This is an update revisiting my attempt at quantifying the Ancestral North African or Ancestral north African related (ANA) admixture in Africans and neighboring populations. ANA in this context would represent a population related to both East Africans and early non-African populations, which is the loose description of the direct ancestors of North Africans; hence the title “ANA”. North Africans of course, highlighted by the genome of the Iberomaurasian (Taforalt), would have had additional non-African ancestry from west Eurasia dating to sometime before 17Kya.1 Here I used Taforalt and an ancient east African (Mota) to remodel potential ANA ancestry as absorbed by modern and ancient populations.
The methodology was updated from the last post’s in which this time, I’ve added more insight by calculating the amount ANA ancestry that is likely shared by the direct ancestor of Taforalt. This is useful as the ancient genetic landscape spanning from East to North Africa has yet to be elucidated. So in the case where ANA is solely defined as just the ancestor of the Iberomaurasian we could in theory visualize and compare the outlying related East African component.
Also for more resolution, I’ve ran the equations with multiple populations for (Y). To put it shortly, population Y would represent an Early Eurasian or East Asian population who in conjunction with our early West Eurasian reference (Sunghir IV), would capture the majority of Eurasian diversity. This is done to see which non-African population’s could have ANA/African ancestry as well as parse out the Eurasian ancestry of the African populations analyzed. See the breakdown for more information.
Once again I ran the equation with the Y population being the ancient sample discovered in Laos. (Haobinhan) This sample was previously used because it showed signs of having deep ancestry either belonging to a “basal” Eurasian or Early Eurasian people, as well as capturing Early East Eurasian ancestry2.
Note*: In the previous ANA ratio chart there was a calculation error involving the South African Hunter-gatherer (Ballitobay) related ancestry which resulted in some minor differences in the overall amount of ANA related ancestry. The results of total ancestry may vary per individual.
Updated Estimates with Hoabinhan as Y
This time we can still see that pastoral Neolithic samples of East Africa report the highest amounts. Following them are Horn Africans led by the Oromo, and North East Africans led by the Beja (Hadendowa). The Toubou scores the highest among modern West/Central Africans and significantly the 230 year old Congolese “Kindoki” sample scored the highest among ancient Central Africans. Once again just as reported before the Congolese sample of 150 years ago reported extremely low coverage to which their results are insignificant. Of the ancient East Africans the 900 year old sample from Kakapeli rockshelter highlighted the most ANA related ancestry as did last time though insignificant due to low genetic coverage. However, a nearby individual discovered in the Molo Cave (GoJi3)3, had the highest significant amount of said ancestry. And among Ancient and modern North Africans, the Early Neolithic Moroccans from Ifri n Amer Moussa and the Saharawi who slightly edges the Copts of modern Egypt/Northern Sudan were estimated to have the highest amounts of ANA ancestry respectively.
Surprisingly, among Non African populations the Minoan individuals from Odigitria report the highest amounts of ANA/African-related ancestry with Haobinhan as Y. Otherwise as expected, early neighboring populations of Israel associated with the early Pre-Pottery Neolithic B and Natufian cultures are estimated to have the highest amounts.
Tips: Click and drag over the bars to zoom in on the graph. Double-click to revert back to the default zoom/view. Click and drag the ticks at the Y or X axis’ to scroll up & down or left & right respectfully. Use the black download buttons underneath each chart to download the corresponding graphs faceted in pdf format.
Zlatý kůň as Reference Y
In contrast when using the 43,000 year old individual found in Zlatý kuň, Czechia as population Y some differences become apparent. One of which includes a decreased estimate within Southern Africans, West/Central Africans and Ancient East Africans. Conversely, Horn Africans, neighboring ancient Europeans, North Africans and most pastoral-neolithic East Africans show a minor overall increase. Interestingly, Northeast Africans mostly of Sudan but also including the Ancient Egyptians of Abusir el Meleq show minimal or negligible changes between Y populations. This pattern could be explained by either variation among Early Eurasian populations as they relate to Africans or by ANA substructure which was poorly encapsulated by using the Haobinhan sample as a reference population. This could be exaggerated by the evidence of the former having “deep” or Basal (Eurasian) ancestors who could’ve been or carried variants shared with a relevant but extinct African population.
Bacho Kiro & Ust Ishim as Y
For further investigation, we can compare the result of the ancient Czech individual to other more contemporaneous Eurasians (Bacho Kiro and Ust Ishim below). When generally analyzing the pattern of distribution among the test samples the Haobinhan run appears to be the outlier as expected. And congruent with the idea that the Haobinhan sample’s deep ancestry could dampen the ANA estimates we do see a general increase of said component in neighboring Eurasians and Eurasian admixed populations when Y is an early Eurasian. What’s interesting to note is while the Zlatý kuň sample was reported to have the most fresh set of neanderthal DNA,4 she shows more potential correspondence with African related DNA when compared with her early Eurasian contemporaries. The individuals from Bacho Kiro predictably showed evidence of the opposite trend as overall estimates had increased the most with them as Y. This is inline with the hypothesis that they received or retained additional neanderthal ancestry in comparison to Ust Ishim and the Zlatý kůň individual.5
Using Iran Neolithic as Y
Lastly, I’ll share what happens when we use neolithic samples from Iran as Y. Two things should be noted when examining this equation in particular. Firstly, some of our test populations have shown ancestry related to or descendant from the neolithic Iranian group. 6–13The equation as explained before works under the assumption that the Y population would only share common non-African variation reflective of the out of Africa (OOA) bottleneck. Direct admixture from population Y could mildly if not significantly decrease ANA estimations. Secondly, the Iranians have been predicted to have some of the most (if not the most putative) Basal Eurasian ancestry which was also hinted by their diluted neanderthal ancestry.14–16 It hasn’t been resolved how much the ghost population, Basal Eurasian, relates to post OOA Africans or more specifically, Northeast Africans and ANA.17 Being so, there is a possibility that estimates using the Neolithic Iranians as Y would fail to parse and or conceal ANA ancestry especially within Non-African individuals.
Here the results were as expected for the most part. Africans especially those who lack Eurasian or related ancestry showed negligible changes and the others showed a notable decrease in ANA estimates. However there are a few interesting inconsistencies. For starters, the Toubou or Teda who’ve shown to be about 30% non-African18 didn’t show any marked decrease with Iran as Y. It should be expected that they’d show a decrease given their (uniparental) coalescence with populations related to early European farmers or Sardians and near Eastern populations.19,20 For comparison, all of the latter populations mentioned showed significant decrease in ANA ancestry. On the contrary the people of South Sudan who haven’t shown any evidence of Eurasian admixture at all (Dinka), shown a decrease along with many other east African samples. Among the Eurasian samples, the early farmers of Raqefet cave, Israel, and associated with Natufian culture were the only group to maintain a non-negligible amount of African ancestry, cementing the idea that they do have East African derived or related ancestry of some-sort.21 Lastly and most surprisingly, the late neolithic individuals found at Kehf el Baroud Morocco were also estimated to have negligible or no ANA ancestry with the neolithic Iranians as Y. This is quite surprising as they’ve been shown to have up to roughly 40% of their ancestry attributed to Early Neolithic Morrocans who could be more than half ANA.12,22-24
So long as the equation is respectable, there are a few scenarios which can make sense of this pattern. One of them could simply be that Iranian-related ancestry had permeated all through Africa but had little impact on West Africa. Prior to widespread distribution of Iranian lineages, the Natufian samples could have received ANA or East African ancestry and the Eurasian source for admixed West Africans could have remained in isolation and subsequently radiated into Africa. Another explanation is that there is significant overlap between the variants we associate with Basal Eurasian in the neolithic Near and Middle Eastern samples and ANA. And substructure among Ancestral north Africans could be the reason why East Africans (including those in the Northeast) show the most significant differences regardless of whether or not they’ve had Eurasian ancestors. However, both of these explanations would need to take into account the core genetic similarities between the Neolithic Iranian samples and other neolithic West Eurasians outside of Basal Eurasian or ANA-related ancestry.
There is more to be seen from the sample set we have available. There are also some limitations to point out regarding some of the results presented such as the poor overlap with some of the samples. It remains the same as with my previous publication on the matter (see the table). Though this time there are more samples such as the Fulani who also shows surprisingly low ANA%s but also have poor overlap with others in this dataset. Another possible task is replacing Bayira, the 4500 year old boy excavated from Mota cave Ethiopia24 as ANA1 with a more suitable population. There is a possibility that another available sample could give deeper insight being that they’re more suited to represent a pure Ancient East African with less shared variants with Neanderthal and other African hunter-gatherers.
Note: I’ve also used a few other East Asian samples as Y whose results are available for download below.
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2. McColl, H. et al. The prehistoric peopling of Southeast Asia. Science (80-. ). 361, 88–92 (2018).
3. Wang, K. et al. Ancient genomes reveal complex patterns of population movement , interaction , and replacement in sub-Saharan Africa. 1–15 (2020).
4. Prüfer, K. et al. A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia. 5, (2021).
5. Vallini, L., Marciani, G., Aneli, S., Bortolini, E. & Benazzi, S. Genetics and material culture support repeated expansions into Paleolithic Eurasia from a population hub out of Africa. 1–14 (2021).
6. Chiang, C. W. K. et al. Supplementary Figures for Population history of the Sardinian people inferred from whole-genome sequencing. Chart (2016).
7. Marcus, J. H. et al. Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia. Nat. Commun. 11, 1–14 (2020).
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11. Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014).
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Excellent work
It seems kind of peculiar to define “ANA” ( Ancestral North African)
as U6 + E1b1b
when U doesn’t even originate in North Africa
What about The Aterian sites suchs Jebel Irhoud remains in Morocco?
or Ain el Hanech, in Setif
I dont think “ANA” is a fair category since it is defined above by U6 bearing
remains of Taforalt and we don’t know what mitochondrial haplogroups may have been in North Africa prior to that.
So if we are dealing with what Lazardis called a “mixed” ancestry, U6 + E1b1b
I don’t think it’s right calling U6 “Ancestral North African”
and then start using that combination to determine that the maternal DNA of some other population in North Africa does not have “ANA” .
And Schuenemann et al in their 2017 article on the mummies at Abusir el-Meleq
“Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods”
was very presumptuous to conclude, make generalizations based on an analysis only at one site of 90 mummies only of maternal DNA except for 3 mummies (one of them E1b1b1), the vast majority of them being late period , the oldest, only about 4 mummies from no earlier than the New Kingdom
” Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times.”
No it is what is, not “the Ancient Egyptians”
it’s the Egyptians at Abusir el-Meleq
and ANA if defined by E + U6 is not Ancestral North African
it’s Iberomaurusian DNA or related synonym Mechta-Afalou
and that is not the whole picture in North Africa, nor the oldest industries.
U6 is also not dominant on the Eastern side of North Africa.
Mota man in Ethiopia was E1b1a and that also distinguishes him Taforalt because all 7 individuals at Taforalt were E1b1b
So these various categories “ANA” “Basal Eurasian” “ANE”
etc. they are simplifications that often lead to simplistic conclusions, sometimes misleading ones, in my opinion
Thank you for the question,
First I’d like to point out that Ancestral North African (ANA) actually isn’t defined by U6 and E-M35 or any individual uniparental haplogroup for that matter. It is a placeholder for the Autochthonous population(s) who may have been residing in Northern Africa after the initial major migrations out of Africa. Yes, the categories of Basal Eurasian, ANA and Ancestral North Eurasian (ANE) are oversimplifications. But they’re established to overcompensate for missing data due to gaps in samples sequenced and analyzed in genomic publications. In the context of Africa, there are many of these gaps, one of the biggest being exemplified by the Sub-Saharan – Eurasian dichotomy. The modern genetic landscape makes it difficult to visualize a native Ancient North African population because of the extensive history of bidirectional migration and settlements between Africa, West Asia and Europe. In this case we simply sought out to statistically bridge that gap to estimate the potential distribution of their ancestry.
Let me update what I said because I had forgotten that they also found L3 with Mota man, Ethiopia
So genetically we have several 15kya Moroccan individuals + one 4.5Kya individual horn African (Mota)
This you say is good enough to establish Ancestral North African DNA
Taforalt
E-M215 (E1b1b)
U6
Mota
E-V38 ( E1b1a2)
L3
Lazaridis said
“Our co-modeling of Epipaleolithic Natufians and Ibero-Maurusians from Taforalt confirms that the Taforalt population was mixed”
the oldest U6 thus far is 35,000 years old found in Romania
in the Peștera Muierilor cave.
So is it fair to include the maternal DNA at Taforalt
part of “Ancestral North African DNA” ?
The term “North Africa” itself is problematic since it’s boundaries can be defined in too many different ways.
and here you include Ethiopia
“North Africa” in my opinion is too problematic a term to use in anthropology.
Instead having two categories “Maghrebian Ancestry” and “Nile Valley Ancestry” are a more appropriate than lumping them into a “North Africa”.
Ethiopia is “Horn Africa”
Ancestral Nile Valley DNA ancestry can’t be determined at this time because there are no samples older than 4,000 years (Djehutynakht) and that was maternal determination only (U5)
And likewise with Mota, one individual
I wouldn’t use the term “ancestral”
aDNA findings in Africa are far few scant, in my opinion to come up with these categories which sound like yardsticks.
The terms “ancient” and “ancestral” are also to imprecise”
This is the trend now, Lazaridis with his three letter abbreviations and discussion of “basal eurasians” as if they exist yet no skeletal remains.
It’s too hypothetical and too simplified.
We should at least continue to us terms like “Neolithic” and “Paleolithic” attached to such terms to give a little more sense of time period.
For instance, Taforalt is Middle Paleolithic while
Mota is Neolithic, whatever term is used at least these
imply there could be a 10,000 year difference between them
With the same data you are using to generate these charts if Instead of “ANA”
you used these categories
Paleolithic Maghrebian
Neolithic African Horn
using the same data, two categories instead of one
what is the result?
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