Saturday, October 14, 2017

3,000ybp Pastoralist proves an old point

Well, a while ago now I pointed out that, simply using modern DNA, various Southeast Africans clearly looked partly descended from peoples closely related to modern Somalis and other Horn-Africans of Erythraeic and Ethiosemitic speaking origins (see here and here) and it seems ancient DNA is now backing this up:

[1] "distance%=0.3802 / distance=0.003802"

Masai_Kinyawa

Tanzania_Luxmanda_3000BP 50.7
Dinka 49.3


That's an nMonte model above utilizing a new 3,000 year old pastoralist sample from Tanzania belonging to the Savanna Pastoral Neolithic culture strongly tied to South-Erythraeic speaking people who began leaving the Horn of Africa for Southeast Africa some 3,000-4,000 years ago. You can see the fit is decent, showing significant Savanna Pastoral Neolithic related ancestry in this average for the Maasai Kinyawa samples in the Global-10 PCA.



We owe this new sample to a study headed up by Pontus Skoglund and it comes with a lot more details I'll be poring over to some extent quite soon but for now; I'm just putting this paper out there and sharing that we finally have some aDNA backing for what modern DNA, archaeology and linguistics have been positing for quite a while now regarding South-Erythraeic speakers and their influencing of Southern and Southeastern Africa.

Do read the study in the meantime, though.


References:


Reconstructing Prehistoric African Population Structure, Skoglund et al.

12 comments:

  1. Hey Awale! Is there any way to run the same exercise with my raw dna to assess my affinity to the Tanzania_Luxmanda_3100BP and Tanzania_Pemba_600BP samples?

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    Replies
    1. Sure, but you'd need to send your raw data to David over at Eurogenes and get him to put you in the Global-10 PCA. Then all I'd need would be your coordinates and I can run the same model for you quite easily.

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  2. It would be great if we could also include the Dinka and South Africa_2000BP in the analysis.

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    1. I included Bantu_Kenya and South_Africa_2000BP below:

      [1] "distance%=0.3376 / distance=0.003376"

      Masai_Kinyawa

      Tanzania_Luxmanda_3000BP 53.30
      Dinka 37.65
      Bantu_Kenya 9.05
      South_Africa_2000BP 0.00

      And removed Bantu_Kenya below:

      [1] "distance%=0.3802 / distance=0.003802"

      Masai_Kinyawa

      Tanzania_Luxmanda_3000BP 50.7
      Dinka 49.3
      South_Africa_2000BP 0.0

      Used South_Africa_1300BP below:

      [1] "distance%=0.3802 / distance=0.003802"

      Masai_Kinyawa

      Tanzania_Luxmanda_3000BP 50.7
      Dinka 49.3
      South_Africa_1300BP 0.0

      To be fair, this Luxmanda sample has notable South_Africa_1300BP related ancestry which is probably dipping into whatever these Masai may have independent of Erythraeic speaker-related ancestry.

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  3. Replies
    1. No problemo, and thank you for the kind words.

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  4. After the paper covering North African Neolithic genomes came out, I really started to think about the possibility of a para-Eurasian population hailing from NE Africa, both rich in and associated with the bifurcation and spread of Hg E. The populations I suspect of being rich in this ancestry are: IAMs, Natufians Old Kingdom Egyptians, Garamantians, Copts, and modern North Africans. It remains to be seen if this was indeed a separate branch basal to the Basal Eurasians or just a more pristinely Basal Eurasian population than current basal-rich pops on file. I lean more towards the former.

    At any rate, I attempted to model Tanzania_Luxmanda on nMonte and obtained the following fits:

    [1] "distance%=1.8585 / distance=0.018585"

    Tanzania_Luxmanda_3000BP:I3726

    Ethiopia_4500BP:mota.SG 60.2
    Levant_N:I1704 39.8


    [1] "distance%=1.2394 / distance=0.012394"

    Tanzania_Luxmanda_3000BP:I3726

    Ethiopia_4500BP:mota.SG 60.3
    Natufian:I1072 39.7

    and

    [1] "distance%=1.1818 / distance=0.011818"

    Tanzania_Luxmanda_3000BP:I3726

    Ethiopia_4500BP:mota.SG 56.9
    Natufian:I1072 22.8
    Saharawi 11.4
    Natufian:I0861 9.0

    The fit improved considerably when I used Natufians as a stand in, though still far from satisfactory. It improved only marginally when Saharawis were added, who I'd suspected of having more of the IAM-modal ancestry. This is probably because they have Mende-related ancestry, which outweighs them potentially being enriched in this ghost ancestry. Also, now that I think about it, their non-Mende ancestry is likely to be comprised of smth KEB-like not IAM-like, so perhaps they're not so enriched in it, after all.

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    1. "It improved only marginally when Saharawis were added, who I'd suspected of having more of the IAM-modal ancestry. This is probably because they have Mende-related ancestry, which outweighs them potentially being enriched in this ghost ancestry. Also, now that I think about it, their non-Mende ancestry is likely to be comprised of smth KEB-like not IAM-like, so perhaps they're not so enriched in it, after all."

      Agree with your logic entirely here.

      "The fit improved considerably when I used Natufians as a stand in, though still far from satisfactory."

      It's the same for thoroughly West-Asian admixed Horn-Africans such as Somalis and Habeshas. Something Natufian-like seems like the bulk of the West-Asian ancestry in the region rather than something Levant_N-like based on nMonte, unlike qpAdm. It makes some sense given the recent North-African samples.

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    2. Yeah, I can't believe they didn't think of using Natufians in their qpAdm modeling. Have you seen any qpAdm models on 'genica and elsewhere using Natufians for Horners, though?

      Can't wait till the IAM genomes come out so that Dave and others can run elucidating formal stats on them the authors didn't.

      In the meantime, there's this new, not-very-rigorous, paper on the Guanche:
      http://www.cell.com/current-biology/fulltext/S0960-9822(17)31257-5

      They appear to be like the KEB samples. There is mtDNA L3(as in ancient Egyptian samples), but no L2 unlike in modern Maghrebis and Egyptians. Also, unlike Tunisians, Algerians and other "lowland" Arabophone Maghrebis, the Yoruba-like signal, which Natufians get at low K as well, disappears in Berbers and Guanche early on. Whether it's ancient SSA or some para-Eurasian admixture is still unclear.

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    3. "Can't wait till the IAM genomes come out so that Dave and others can run elucidating formal stats on them the authors didn't."

      Or even get to throw them into Global-10 (I'm not that wild about qpAdm, to be honest) if there are enough markers.

      "In the meantime, there's this new, not-very-rigorous, paper on the Guanche:
      http://www.cell.com/current-biology/fulltext/S0960-9822(17)31257-5

      They appear to be like the KEB samples. There is mtDNA L3(as in ancient Egyptian samples), but no L2 unlike in modern Maghrebis and Egyptians. Also, unlike Tunisians, Algerians and other "lowland" Arabophone Maghrebis, the Yoruba-like signal, which Natufians get at low K as well, disappears in Berbers and Guanche early on. Whether it's ancient SSA or some para-Eurasian admixture is still unclear."

      Thanks for sharing, I'll comment more on this later.

      "Yeah, I can't believe they didn't think of using Natufians in their qpAdm modeling. Have you seen any qpAdm models on 'genica and elsewhere using Natufians for Horners, though?"

      I think they're just automatically assuming Natufians or people very similar to them didn't contribute to any modern populations and instead it had to be Neolithic Levantines did and there's also the fact that qpAdm tends to make Natufians fit quite poorly with Horn-Africans:

      http://anthromadness.blogspot.com/2016/07/somali-qpadm-models-using-new-ancient.html

      Anyway, I did some runs on Somalis and the like and shared them at 'genica:

      http://www.anthrogenica.com/showthread.php?12080-Reconstructing-Prehistoric-African-Population-Structure&p=302068#post302068

      As I say in the thread, I didn't used to get those results for Somalis in the past but now interestingly do. It seems like most modern Horn-Africans are some older, more Natufian-like West-Asian component + a later Arabian~Egyptian (particularly Copts when speaking of Egyptians) component whilst the Luxmandan seems to entirely lack the later Arabian~Egyptian stuff which I assume to some degree came with the Proto-Ethiosemitic speaking community around 2500-3000ybp and there MIGHT be something that predates that as touched upon here:

      http://anthromadness.blogspot.com/2016/01/the-later-west-eurasian-element-in-agaws.html

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  5. It's pretty clear that Somalis have two(or possibly more) distinct sources of Eurasian ancestry if we assume they have a real Tanzania_Luxmanda-like substrate(which I suspect to have harbored ancestry from the aforementioned potential ghost population).

    The question is when the second layer, carrying a bit of Iran_N-related DNA with y Hg T present, started arriving.

    What do you know about the origins of Puntite civilization so far? Could there have been a migration into the region by actual Egyptians acting as mediators for Iran_N ancestry? I thought about ancient South Arabia, too, but Iran_N ancestry there seems to be associated with a high frequency of y Hg J. As I understand, it's not a Hg that's well represented in Somali clans.

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    1. "The question is when the second layer, carrying a bit of Iran_N-related DNA with y Hg T present, started arriving."

      I doubt this has much to do with the T-M70 in the Horn and Somalis. For one, T-M70 definitely looks like it existed among South-Erythraeic speakers like the ancestors of this Luxmanda sample as it even appears in modern Iraqws and at lower frequencies in SE African populations that seem South-Erythraean admixed:

      http://anthromadness.blogspot.com/2015/05/south-cushitic-admixture-in-southeast.html

      T-M70 is more likely tied to the earlier strain of West-Asian ancestry in the Horn. The strain that looks Natufian in nMonte and Levant_N in qpAdm. The Y-DNA J1 (and a bit of J2) in the region is another story entirely, though:

      http://anthromadness.blogspot.com/2016/10/sudanese-arab-and-nubian-mtdna-is.html

      "What do you know about the origins of Puntite civilization so far? Could there have been a migration into the region by actual Egyptians acting as mediators for Iran_N ancestry?"

      Punt, as far as I know, was probably anywhere from the northern Eritrean coast down to the north-central Somali coastline (I lean Eritrea) and it wasn't all that extensive whilst probably just being some small pre-historic fiefdom of some sort that happened to be sitting on bountiful land the Egyptians liked to trade with. I doubt much admixture was acquired through it at all, certainly not enough to influence the entire Horn region as the ancestors of Somalis, Habeshas and the like were already linguistically broken up at this point (Central-Erythraeic and East-Erythraeic had already become distinct) and were unlikely to be one small community living in a small area of the Horn together.

      "I thought about ancient South Arabia, too, but Iran_N ancestry there seems to be associated with a high frequency of y Hg J. As I understand, it's not a Hg that's well represented in Somali clans."

      There is plenty of Y-DNA J among our various Ethiosemitic and Erythraeic speaking neighbors. Oromos, Alabas, Afars, Tigrinyas, Amharas, the Gurage... All about 20-25% J1 from what I've seen. Somalis normally just show low frequencies for J1 (1-4%) but it appears in several different datasets and seems geographically well-spread (appearing in Northeast Somalia to Jijiga in Ethiopia to even among Garre-Somalis). Granted, some of it can, at times, be recently acquired like how it seems with a relative of mine:

      http://www.anthrogenica.com/showthread.php?5584-Interesting-case-of-a-South-Arabian-J1-subclade-present-in-a-non-mixed-looking-Somali

      Anyway, it's possible we were more minorly influenced by South-Arabians than our neighbors and our clear founder-effects for the local E-V32 & T-M70 Y-DNA Haplogroups proved too predominant for J1 to ever take any sort of root. Can't be sure... As I said over at 'genica, Somalis showing something like ~10% Yemenite-Jew-like ancestry is new to me, honestly. Still figuring out how this makes sense. :-)

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