Neanderthals in Africa?

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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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

On the Diversity of Africans

In a recent post I wrote about the Neutral Theory of molecular genetics, and its shortcomings. Today's post will explore the African genetic diversity, a foundation on which the Out Of Africa (OOA) theory is based.

There are several questions that should be answered: Do modern Africans reflect the genetic makeup of ancient Africa 100,000 or 75,000 years ago? Is a modern Nigerian, Gambian, Angolan African representative of the ancient population from which the Out of Africa migrants split? Have other events taken place within Africa in other populations that were isolated from the sub-population that was the root or base from which modern H. sapiens migrated into Eurasia?

Admixture with archaic hominins after the OOA event (such as H. naledi), admixture between many separate and formerly isolated hunter gatherer sub-populations due to migrations like the Bantu migration could have led to a modern highly diverse African population, while the original OOA root was far less diverse.

The image below is a crude attempt to reflect the isolated populations within Africa at the time modern Humans appeared. Each circle is a population. They all contain allelles (colored red, blue, yellow, etc.) some shared, others unique to each population. The black arrows show the migration Out of Africa, with humans dispersing across Eurasia towards Siberia, Europe and Oceania, and America. They lose diversity on the way due to Genetic Drift.

The dashed red arrows converging on a circle shows the internal migrations within Africa by which these formerly isolated sub-populations of humans admixed and the final, contemporary population has an even higher diversity than the original root of the Out of Africa migration (set in the horn of Africa).

It does not show any back-flow of humans from Eurasia into Africa, or archaic introgression either in Africa or in Eurasia (Neanderthals, Denisovans).

Genetic Drift out of Africa. Copyright © 2026 by Austin Whittall

Population structure in Africa

The humans in Africa were not a uniform population. A paper published in Nature suggested that there were "low levels of gene flow among archaic populations before the emergence of anatomically modern humans — that is, they imply the existence of ancestral population structure." It also hints at admixture with primitive, archaic, hominins in Africa: "There is also growing evidence that some highly divergent genetic lineages might have entered our genome through hybridization between an expanding anatomically modern human population and archaic forms of humans."

Another article published in Nature, questions the use of modern Africans to model the OOA event. While highlighting the high diversity within Africa, the paper also states that "we will need to establish whether selection has continued to operate effectively on complex traits, leading to unbiased estimates from these populations. If not, it may still be inappropriate to use a specific modern African population as a proxy for the ancestral population of modern humans."

Additional research (Source) looks into the effects of the structured population within ancient pre-OOA Africa: "Several studies have indicated that ancestral populations were geographically structured before modern humans migrated out of Africa. For example, it has been suggested that the deep coalescence times of mtDNA and X-chromosome lineages are consistent with a demographic scenario of ancient population structure in Africa. A recent analysis of cranial shape variability in anatomically modern human fossils (dating to 200–60 kya) from Africa and the Middle East also reported a high level of morphological divergence among these fossil hominids which was interpreted as evidence for ancestral population structure in Pleistocene Africa. Thus, arguably, a considerable amount of genetic and phenotypic diversity may have been present at an early stage of modern human evolution."

Indeed! And not all of this diversity was found in one population, each sub-population had their own alleles, later admixed into modern Africans (minus alleles lost due to genetic drift) and plus backflow from Eurasia with introgressed Neanderthal genes, and the mutations added by an additional 100 ky of evolution in Africa, subjected to natural selection and random mutations over that period of time.

This paper also mentions the backflow: "The reverse migration of non-Africans into Africa was also shown to contribute to the gene-pool of modern African populations"

The variations observed in skulls mentioned above was reported by a paper published in Nature. Different skull shapes mean that different sets of genes were working and they were not the same alleles in each sub-population.

"Late Middle Pleistocene (LMP, from 350 to 130 ka) African fossils [were highly variable]... Even when excluding the H. naledi material, African LMP fossils exhibit extremely variable morphologies. The Omo I22 and Herto specimens have a modern-like anatomy... and are generally considered the earliest undisputed remains of H. sapiens. All other LMP African fossils show a mosaic of derived and archaic characters. For instance, the Jebel Irhoud remains were originally described as showing strong similarities with Neandertals, while the study of the new Irhoud remains emphasises their affinities with H. sapiens, despite the absence of key modern humans apomorphies. The Guomde, Ngaloba, Eliye Springs and Florisbad specimens along with Omo II... have been mostly referred to as ‘archaic H. sapiens’, a category grouping isolated fossils with disparate morphologies. This situation challenges any attempt at identifying the evolutionary mechanisms that may explain the morphological pattern in the African LMP fossil record, as well as identifying the ancestral population, or populations, of modern humans"

The Admixture Within Africa

These different groups of humans must have later admixed into the base from which modern Africans come from. Possibly after the basal Homo sapiens left Africa in its OOA journey.

Yet another paper from Nature investigated contemporary African diversity. It looked at the genes and ancient migrations in different populations, including the Hunter gatherers (HG) and the supposedly most ancient group of humans, and the most diverse one, those living in sub-Saharan Africa (SSA), to define the current genome of Africans. It found an important effect from Eurasian admixture and a strong influence of natural selection modelling modern genes:

"Eurasian ancestry has a substantial impact on differentiation among SSA populations...
We found evidence for historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA. Specifically, ancient Eurasian admixture was observed in central West African populations (Yoruba; ∼7,500–10,500 years ago), old admixture among Ethiopian populations (∼2,400–3,200 years ago) consistent with previous reports, and more recent complex admixture in some East African populations (∼150–1,500 years ago). Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period.
We also find evidence for complex and regionally distinct HG admixture across SSA, with ancient gene flow (∼9,000 years ago) among Igbo and more recent admixture in East and South Africa (multiple events ranging from 100 years ago to 3,000 years ago), broadly consistent with historical movements reflecting the Bantu expansion. An exploration of the likeliest sources of admixture in our data suggested that HG admixture in Igbo was most closely represented by modern day Khoe-San populations rather than by rainforest HG populations.
Positive selection in SSA
We examined highly differentiated SNPs between European and African populations, as well as among African populations to gain insights into loci that may have undergone selection in response to local adaptive forces. To account for confounding due to Eurasian admixture, we also conducted analyses after masking Eurasian ancestry. On examining locus-specific Europe–Africa differentiation, enrichment of loci known to be under positive selection was observed among the most differentiated sites (P = 1.4 × 10−31). Furthermore, there was statistically significant enrichment for gene variants among these, indicating that this differentiation is unlikely to have arisen purely from random drift..."

So modern African diversity is the result of recent admixture across the continent and the forces of natural selection. These people are not the same people that saw the OOA migration depart.

Archaic introgression in Africa

Regarding introgression of archaic human in Africa, I had posted back in 2019 about it (See post: Archaic Ghost population admixed with Modern Humans in Africa) which quotes a paper by Lorente-Galdos et al. that reported that: "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."

Another paper form 2020, published in Science found the same effect in Western Africa: "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. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations."

This introgression took place in West Africa after the OOA: "the admixture time ... 43,000 years B.P. (95% HPD: 6000 to 124,000), and the admixture fraction ... 0.11 (95% HPD: 0.045 to 0.19).", that is 11% mean (4.5 to 19%). And then subject to selection as it was an adaptive introgression.

This surely contributed to the diversity of the alleles in these people compared to those who left Africa in the OOA migration.

Other confounders

Finally, there is the question of back-migrations from Eurasia into Africa. These people who returned "Into Africa" or "Out of Asia" back flow carried with them genes from people who had left Africa, plus admixture with Neanderthals (and maybe, Denisovan, ultra-archaics, first wave humans who left before the final OOA event). This surely contributed to the genetic diversity of Africa.

Another element to consider is the mutation speed or faster evolutionin Africa which could have fueled diversity starting even before the final OOA event 60-100 ky ago. But that is the subject of a future post.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

Neanderthal genes in Africans: a confirmed fact

Last October I posted about a paper that disclosed that Africans had a higher Neanderthal signature in their mtDNA than Asians or Europeans.

African lack of Neanderthal DNA (and mtDNA) is used as proof of the Out of Africa (OOA) event, because it is said that Neanderthals and Homo sapiens admixed outside of Africa after H. sapiens migrated from Africa on their OOA journey.

A recent paper cast a shadow of doubt on this assumption: they have found signals of Neanderthal DNA in Africans!

The paper is: Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals by Lu Chen, Aaron B. Wolf, Wenqing Fu, Liming Li, and Joshua M. Akey. Chen et al., 2020, Cell 180, 1–11 February 20, 2020 https://doi.org/10.1016/j.cell.2020.01.012.

It summarizes their research as follows:

"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"

The paper finds that some of the ancestors of modern Europeans back migrated into Africa after they had split from those who would later become East Asians.

They found 13 African-specific high-frequency Neanderthal haplotypes which are unique to Africans, and only found in Africa, and another 31< haplotypes shared with Europeans. Specific African genes means that selection preserved them because they gave those carrying them some immune benefits and also protection against UV radiation in sunlight.

So now we know that ALL humans have Neanderthal genes in their genome, including Africans.

This gene flow, which had not been recognized until now also caused biased estimations of Neanderthal admixture in Asians and Europeans: East Asians seemed to have 20% more Neanderthal DNA than Europeans, which was odd, considering that Neanderthals lived in western Eurasia so admixture there would have been higher than in the Far East.

But now it seems that roughly 0.3 to 0.5 % of African genome was inherited from Neanderthals (vs. 1.8% in Non-Africans).

So factoring in this African Neanderthal content, the East Asians ended up with only 8% more Neanderthal genes than Europeans.

The study found "[in] African populations, we identified approximately 17 Mb of putative Neanderthal sequence per individual"

Compare thiese 17Mb with what they found in Europeans and Asians:

"we found similar levels of Neanderthal ancestry in Europeans (51 Mb/individual), East Asians (55 Mb/individual), and South Asians (55 Mb/individual)"

So Africans have roughly one third of the Neanderthal admixture that non-Africans have! See the image below which shows exactly this (non-Africans in Blue, Africans in brown):

Neanderthal genetic admixture in humans. From Fig. 2 in Chen et al.

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Finally, around 94 percent of Neandertal DNA sequences found in Modern Africans is also shared with Non-Africans.

The paper explains the Neanderthal admixture into Africa as follows: "In summary, these data indicate that both pre-OOA human-to-Neanderthal gene flow and elevated historic backmigration contribute to the signal of Neanderthal ancestry detected in Africans.".

The first wave of humans to leave Africa between 250 and 150 kya, mixed with Neanderthals in Eurasia and passed on to them some archaic human genes. These were lost as this pre-OOA wave became extinct. The Neanderthals then mixed with the OOA wave and part of these admixed modern Humans returned to Africa bringing the genes with them.

Perhaps further studies -Science news reports an unpublished study that ratifies Chen et al. findings: "as-yet-unpublished work by Sarah Tishkoff, an evolutionary geneticist at the University of Pennsylvania. She told Science she has also found higher-than-expected levels of apparent Neanderthal DNA in Africans."

I have written many posts about "into Africa events", but this one is the first paper to conclusively prove the presence of Neanderthal genes in modern Africans.

This will open the gates to more scrutiny on the origin of the higher "African" diversity when compared to the rest of humankind. This diversity is surely due to admixture with archaic populations and not only to bottlenecks caused by an OOA migration.

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2020 by Austin Whittall © 

Skin color and Neandertals

Qiliang Ding et al., (2014) published a paper (Neanderthal origin of the haplotypes carrying the functional variant Val92Met in the MC1R in modern humans, Molecular biology, DOI:10.1093/molbev/msu180) which looks into the pale skin of Eurasians in general as due to admixture between Homo sapiens and Neandertals.

The color of our skins is due to the combination of two pigments, one red (phaeomelanin) and one black (eumelanin), and the proportion of this color blend is in part defined by the Melanocyte-stymulating hormone or MSH. MSH is encoded by a gene called MC1R.

If the function of this gene is altered by mutations, it impacts on MSH and therefore on skin color.

Five "loss-of-function" variants of MC1R have been discovered to date, and are linked to fair hair (red or blond) and fair skin:

1. Val60Leu (rs1805005*T)
2. Val92Met (rs2228479*A)
3. Arg151Cys (rs1805007*T)
4. Arg160Trp (rs1805008*T)
5. Asp294His (rs1805009*C)

Neanderthals also carried (but we, modern humans don't), another variant of MC1R (Arg307Gly)

Qiliang's team found that "...almost all of the derived alleles at the Val92Met variant of MC1R (rs2228479*A) in the human gene pool are carried by the putative introgressive haplotypes", by "putative introgressive haplotypes" they mean "haplotypes from Neanderthal introgression in modern Eurasians".

It is found at roughly 5% introgression rates in Europeans (not very high), up to 30% in East Asians (Chinese for instance) and at a surprising high introgression rate of 60 to 70% in the Taiwanese aborigine people (the Atayal and the Ami).

They don't know why this cline exists and conjecture: " Therefore, we cannot rule out demographic effects such as population bottleneck as an explanation for the unusually high frequency of rs2228479*A in Atayal and Ami although positive natural selection is also a possibility"

Its origin is linked to the Altai Neanderthal branch and the time line is the following:

"Based on the values, it could be estimated that the putative introgressive haplotypes diverged with the AMH 552.5 ka, then diverged with the Denisovan 159.0 ka, and then diverged with the Altai Neanderthal 103.3 ka (fig. 2). It could be observed that the divergence time between the putative introgressive haplotypes and the Altai Neanderthal (103.3 ka) postdates the reported Neanderthal–AMH divergence time (>270 ka), which indicates the presence of postdivergence introgression"

Altai, Japanese and Africans

The paper reports that "Remarkably, it was observed that all putative introgressive haplotypes carry the derived allele of the Val92Met variant (rs2228479*A), and almost none [except a Japanese subject NA19084_a]... of the nonintrogressive haplotypes carries the rs2228479*A. This suggests that the rs2228479*A carried by the putative introgressive haplotypes might be from archaic hominin lineage. However, rs2228479*A was not found in the Altai Neanderthal genome."

They explain the lack of rs2228479*A in the Altai Neanderthal as follows: " 1) The rs2228479 is polymorphic in Neanderthal populations, and 2) the mutation creating rs2228479*A occurred on the putative introgressive haplotype shortly after it entered modern human gene pool (...) The rs2228479*A was found in one (out of 41) sequencing read of Altai Neanderthal and one (out of 20) sequencing read of Denisovan. All of the relevant sequencing reads and base calls passed quality control filter. Therefore, it could be possible that the Neanderthal and Denisovan are heterozygous at the rs2228479, and some unknown reason caused the imbalanced observation of ancestral and derived alleles of rs2228479 in sequencing reads."

The Japanese subject NA19084-a is among the non-introgresses subjects, so the derived allele at rs2228479 "might be from recurrent mutation, double recombination, or biased gene conversion".

Interestingly they found this allele at rs2228479 in three African subjects: "...among all HapMap African individuals, it was observed that one YRI (Yoruba in Ibadan, Nigeria; NA18852) and two MKK (Massai in Kinyawa, Kenya; NA21339 and NA21574) carry heterozygous alleles at the rs2228479".

They propose three possible explanations for this odd situation:

"Presence of derived alleles at Val92Met (i.e., rs2228479*A) in Africans could be explained by three models: 1) The rs2228479*A existed in the human gene pool before the Neanderthal–AMH divergence and was drifted to very low frequency in modern Africans whereas preserved in the Neanderthals and modern Eurasians (i.e., the “ancestral polymorphism model”), 2) recent gene flow from modern Eurasians to Africans, or 3) independent origin (such as recurrent mutation)."

They reject (1) but consider (2) and (3) as feasible. That is, it originated independently in Africa or there was a recent flow into Africa carrying Neanderthal genes i.e. contemporary Eurasians, which is quite reasonable, nevertheless, I would add, Neanderthals could have entered Africa and mixed there with Massai in Kenya and Yoruba in Nigeria.

Another surprising find was that it appears ata 50% frequency among the Cheyenne people of America. That is high, and rather unique in the New World, where it is hardly found at all.

Below is a map with its global distribution:

It is important to point out that Norton, Werren, and Friedlaender,(2015) found this Val92Met polymorphism in over 600 Melanesians sampled on different islands, reporting that the frequency of the derived allele ranged from 4 to 33% yet it seemed to have no influence whatsoever on the skin or hair color of the individuals. This suggests that it must interact with other genes to define the tone of hair and skin.

The same thing can be seen in East Asians: they have black hair just like Africans - and unlike brown of fair haired Europeans- despite carrying this derived gene that promotes fair hair.

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall © 

Another paper on "Out of China" (H sapiens originated in China)

A few days ago I wrote a post about an Asian origin for modern humans, written by Shi Huang. Today I found an earlier paper where Huang is one of the authors Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA (Dejian Yuan et al., 2018). As expected mankind originated in China and spread across the globe (into Africa too!).

The paper is quite interesting as it details its objections to the current Out of Africa theory and also highlights some interesting points:

On Negritos and Australian Aboriginals: "Analyses of autosomes, Y and mtDNA all suggest that Denisovan like humans were archaic Africans with Eurasian admixtures and ancestors of South Asia Negritos and Aboriginal Australians.".

"Origins of Negritos and Aboriginal Australians. The Andamanese and the African pygmies seem obviously related in multiple aspects, including traits, Y relationship with the African megahaplogroup ABDE, and mtDNA haplotype M being closely related to African L.
... Using the published genomes of 10 individuals from the Jarawa (JAR) and Onge (ONG) populations in the Andaman Islands (19), we found that Andamanese are relatively closer to Africans...
We also examined the Aboriginal Australian (AUA) samples ... These results showed similarity between AUA and Negritos, indicating similar ancestry in Neanderthals and Denisovans."

On Africans, Chimpanzees, Denisovans and Neanderthals: "... previous studies have found Neanderthals to be outgroup to AMH and used D-statistics to show Neanderthal gene flow into non-Africans but oddly not Africans (9, 10).
The assumption of D-statistics is that all modern groups are equidistant to chimpanzees so that presence of derived alleles (different from chimpanzees) was due to gene flow from Neanderthal. If in fact Africans are closer to chimpanzees or carrying more ancestral alleles in general, the conclusion of gene flow into non-Africans would become invalid. We examined this by measuring genetic distance between 1000 genomes and 10 previously sequenced chimpanzee genomes (49). Using the random 255K SNPs set, we found closer hom distance between Africans and chimpanzees than between non-Africans and chimpanzees....
Making use of the published Neanderthal genomes (9, 10, 50), we calculated the genetic distance in slow SNPs between 1000 genomes and Neanderthals (Altai, Vindija 33.16, 33.25, 33.26, and Mezmaiskaya) or Denisovan (Fig. 4A). These ancient genomes showed closer distance to Africans except Vi33.25 to ASN and Vi33.26 to AMR. Denisovan was closer to Africans than Neanderthals were..."

The previous conclusions are completely opposite to current prevailing theories (Africans lack links to both Denisovans and Neanderthals as any admixture with these groups took place in Eurasia with Eurasian people that migrated out of Africa).

On SE Asian features in Africa: "Fossils or traits indicating AMH migration from East Asia into Africa or Europe have been noted before. First, native Africans such as Khoisans are well known to have certain East Asian features such as shoveling teeth, epicanthic fold, and lighter skins. Mbuti pygmies look very much like the Andamanese. The much lower frequency of shoveling teeth in African fossils and Khoisan relative to ancient and modern Chinese suggests that this type of teeth could only originate in China with its African presence due to migration. The type of shoveling teeth found in Neanderthals and Pleistocene Homo from Atapuerca-Sima de los Huesos may either be a different type from that of Asians and Africans or come from early disposal of Homo from Asia to Europe (81, 82)...".

I found the article amusing and their arguments against the "Out of Africa" theory worth investigating in depth.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall © 

Neanderthal admixture in Africans (into Africa? or back to Africa?)

Time and time again you read that only non-Africans carry Neanderthal DNA because it was the wave of humans leaving Africa in an Out-of-Africa migration that encountered the Neanderthals in Eurasia and mated with them, mixing our and their genes. Africans who remained in the cradle of mankind, didn't admix and therefore carry no Neanderthal DNA.

A paper published in 2018 (Neandertal signatures in modern human mitochondrial genome haplogroups?, Renata C. Ferreira, Camila R. Rodrigues, James R. Broach,Marcelo R. S. Briones, BioRxiv, 18/Sep/2018. doi: https://doi.org/10.1101/190363) puts this idea upside down: the authors state that "...contrary to what is observed in the nuclear genome, African mitochondrial haplogoups have more potential Neandertal signatures than Asian and European haplogroups.".

Let's look into this surprising and contradictory finding.

The authors repeat the current orthodox view of an admixture outside of Africa:

"Intercrosses between Neandertals and ancient Homo sapiens lineages, or archaic Anatomically Modern Humans (AMH) who migrated from Africa into the Middle East and Europe in the last 50,000 years might explain the presence of Neandertal signatures in extant human genomes (Prüfer et al., 2014; Simonti et al., 2016). The spatio-temporal overlap of Neandertals and AMH is estimated to be approximately 22,000 years since the first AMH arrived in Europe around 50,000 years ago..."

Neanderthal mtDNA is liniked to certain diseases in modern humans, and the study found evidence of this too, and this included Africans: "Four of these disease associated N-SNVs were observed in African haplogroups (L0, L1, L2, L3, 10 L4, L5 and L6)", N-SNVs stands for Neanderthal SNVs. and the haplogroups they mention are considered the oldest and most basal ones. So how did the Neanderthal DNA admix with these "basal" haplogroups?

The autors explain this as follows: "A back to Africa hypothesis has been proposed in which humans from Eurasia returned to Africa and impacted a wide range of sub-Saharan populations (Henn et al., 2012). Our data suggest that Neandertal signatures might be present in all major African haplogroups which supports the “Back to Africa” contribution to the modern mitochondrial African pool."

They also conclude that modern human males introgressed with female Neanderthals more frequently in the Africans than in the Europeans (where the opposite took place: modern women were impregnated by Neanderthal men):

"Our data is compatible with a scenario in which the AMH-Neandertal crosses occur in Europeans, East Asians and African lines of descent. However, in the African haplogroups the crosses between AMH males and Neandertal females would have a higher frequency than in European lines of descent, where the reverse crosses would be predominant. Based on the comparison of Neandertal signatures in nuclear and mitochondrial genome haplogroups we hypothesize that the African lines of descent would have a higher female Neandertal contribution whereas European lines of descent would have higher male Neandertal contribution."

It is interesting to point out that Africans, Eurasians and Neanderthals share the N-SNV 16,278, which "is found in African haplogroups 34 (L0, L1, L2, L5 and L6) and two Eurasian haplogroups (X3, U2c and P2) and in all Neandertal sequences..."

What is also interesting is the link between Amerindians, Eurasians and the Altai Neanderthals, hinting at an admixture in Siberia : "... N-SNV 16.298 is found only in Eurasian-Native American 36 haplogroups (V1, V2, M8, C1, C4, C7 and Z1) and only in the Altai Neandertal."

The heat map (Fig. 4) in the paper shows a surprisingly strong introgression of Neanderthal genes in Africans, compared to Europeans, Asians, people from Oceania and Amerindians:

You would expect this admixign to have happened in non-Africans, instead it took place with Africans.

Could this enrichement of African DNA be caused by an actual into-Africa migration? One where modern humans -of Eurasian origin- with Neanderthal admixture entered Africa, and admixed there with the locals?

The gradient displayed in the image above, from a low (Oceania - Americas) to mid (East and western Asia - Europe) to high (Africa) Neanderthal genetic content clearly marks a migration path through Neanderthal territory (central Eurasia) into Africa.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Super Archaic Hominin admixture with Denisovans, Neanderthals and Africans

Our ancient relatives, Neanderthals and Denisovans not only introgressed with humans, they also admixed with an archaic hominin population, and passed some of the archaic's DNA to us!

A paper (Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph, Melissa J. Hubisz, Amy L. Williams, Adam Siepel, BioRxiv, June 30, 2019. doi: https://doi.org/10.1101/687368), used its computer simulation model (ARGweaver-D) to find:

" We identify 1% of the Denisovan genome as introgressed from a super-archaic hominin [Sup], which is double our estimated false positive rate for this event. The fact that we found much less than the ∼6% estimated by previous methods might suggest that the super-archaic divergence time is closer to 1Mya, since we would expect to have more power with a higher divergence time. Still, this analysis resulted in 27Mb of sequence that may represent a partial genome sequence from a new archaic hominin. ARGweaver-D also predicted a small fraction of the Neanderthal genomes as introgressed from a super-archaic hominin (0.75% for Altai and 0.70% for Vindija). These amounts are only slightly above the estimated false positive rates (0.65%), and the Sup→Nea event has not been previously hypothesized."

It adds more information on Denisovan admixture with Super-archaics:

"ARGweaver-D also identified 1% of the Denisovan genome as introgressed from a super-archaic hominin. Previous studies have estimated the total amount of Sup→Den as roughly 6% [8], but this is the first study to be able to identify specific introgressed regions. The fact that we only find a small fraction of the total amount suggests that the introgressing population was not too highly diverged from other hominins; this low power is much more consistent with a divergence time of 1Mya than 1.5Mya. Still, we report 27Mb of putative super-archaic sequence from this previously-unsequenced hominin, and we note that 15% of these regions have been passed on to modern humans through Den→Hum introgression. "

And also mentions Africans admixin with the super-archaic hominins but found it hard to track due to the large size of the "recipient" population (Africans):

"There have been several studies suggesting super-archaic introgression into various African poulations. However, ARGweaver-D only detected a small amount of Sup→Afr introgression, which was somewhat lower than our estimated false positive rate. One aspect to note here is that the power to identify introgression from an unsequenced population is highly dependent on the population size of the recipient population..."

The interesting find is that Neanderthals received an imput from humans in an admixture event some 300 kya.:

" We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya."

Where did this event take place? Not in Africa because there is no Neanderthal DNA there. So this means ancient humans left Africa and bred with Neanderthals in Asia 200-300,000 years ago, long before any currently accepted Out Of Africa migration date.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall © 

On the genes that regulate teeth, archaic hominins and Africans

A paragraph in this paper: Neanderthal and Denisova tooth protein variants in present-day humans) by Clément Zanolli , Mathilde Hourset, Rémi Esclassan, Catherine Mollereau (Published: September 13, 2017https://doi.org/10.1371/journal.pone.0183802) caught my eye. It pointed out an anomaly: Africans sharing a trait with Neanderthals and Denisovans!

This is what it says:

"The finding in living Africans of rare derived polymorphisms that were present in Neanderthals (Fig 2: ENAM G389S, 5%) or Denisova (Fig 3: CEMP1 R80H, 0.5%) is difficult to reconcile with the fact that interbreeding of AMH with Neanderthals occurred out of Africa [75, 76]. However, as mentioned above, this could be explained by the inside Africa admixture between the ancestors of AMH and archaic hominins, or by the possible back migration of Neanderthal gene flux. Further genome analysis of the Neanderthal and Denisova polymorphisms in AMBN, ENAM, and CEMP1 certainly deserves attention as they could trace back an African ancestor common to Neanderthals, Denisova and early anatomically modern humans."

Well, it is not "difficult to reconcile" if the fact is wrong and AMH interbred with Neanderthals inside Africa...

The ENAM G389S variant is found not only in Africa at 5% but also at very low frequencies in the Americas 0.3% (maybe imported by African slaves or perhaps a genuine Amerindian-Neanderthal admixture). Its global prevalence is only 1.3% and is virtually absent in Asia and Europe. Denisovans carried the ancestral "G" type, found in chimps and gorillas. Neanderthals and modern humans carry the derived "S" type.

They also found a some proteins in Denisovans (K55 E variant) that appear at 26% frequency among Africans and 7% globally (the highest outside of Africa being in America at 2% and far lower elsewhere). This is the ancestral type, found in Denisovans, chimpanzees and modern humans, but it was not found in Neanderthals.

The paper also hints at an admixture in Africa between H. Sapiens and some archaic homo 35,000 years ago:

"Most of the amino acid changes are found in the dentin and enamel proteins that are encoded by genes located in two close clusters on the chromosome 4 (Fig 4) and supposed to derive from an ancestral gene encoding a secretory calcium-binding protein [68]. These clusters fall apart from known haplotypes on chromosome 4 and do not correspond to candidate Neanderthal or Denisovan gene flow regions in non-African living humans [69, 70]. However, a signal of archaic introgression in the locus 4qMB179 on chromosome 4 has been evidenced in Central African populations, and is supposed to result from admixture with an archaic Homo some 35 kya [71]."

Admixture with archaic hominins in Africa would "enrich" the diversity of African DNA and therefore contradict the prevailing theory that Africans are more diverse and therefore they are the "original" source of humanity.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Into Africa gaining strength

A paper pubished in Science (Gallego Llorente et al., 2015. Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent, Science DOI: 10.1126/science.aad2879 two days ago, reveals what has been suspected for some time: All Africans have a Eurasian component in their genes.

The abstract says so clearly:

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.

As it is behind a pay wall, I checked the web and found the following additional data:

• "the scientists believe up to 25% of the DNA of modern Africans can be traced back to this event."
• "... if you go to the corners of Africa, all the way to West Africa or South Africa, even populations that we really thought were purely African have 5-6% of their genome that dates back to these western Eurasian farmers."
• "...it is also interesting to discover now that even sub-Saharan Africans have a bit (0.3-0.7%) of Neanderthal ancestry."

Who knows, perhaps this is the first step into a serious analysis of the real roots of mankind, and may lead to a revision of the conclusions of another recent paper (L. Pagani, 2015, Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians Cell):

"... the Ethiopian and Egyptian genomes showed different patterns. In particular, the Egyptian0 genomes displayed a more recent split from both the West African (21,000 years ago) and the non-African (55,000 years ago) genomes than did the Ethiopian genomes (37,000 and 65,000 years ago, respectively). This suggests a higher similarity between non-African and Egyptian components than between non-African and Ethiopian components, which is consistent with the fact that Egypt is the last stop on the way out of Africa. Such split dates also hint at a recent interaction between Egyptians and West Africans..."

They too noticed a similarity between Egyptian and Eurasian genes, but their conclusions are different.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall ©