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Thread: Africa before ancient DNA: The deepest splits

  1. #1
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    Africa before ancient DNA: The deepest splits

    Alright, I plan to make a somewhat short post about this at Anthromadness in due time but Uni-work and other posts due before it have had me distracted for the time being but here goes:





    I basically asked David to run the South-Sudanese, the Gumuz, Yorubas & Mandenkas, Mbutis & Biakas and, finally, the "San" to sort of try and represent the deepest splits we so often notice via ADMIXTURE in PCA form:

     



    So... My two cents based on the above would be:

     


    Sent to an old friend (Lank) in private via email


    So... Theorize away. What do you think ancient DNA from across Africa will do to the diversity that PCA displays. Have you noticed other deep splits across the continent that I haven't? Share away if so. Consider this a place to dump some theories and discuss said theories whilst gauging how probable they are (share evidence you think back up your theories as well). It'll be interesting to see how much many of you have picked up on before we see plenty of aDNA from Africa someday.

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    Not a theory, but I'm curious why you did not include MOTA. I'm also curious to see whether those upcoming ancient Turkana samples would deviate further to the north than contemporary Nilotes.

    Nonetheless, I'd be curious if the genetic distance we see between West Africans and East Africans is drift or admixture, or both. West Africans carry a lot of Y-DNA and mtDNA lineages that are subsets of East African ones, but also very unique lineages to West Africa. There was probably a (now extinct?) hunter-gatherer population in West Africa that was absorbed by E-V38, mtDNA L2* + L3b'd'e "Proto West Africans". L1b* and L2a1 are hella old, and E-V33 is from the southwestern Sahara.

    I find it interesting that the Pygmy groups deviate from one another so drastically. Are the Mbuti closer to the San than the Biaka? Bantu admixture in the Biaka I'd guess.
    Last edited by pgbk87; 12-23-2016 at 02:52 PM.

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    I am interested in seeing if populations that seem like a composite of ancestries still look the same in ancient DNA.

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    Quote Originally Posted by beyoku View Post
    I am interested in seeing if populations that seem like a composite of ancestries still look the same in ancient DNA.
    Ie. South Sudanese/Anuak vs Gumuz.

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    Interesting! are there any genetic studies on coastal East Africans like the Swahili? it will be interesting to see the genetic composition of different Swahili tribes as well as the ancient component. Not much genetic research has been done on Swahili people which is a shame considering the multi-ethnic and multicultural diversity in the Coast of East Africa.

    Before the Swahili became Swahili they were bantu people living in Eastern Congo. There were Cushitic and Nilotic groups living in the East Coast of Africa at that time. The migration towards Ethiopia and Southern Somalia was due to the bantu migration as well as the harsh tropical climate. These Bantu people converted to Islam long before the Arabs and Persians were in the East Coast of Africa. This could suggest that the Bantu people living in Southern Somalia or Shungwaya had relations to the Axumite and Cushitic East African kingdoms in East Africa?

    The migration with the Bantu from Southern Somalia towards South Eastern Africa was due to war and conflict with the Oromo. These Bantu people became Swahili meaning people living in the East Coast of Africa. Later on some Swahili people intermarriage over time with first Persian Shirazis, Yemenis, East Asians then Omanis, Portuguese and South Asians.

    It really would be interesting to support this historical research with Genealogy.

    Cheers Abdurashid

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    Such a shame that we lack African ancient DNA so far. However, I wouldn't be surprised if E1a (my own Y-DNA) turns out to be dominant in Pre-Neolithic samples from the Maghreb and West Africa.
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    I'd wager that there's much diversity not being captured between San and Mbuti. Though they're both Hunter Gatherer groups and have some sort of relation which is well established, that PCA placed them in a position which isn't really intuitive. There's definitely something else going on there. The first dimension is not showing their divergence in the way that it shows HG vs. Farmer divergence, but I'd expect it to be overt simply because these populations allegedly separated very early.

    I'm also really curious about West African ancients and wonder if there are some extreme populations hidden within the region. Although there is marked modern diversity, the continent doesn't seem to meet my expectations as "the most diverse" when Eurasian admixture is accounted for. Again, something else is going on here, or I'm missing something (ascertainment bias?).

    Edit: Further, the enormity of African diversity which was mentioned frequently say, 5 or so years ago, hasn't really been captured autosomally, as far as I can tell anyway. One must wonder why this intra-African diversity isn't as apparent as we'd expect given the origin of Homo Sapiens.
    Last edited by xKeleix; 12-23-2016 at 05:28 PM.
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    I'll paste my response here too then.


    Agreed on all counts. I definitely think the admixture in African prehistory will be at least as complicated as in Eurasia, given the much longer history of modern humans on the continent. Once technology and available resources permit ancient DNA analysis more widely in Africa, we will certainly find a very complicated history, including but not at all limited to archaic humans. We will be seeing divergence on the order of hundreds of thousands of years, not merely tens of thousands of years as in Eurasian modern human structure and admixture.
    The common ancestor of Neanderthals/Denisovans and Homo sapiens, Homo heidelbergensis, is believed to have migrated out of Africa around 600 kya. Homo sapiens is estimated to be 200 ky old based on a combination of fossils (Omo 1), mtDNA and Y-DNA, although the A00 Y found in recent years is a bit older than 200 ky). But this division between modern and archaic is somewhat arbitrary, since modern humans were at least somewhat compatible with Neanderthals/Denisovans, and evolved in Africa continuously ever since that split. And the "modern behavioral package", i.e. LSA/UP technology, only dates to 50 kya, so there are those who only consider humans since 50 kya to be "modern" (although Khoisan, who split from the rest 200 kya, are also "behaviorally modern").

    However, if we accept that 200 kya limit for AMH, it is quite likely that Africans have some ancestry from groups more divergent than that. There are plenty of African fossils with a mixture of modern and archaic traits, and there is a lot of variety in Middle Stone Age African cultures. This fits with the population boom we see in proto-Sapiens from genetic data after the split from Neanderthals/Denisovans, whereas the latter had a population crash, no doubt due to the harsh Eurasian climate. There were a lot of different groups. Many of these would have been more archaic than the 200 kya TMRCA, but not at all as divergent as Neanderthals (e.g. the A00 dudes). And I wouldn't be surprised if some who were even more divergent than Neandeerthals survive in some of our DNA (as has been reported at least in Pygmies)."

    Mota's sequence came as a pleasant surprise, somewhat confirming earlier speculation that Paleolithic Ethiopians were Omotic-like (without Eurasian admixture). Let's hope we have more such surprises in 2017! Some of these, such as Epipaleolithic (E-M35?) North Africans may be relevant for Eurasians as well. Late MSA Africans, forming the predominant ancestry of all modern humans, certainly would be. Hofmeyr, the LSA South African who supposedly had craniometric similarities to Upper Paleolithic Eurasians, was apparently sent to the aDNA lab in Copenhagen over two years ago.

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    Quote Originally Posted by xKeleix View Post
    I'm also really curious about West African ancients and wonder if there are some extreme populations hidden within the region. Although there is marked modern diversity, the continent doesn't seem to meet my expectations as "the most diverse" when Eurasian admixture is accounted for. Again, something else is going on here, or I'm missing something (ascertainment bias?).

    Edit: Further, the enormity of African diversity which was mentioned frequently say, 5 or so years ago, hasn't really been captured autosomally, as far as I can tell anyway. One must wonder why this intra-African diversity isn't as apparent as we'd expect given the origin of Homo Sapiens.
    One important point to make is that Africans are less drifted, due to higher effective population sizes. This is why Fst distances between African groups are relatively low; much of the great African diversity is found within groups rather than between them. Yet analyses based on IBD, mtDNA and Y-DNA reveal fairly deep divergences do exist, even between the less isolated East and West Africans (after accounting for Eurasian admixture in the former).

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    Quote Originally Posted by Power77 View Post
    Such a shame that we lack African ancient DNA so far. However, I wouldn't be surprised if E1a (my own Y-DNA) turns out to be dominant in Pre-Neolithic samples from the Maghreb and West Africa.
    To be pedantic: There is one ancient African genome, namely Mota from Ethiopia: http://science.sciencemag.org/conten...cience.aad2879
    Last edited by rozenfeld; 12-23-2016 at 08:09 PM. Reason: typos

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