Ancient North African genomes show migration from Levant and Europe

[Angela]

See:
Rosa Fregel, Fernando L. Méndez, Youssef Bokbot, Dimas Martín-Socas, María D. Camalich-Massieu, Jonathan Santana, Jacob Morales, María C. Ávila-Arcos, Peter A. Underhill, Beth Shapiro, Genevieve Wojcik, Morten Rasmussen, André E. R. Soares, Joshua Kapp, Alexandra Sockell, Francisco J. Rodríguez-Santos, Abdeslam Mikdad, Aioze Trujillo-Mederos, and Carlos D. Bustamante

"Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe"

http://www.pnas.org/content/early/2018/06/11/180085


"The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals’ genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.

Unfortunately, it's behind a pay wall, even the SI.

[bicicleur]

it's been printed last year :

https://www.biorxiv.org/content/earl...1/191569?rss=1

probably there is some additional info

[Angela]

Some new, I think, formal statistical analysis, and a test for SSA admixture.

Interestingly, PCA revealed that IAM individuals are similar to North African Later Stone Age samples from the Taforalt site in Morocco, dated ∼15,000 y ago (Fig. 2 and SI Appendix, Supplementary Note 6). When projected, IAM samples are halfway between Taforalt and modern North Africans, in the Levantine corner of the PCA space (Fig. 2). Southern Iberian Neolithic individuals from TOR cluster with Sardinians and with other Anatolian and European Neolithic samples. Moreover, KEB samples are placed halfway between the IAM and Anatolian/European farmer clusters, in close proximity to Levant aDNA samples and also to Guanche samples (16) (from the indigenous population of the Canary Islands known to have a Berber origin; ref. 23).



Recent aDNA analysis of Moroccan Later Stone Age samples from the Taforalt site indicates that at least one-third of Taforalt ancestry derives from sub-Saharan African populations. When Taforalt and sub-Saharan African samples are included in the unsupervised clustering analysis (SI Appendix, Supplementary Note 7), we observe that IAM and Taforalt cluster together at K = 7, as observed for the MEGA-HGDP ADMIXTURE analysis. However, as reported by van de Loosdrecht et al. (17) for Taforalt, we can detect both West African (maximized in Gambians and Yoruba) and East African (maximized in Hazda) components in IAM at lower K values. In contrast, TOR does not show any sub-Saharan African ancestry and KEB is again in an intermediate position, with lower sub-Saharan African ancestry than IAM.

To compare our samples directly to the genomes of ancient and modern populations, we calculated pair-wise fixation index (FST) distances, which, unlike PCA and global ancestry analyses, are insensitive to the inclusion of large numbers of individuals from modern populations. FST values (noted in parentheses) indicate that the IAM samples are as differentiated from all other populations as Yoruba are from non-Africans (SI Appendix, Supplementary Note 9), with the exceptions of Taforalt (0.049) and, to a lesser extent, KEB (0.090; similar to the distance between Yoruba and Mbuti), the Guanches (0.125; similar to the distance between Somali and Mbuti), and modern North African populations (0.115 to 0.138). The same pattern is observed for Taforalt samples, which shows its lower FST distance with IAM, followed again by KEB (0.129), the Guanches (0.150), and modern North Africans (0.130 to 0.149). Given the relatively low heterozygosity and high identity-by-descent proportions observed in IAM (SI Appendix, Supplementary Note 8), this differentiation could be driven by isolation and genetic drift. IAM is divergent from the other populations, with the exception of populations that either could have shared genetic drift with them or received genetic influx from them. This raises the possibility that Taforalt/IAM people were isolated in North Africa since Paleolithic times, when a back migration from Eurasia brought mtDNA haplogroups M1 and U6 to the Maghreb (19). Although IAM is clearly more similar to KEB than most populations, the converse is not true. KEB has lower FST distances with ancient Anatolian (0.032), Armenian (0.025 to 0.053), European (0.036 to 0.041, excluding European hunter-gatherers), Levantine (0.020 to 0.079), and Iranian (0.081 to 0.081) populations, as compared with IAM. In the modern DNA reference panel, KEB is similar to North African, European, and Middle Eastern populations. Among the ancient populations, TOR is more similar to Middle Neolithic/Chalcolithic Europeans (0.029 to 0.031), and, among modern populations, TOR is more similar to those from Spain, North Italy, and Sardinia.



To further investigate the genetic affinities of IAM, KEB, and TOR samples, we conducted outgroup f3-statistic analysis (24). When using an outgroup population that has not experienced any postdivergence gene flow with either one of the compared populations, the f3-statistic calculated in the form f3(PopA, PopB; outgroup) allows us to determine the amount of shared drift between two populations, PopA and PopB. We selected the Ju\ʼhoan population as the outgroup, and compared our three ancient populations (IAM, KEB, and TOR) against all of the ancient populations in the Human Origins panel, as well as the Taforalt and Guanche samples. The highest f3 values for IAM are observed for Taforalt (0.3060) and KEB (0.2296). Consistent with previous results, when Taforalt, KEB, and Guanches (f3 = 0.2196) are excluded, IAM shares more drift with ancient Levantine populations, such as Epipaleolithic communities (Natufians; f3 = 0.2296) and Pre-Pottery Neolithic individuals (f3 = 0.2167) (Fig. 3 and SI Appendix, Supplementary Note 10), than with any other ancient population. This confirms previous results for Taforalt (17) indicating a Levantine intrusion in North Africa in Paleolithic times.

[berun]

I think that the authors jump into conclusions too quickly:

FST and outgroup-f3 distances indicate a high similarity between IAM and Taforalt. As observed for IAM, most Taforalt sample ancestry derives from Epipaleolithic populations from the Levant. However, van de Loosdrecht et al. (17) also reported that one third of Taforalt ancestry was of sub-Saharan African origin. To confirm whether IAM individuals show a sub-Saharan African component, we calculated f4(chimpanzee, African population; Natufian, IAM) in such a way that a positive result for f4 would indicate that IAM is composed both of Levantine and African ancestries. Consistent with the results observed for Taforalt, f4 values are significantly positive for West African populations, with the highest value observed for Gambian and Mandenka (Fig. 3 and SI Appendix, Supplementary Note 10). Together, these results indicate the presence of the same ancestral components in ~15,000-yold and ~7,000-y-old populations from Morocco, strongly suggesting a temporal continuity between Later Stone Age and Early Neolithic populations in the Maghreb. However, it is important to take into account that the number of ancient genomes available for comparison is still low and future sampling can provide further refinement in the evolutionary history of North Africa

even if autosomaly it could be a logic process, the Y-DNA is telling another history

from Quiles' blog

Attachment 10272

the Y-DNA of the Iberomaurisians of Taforalt was E1b1b1a1 (M78), E1b1b1a1b1, and E1b1b (M215*), but the Y-DNA found in the Neolithic herders/farmers of IAM was E1b1b1b1 (L19), so a big difference like to find R1b in Mesolithic Estonia and R1a in Neolithic Estonia...

Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people.

Really I can't see it in autosomals, Taforalt and IAM share four components (some 25% SSA, 50% Anatolian, 10% Hadza, 20% CHG-related) but in the 3600 BC samples of KEB it is left 5% SSA, 80% Anatolian, 2% Hadza and 15% CHG, so that an Iberian migration is in fact denied by lack of WHG component.... so that the autosomal change must come from a different source, from the east (Levantines had Anatolian and CHG components). By the way the autosomal upheaval is accompanied by Y-DNA novelties.

[berun]

Doing rough maths, seeing that KEB loss 1/5 of SSA and 1/5 Hazda, if being it not coincidental, 1/5 of Anatolian would be 10% and 1/5 of CHG would be 4%, leaving so and increase of 70% Anatolian and 10% CHG in KEB, so, which peoples before KEB would be roughly 3/4 Anatolian and 1/4 CHG?

[Olympus Mons]

Doing rough maths, seeing that KEB loss 1/5 of SSA and 1/5 Hazda, if being it not coincidental, 1/5 of Anatolian would be 10% and 1/5 of CHG would be 4%, leaving so and increase of 70% Anatolian and 10% CHG in KEB, so, which peoples before KEB would be roughly 3/4 Anatolian and 1/4 CHG?

Anatolian and CHG? --- There is a crazy guy, that said that the same population that is later seen in steppe, since it was originally a south caucasus population, is later seen (4800bc) i tell tsaf (israel), in Egypt Delta Nile as Merimde bene salama (4600bc).... and arriving to iberia by 3300bc so 600 years of Merimde being abandoned.

Who knows, crazier things have happened in the world :)
https://shulaveri2bellbeaker.blogs.sapo.pt/

[Govan]

What are you talking about anyway ? There is no CHG whatsoever in either IAM nor Taforalt , both are Natufian-like but distinct, with IAM more shifted towards Levantines.

KEB is a mixture of IAM and Neolithic Anatolian ancestry with new lineages , on the PCA plot KEB cluster very close to Guanches , and the current Berbers also.

[Govan]

Anatolian and CHG? --- There is a crazy guy, that said that the same population that is later seen in steppe, since it was originally a south caucasus population, is later seen (4800bc) i tell tsaf (israel), in Egypt Delta Nile as Merimde bene salama (4600bc).... and arriving to iberia by 3300bc so 600 years of Merimde being abandoned.

Who knows, crazier things have happened in the world :)
https://shulaveri2bellbeaker.blogs.sapo.pt/

yeah crazy world , crazy people to rainbows it . Israelites probably invaded Portugal bringing the faith and CHG too ? In all seriousness , CHG ancestry appears in midlle Bronze Age in Iberia , alongside RM269 and weapons of Danubian\Rhine origins. There's no link with Abydos Egypt , which is much later

[berun]

What are you talking about anyway ? There is no CHG whatsoever in either IAM nor Taforalt , both are Natufian-like but distinct, with IAM more shifted towards Levantines.
KEB is a mixture of IAM and Neolithic Anatolian ancestry with new lineages , on the PCA plot KEB cluster very close to Guanches , and the current Berbers also.

Look at Iran Neolithic, it is what K7 provides in the paper.

Forget any extra Anatolian ancestry without WHG coming from Europe.

[Govan]

Look at Iran Neolithic, it is what K7 provides in the paper.

Forget any extra Anatolian ancestry without WHG coming from Europe.

You're smart ass in genetics aren't you ? That's not CHG ancestry but Basal rich ancestry exp
in ancient West Asians. so you went on your own labeling the colors fi

[berun]

my own labeling of colours was "CHG related", you just need to read again or wake up

[Govan]

my own labeling of colours was "CHG related", you just need to read again or wake up

It's neither CHG , nor CHG-related , nor any of your other labeling , leave the paper to actual scientists rofl .

[berun]

You will need to discuss with a little bunch of "actual scientists", maybe you alone, as the same authors even label it with a modern pop: "the violet component being higher in the Bedouins"

[ratchet_fan]

I think that the authors jump into conclusions too quickly:



even if autosomaly it could be a logic process, the Y-DNA is telling another history

from Quiles' blog

Attachment 10272

the Y-DNA of the Iberomaurisians of Taforalt was E1b1b1a1 (M78), E1b1b1a1b1, and E1b1b (M215*), but the Y-DNA found in the Neolithic herders/farmers of IAM was E1b1b1b1 (L19), so a big difference like to find R1b in Mesolithic Estonia and R1a in Neolithic Estonia...



Really I can't see it in autosomals, Taforalt and IAM share four components (some 25% SSA, 50% Anatolian, 10% Hadza, 20% CHG-related) but in the 3600 BC samples of KEB it is left 5% SSA, 80% Anatolian, 2% Hadza and 15% CHG, so that an Iberian migration is in fact denied by lack of WHG component.... so that the autosomal change must come from a different source, from the east (Levantines had Anatolian and CHG components). By the way the autosomal upheaval is accompanied by Y-DNA novelties.

So Taforalt is 30-35% African and 65-70% West Asian? How does the ANA component play into this?

[Regio X]

So Taforalt is 30-35% African and 65-70% West Asian? How does the ANA component play into this?

This was already "corrected" by Lazaridis et al.

https://www.biorxiv.org/content/bior...1/423079-1.pdf

"The analysis using the All set showed that Levantine (Natufians and PPNB) and North African (Taforalt and Morocco_EN) populations could be modeled as a mixture of Dzudzuana with extra Basal Eurasian ancestry. The study of the Ibero-Maurusian remains from Taforalt was initially interpreted as suggesting that this population was formed by admixture between Natufians and a Sub-Saharan population15. However, the admixture graph model suggests the opposite scenario: that Natufians were formed by admixture from a Taforalt-related population and a Dzudzuana-related one"
(...)
"Taforalt could not be modeled as any 2-way mixture. The best model involving Natufians and an African population (Yoruba) could still be strongly rejected (p=2.7e-13). Taforalt could also not be modeled as a 3-way mixture. However, Natufians could be convincingly modeled as a 2-way mixture of ~86% Dzudzuana and ~14% Taforalt (p=0.405) with small standard errors of 1.9%. Thus the affinity between Natufians and Taforalt described in ref.15 may have come about by admixture from a North African/Taforalt-related population into Natufians, rather than by admixture in the opposite direction. The results of our analysis using the All set, as well as the results of the analysis of ref.15 do suggest that Taforalt can be modeled as a mixture of a West Eurasian related population (represented by Dzudzuana in our case) and a Sub-Saharan African lineage. However, when one uses only a single African population as a source without using others as outgroups, this mixture can only be interpreted as evidence of ancestry from a lineage basal to members of the All set, rather than as evidence of ancestry specifically specifically 44 related to the chosen African population. No Sub-Saharan African populations appear to be good sources for the ancestry of Taforalt as described previously. The admixture graph model suggests an alternative possibility: that it is West African populations like the Yoruba that may have ancestry from a North African Taforalt-like population. Under such a scenario, North Africa and the Levant were occupied by populations that experienced gene flow from each other, with more ancestry from a Basal lineage in North Africa, and more ancestry from a West Eurasian specific lineage (represented by Dzudzuana) in the Levant, thus explaining the presence of Dzudzuana related admixture in Taforalt and of Taforalt-related admixture in the Levant. Under this scenario, a North African-related population may have contributed some ancestry to Sub-Saharan populations to its south, perhaps during the Holocene Green Sahara period (~11-6kya)22 that postdates the sampled Taforalt individual which may have facilitated north→south gene flow across the Sahara. Based on the very low presence of Neandertal admixture in Yoruba, it has been estimated that >2.7±0.9% of the ancestry of Yoruba came from West Eurasia 9618 ± 1825 years ago 23 . The admixture graph model predicts that 13% of the ancestry of Yoruba came from Taforalt, which in turn was 55% descended from Dzudzuana and which in turn was 72% descended from Villabruna, for a total of 0.13*0.55*0.72≈5% Villabruna-related ancestry that would have carried Neanderthal DNA. This is consistent with the >2.7±0.9% estimate of ref. 2"
(...)

[kingjohn]

Regio x
Great post
Very informative 👍
This Dzudzuana admixture is fascinating
In natuffians and taforalt🤔
and the 14% taforlat admixture in natuffians
Maybe that what gave natuffians in part there
y haplogroup E .... 🤔

[ratchet_fan]

This was already "corrected" by Lazaridis et al.

Interesting. Seems like Tarofalt is an ANA population that contributed to West Africans rather than being derived from them.