B.P. (95% HPD: 6000 to 124,000), and the admixture fraction to be 0.11 (95% HPD: 0.045 to 0.19). Analyses of three other West African populations (ESN, GWD, and MSL) yielded concordant estimates for these parameters. Combining our results across the West African populations, we estimate that the archaic population split from the ancestor of Neanderthals and modern humans 360 thousand years (ka) to 1.02 million years (Ma) B.P. and subsequently introgressed into the ancestors of present-day Africans 0 to 124 ka B.P. contributing 2 to 19% of their ancestry."
This means that an ancient, relict population that split from the branch leading to Modern Humans and Neanderthals between 360 and 975 ky ago, on avg. 625,000 years ago, mated with Homo sapiens people in Western Africa, and this event ocurred after the OOA event that peopled the rest of the world, this admixture inside of Africa took place roughly 43,000 years ago (0 to 124 ky).
Maybe later there was backflow from Eurasia, but this introgression in Western Africa with an ultra archaic human is the one tha injected Neanderthal-like genes into this population. It must have surely contributed to the diversity of these populations, adding more heterozygosity to them.
This idea is supported by Nina Hollfelder, Gwenna Breton, Per Sjödin, and Mattias Jakobsson, (2021):
"Another possibility is that the large Ne is shaped by multiple introgression events from divergent lineages, which are hard to distinguish without archaic reference sequences. Unfortunately, many studies of archaic or ghost introgression in Africa focus on a few populations and/or use only one method for inference, so that the effect of the identified archaic or ghost introgression is not yet comparable across all major branches of modern humans in a systematic way.
Interestingly, many studies identified a fairly recent time for the introgression from extinct lineages in Africa, with introgression events even after the split from non-African populations, hinting at survival of archaic human populations until relatively recently in time."
Where Ne is the effective population, the large Ne of the African population is considered as one of the factors that created its diversity vs. the rest of the World, with lower Ne's due to bottlenecks and lower diversity. Here, we see that multiple introgression from diverse populations that merge can also lead to the effect of a high Ne!
I personally support the idea of super-archaics mixing with Africans after the OOA event, adding diversity and heterozygosity to their genetic makeup, and I don't exclude a backflow from Eurasia with Neanderthal genes.
No Neanderthals or Denisovans, but an archaic introgression
Last but not least, Lorente Galdos et al., (2019)" found no signals of Neanderthal or Denisovan
introgression in the sub-Saharan individuals... We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage.... Our results suggest interbreeding of AMHs with an archaic ghost population that diverged from the AMH lineage at a temporal scale similar to the one between the Neanderthals and Denisovans. "
The timeline given in this paper is the following: "the AMH lineage and the one from the archaic Eurasian populations
diverged 603 kya (95% credible interval (CI) ranging from 495.85 to 796.86 kya). The ghost XAf archaic population
and the AMH lineage split 528 kya (95% CI of 230.16 to 700.06 kya), whereas the Denisovan and Neanderthal lineages split 426 kya (95% CI from 332.77 to 538.37 kya). Archaic introgression estimates from XAf to African populations range from 3.8% (95% CI 1.7 to 4.8%) in Khoisan and 3.9% (95% CI 1.3 to 4.9%) in Mbuti to 5.8% (95% CI 0.7 to 0.97%) in West Africa. Our analyses also identified the archaic introgression from early AMHs into Neanderthal."
I wonder if the AMH introgression into Neanderthals (also mentioned further up) which is said to have taken place during the early OOA event 250-100 ky ago, isn't just the reflection of the common origin and relatedness between Neanderthals and these early AMHs. They split in Africa and had common genes. Seems a simple, straightforward explanation.
Regarding the ghost archaics XAf population, I have posted about them in the past (see this post, this post, this one, and this post among others), they are indeed a source of diversity, rare alleles, and heterosygosity for contemporary Africans.
Comments
As you can see, many research papers, authors, models, interpolations, algorithms, and softwares used and different interpretations from the same basic genetic samples!
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