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Thread: Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa

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    Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa

    A new study from the Reich lab with some Later Stone Age, Pastoral Neolithic and Iron Age DNA from Kenya and Tanzania.

    Quote Originally Posted by Prendergast et al.
    How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multi-phase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers, while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.
    You can access the paper and supplement for free (the latter includes some qpAdm models). The genotype data is also available.




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    Fantastic stuff, devouring it now. The genotype data has also been released. I'm excited to see them added to the G25.
    Ελευθερία ή θάνατος.

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    Some highlights:

    1) They hypothesize that early Northeast African pastoralists (ENP) were an even mixture of a group related to North African and Levantine populations, and a group related to South Sudanese. This ENP group went on to mix with East African foragers. In some samples, they infer 2 separate admixture events: 5000-6000 years ago, and 4000 years ago. They associate the former with the formation of ENP ancestry in Northeast Africa, and the latter with additional forager admixture in East Africa. We'll see how admixture dating continues to change with further ancient DNA. I'd guess a date around 6000-8000 years ago would fit with the exodus of early pastoralists (proto-Cushites?) from the desiccating Sahara.

    2) 2 possible early pastoralist samples at Prettejohn’s Gully, dated to ~4000 years ago, couldn't be modeled as related to the later Pastoral Neolithic samples. Surprisingly, the male carried Y-DNA E2(xE2b). Today, E2a is very frequent in East African Nilotic speakers, but absent in the South Sudanese, who are mostly A/B, with some E-M35. E2 may have been picked up by Nilotes when they reached East Africa? Unfortunately, Reich's team were unable to extract DNA from the early pastoralists near Lake Turkana, builders of monuments like the Lothagam North Pillar site dated to 5300 ya. Comparing these samples with some data from the Turkana pastoralists would be great to get the full picture.

    3) Individuals from the Savanna Pastoral Neolithic and Elmenteitan were not genetically distinct, even though the Elmenteitan has been associated with early South Nilotic speakers in the past. Both were most similar to modern-day Cushitic speakers. Their Y-DNA was mostly E-M293, with some E-V22, E-V32 and A-M13. The Luxmanda sample from Skoglund's paper is slightly more forager-admixed than most of the new Pastoral Neolithic samples, and 1 of the new samples sticks out as less forager-related (I8759).

    4) They found a single instance of a mutation associated with lactase persistence, the same mutation found in present-day southern/eastern African pastoralists, in a Tanzanian who lived 2000 years ago. Much like in Europe, LP allele frequencies seem to have increased fairly recently in SSA.

    5) The LSA Kenyan samples fall on the previously described East-South African forager cline, and are a bit more "southern" than Mota.

    6) Some Iron Age samples are shifted toward Nilotic South Sudanese and Bantu groups.

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    These samples made it into the Global25 datasheets.

    KEN_Early_Pastoral_N:I12533
    KEN_Early_Pastoral_N:I12534
    KEN_IA_Deloraine:I8802
    KEN_LSA:I8808
    KEN_Pastoral_IA:I12379
    KEN_Pastoral_IA:I12381
    KEN_Pastoral_N:I8758
    KEN_Pastoral_N:I8804
    KEN_Pastoral_N:I8809
    KEN_Pastoral_N:I8814
    KEN_Pastoral_N:I8830
    KEN_Pastoral_N:I8874
    KEN_Pastoral_N:I8918
    KEN_Pastoral_N:I8919
    KEN_Pastoral_N:I8920
    KEN_Pastoral_N:I12384
    KEN_Pastoral_N_Elmenteitan:I8805
    KEN_Pastoral_N_Elmenteitan:I8922
    KEN_Pastoral_N_Elmenteitan:I8923
    KEN_Pastoral_N_Elmenteitan:I10719
    KEN_Pastoral_N_Elmenteitan:I12394
    KEN_Pastoral_N_Elmenteitan:I12398
    TZN_PN:I13762
    TZN_PN:I13977
    TZN_PN:I13979
    TZN_PN:I13980
    TZN_PN:I13981
    TZN_PN_outlier:I13978

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    The Savannah Neolithic Pastoral complex is usually associated with Cushitic speakers. The presence of Natufian ancestry in them makes sense.

    But how did Omotic speakers, who speak presumably the most basal living Afro-Asiatic language, acquire their Natufian ancestry? Gene flow from SPN pastoralists? Or did they acquire it from Natufian-related foragers much earlier? This obviously has implications for the Afro-Asiatic homeland debate, because if AA spread to Ethiopia with a Natufian-rich population from elsewhere, you'd expect some pre-PN Ethiopians (putative ancestral Omotes) to show evidence of it.
    Ελευθερία ή θάνατος.

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    Quote Originally Posted by Michalis Moriopoulos View Post
    The Savannah Neolithic Pastoral complex is usually associated with Cushitic speakers. The presence of Natufian ancestry in them makes sense.

    But how did Omotic speakers, who speak presumably the most basal living Afro-Asiatic language, acquire their Natufian ancestry? Gene flow from SPN pastoralists? Or did they acquire it from Natufian-related foragers much earlier? This obviously has implications for the Afro-Asiatic homeland debate, because if AA spread to Ethiopia with a Natufian-rich population from elsewhere, you'd expect some pre-PN Ethiopians (putative ancestral Omotes) to show evidence of it.
    I think proto-Omotic speakers acquiring Natufian-like forager ancestry from either further north in Africa or via South Arabia, is highly likely. On amateur runs, the Ari (for example) possess about 15 - 20% of a "pure" "Southwest Asian" component as their sole non-African ancestry.

    This is in contrast to Somalis who get some "Anatolian Farmer" and, Ethio-Semites who additionally have some CHG-like ancestry.
    Last edited by pgbk87; 05-31-2019 at 05:48 AM.

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    Quote Originally Posted by Michalis Moriopoulos View Post
    The Savannah Neolithic Pastoral complex is usually associated with Cushitic speakers. The presence of Natufian ancestry in them makes sense.

    But how did Omotic speakers, who speak presumably the most basal living Afro-Asiatic language, acquire their Natufian ancestry? Gene flow from SPN pastoralists? Or did they acquire it from Natufian-related foragers much earlier? This obviously has implications for the Afro-Asiatic homeland debate, because if AA spread to Ethiopia with a Natufian-rich population from elsewhere, you'd expect some pre-PN Ethiopians (putative ancestral Omotes) to show evidence of it.
    After doing a bit of reading about Omotic languages and comparing with what we know from the genetic studies thus far, I've come up with this:

    According to Ethiopian linguist Moges Yigezu, the southern Omotic groups (Aari, Hamer-Banna, etc) may have spoken or been exposed to Nilo Saharan languages before they adopted Omotic.

    And the Chabu, the southwest Ethiopian group that has the most ancestry of the type found in Mota and the South Omotic speaking Aari, speak a language that has more connection to Nilo-Saharan, and their neighbors who carry similar ancestry also speak Nilo-Saharan languages.

    This could suggest that Omotic spread to this area from the northeast relatively late. In turn, that would mean that it would be harder to associate Omotic with an earlier AA forager lifestyle.

    Indeed, looking at the PCA, all of the Afroasiatic groups (which I believe includes Omotic groups, I checked the paper with the modern Ethiopian reference populations in the supplement) fall on a cline towards the Pastoral Neolithic cluster. That leads me to suspect that Omotic groups adopted their current languages from PN related populations.

    It would be great to see some focused aDNA modeling with Omotic populations for sure!

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    Using the same outgroups for qpAdm from the paper:

    Kenya_Early_Pastoral_N (~4000BP):

    50.0% (+/- 0.9%) Levant_N
    22.6% (+/- 3.4%) Dinka
    26.7% (+/- 3.6%) Mota

    qpAdm output:
     

    left pops:
    Kenya_Early_Pastoral_N
    Levant_N
    Dinka.DG
    Ethiopia_4500BP.SG

    right pops:
    South_Africa_2000BP.SG
    Yoruba.DG
    Luxembourg_Loschbour.DG
    Mbuti.DG
    Biaka.DG
    Iranian.DG
    French.DG

    0 Kenya_Early_Pastoral_N 2
    1 Levant_N 12
    2 Dinka.DG 4
    3 Ethiopia_4500BP.SG 1
    4 South_Africa_2000BP.SG 3
    5 Yoruba.DG 4
    6 Luxembourg_Loschbour.DG 1
    7 Mbuti.DG 5
    8 Biaka.DG 2
    9 Iranian.DG 2
    10 French.DG 4
    jackknife block size: 0.050
    snps: 1135527 indivs: 40
    number of blocks for block jackknife: 714
    ## ncols: 1135527
    coverage: Kenya_Early_Pastoral_N 765633
    coverage: Levant_N 839184
    coverage: Dinka.DG 1135405
    coverage: Ethiopia_4500BP.SG 1134612
    coverage: South_Africa_2000BP.SG 1135087
    coverage: Yoruba.DG 1135401
    coverage: Luxembourg_Loschbour.DG 1048865
    coverage: Mbuti.DG 1135367
    coverage: Biaka.DG 1106999
    coverage: Iranian.DG 1107130
    coverage: French.DG 1135340
    dof (jackknife): 620.693
    numsnps used: 634874
    codimension 1
    f4info:
    f4rank: 2 dof: 4 chisq: 5.940 tail: 0.203638453 dofdiff: 6 chisqdiff: -5.940 taildiff: 1
    B:
    scale 1.000 1.000
    Yoruba.DG 0.046 1.766
    Luxembourg_Loschbour.DG 1.396 -0.607
    Mbuti.DG 0.001 0.931
    Biaka.DG 0.020 1.042
    Iranian.DG 1.380 -0.508
    French.DG 1.464 -0.549
    A:
    scale 79.955 730.950
    Levant_N 0.984 0.266
    Dinka.DG -0.908 1.024
    Ethiopia_4500BP.SG -1.099 -1.371


    full rank
    f4info:
    f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 4 chisqdiff: 5.940 taildiff: 0.203638453
    B:
    scale 1.000 1.000 1.000
    Yoruba.DG 0.075 1.725 -1.578
    Luxembourg_Loschbour.DG 1.396 -0.661 0.877
    Mbuti.DG 0.016 0.914 1.377
    Biaka.DG 0.038 1.023 0.422
    Iranian.DG 1.379 -0.571 -0.777
    French.DG 1.464 -0.614 -0.252
    A:
    scale 81.442 736.284 8396.106
    Levant_N 1.015 0.230 1.028
    Dinka.DG -0.885 1.306 0.945
    Ethiopia_4500BP.SG -1.090 -1.114 1.024


    best coefficients: 0.507 0.226 0.267
    Jackknife mean: 0.506807208 0.226173867 0.267018925
    std. errors: 0.009 0.034 0.036


    Somali (Single individual from Garissa, Kenya):

    40.2% (+/- 1%) Levant_N
    54.8% (+/- 3.6%) Dinka
    5.0% (+/- 3.7%) Mota


    qpAdm output:
     

    left pops:
    Somali.DG
    Levant_N
    Dinka.DG
    Ethiopia_4500BP.SG

    right pops:
    South_Africa_2000BP.SG
    Yoruba.DG
    Luxembourg_Loschbour.DG
    Mbuti.DG
    Biaka.DG
    Iranian.DG
    French.DG

    0 Somali.DG 1
    1 Levant_N 12
    2 Dinka.DG 4
    3 Ethiopia_4500BP.SG 1
    4 South_Africa_2000BP.SG 3
    5 Yoruba.DG 4
    6 Luxembourg_Loschbour.DG 1
    7 Mbuti.DG 5
    8 Biaka.DG 2
    9 Iranian.DG 2
    10 French.DG 4
    jackknife block size: 0.050
    snps: 1135527 indivs: 39
    number of blocks for block jackknife: 714
    ## ncols: 1135527
    coverage: Somali.DG 1104854
    coverage: Levant_N 839184
    coverage: Dinka.DG 1135405
    coverage: Ethiopia_4500BP.SG 1134612
    coverage: South_Africa_2000BP.SG 1135087
    coverage: Yoruba.DG 1135401
    coverage: Luxembourg_Loschbour.DG 1048865
    coverage: Mbuti.DG 1135367
    coverage: Biaka.DG 1106999
    coverage: Iranian.DG 1107130
    coverage: French.DG 1135340
    dof (jackknife): 621.987
    numsnps used: 804292
    codimension 1
    f4info:
    f4rank: 2 dof: 4 chisq: 4.187 tail: 0.381342398 dofdiff: 6 chisqdiff: -4.187 taildiff: 1
    B:
    scale 1.000 1.000
    Yoruba.DG 0.060 1.757
    Luxembourg_Loschbour.DG 1.396 -0.641
    Mbuti.DG 0.007 0.932
    Biaka.DG 0.027 1.042
    Iranian.DG 1.379 -0.482
    French.DG 1.465 -0.561
    A:
    scale 80.416 603.495
    Levant_N 1.189 -0.358
    Dinka.DG -0.783 0.412
    Ethiopia_4500BP.SG -0.986 -1.644


    full rank
    f4info:
    f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 4 chisqdiff: 4.187 taildiff: 0.381342398
    B:
    scale 1.000 1.000 1.000
    Yoruba.DG 0.079 1.789 -0.320
    Luxembourg_Loschbour.DG 1.395 -0.592 0.571
    Mbuti.DG 0.017 0.944 -0.502
    Biaka.DG 0.038 1.057 1.246
    Iranian.DG 1.379 -0.432 -1.760
    French.DG 1.465 -0.505 0.820
    A:
    scale 81.353 638.351 9431.717
    Levant_N 1.204 -0.457 1.062
    Dinka.DG -0.781 0.519 1.057
    Ethiopia_4500BP.SG -0.969 -1.588 0.868


    best coefficients: 0.402 0.548 0.050
    Jackknife mean: 0.402115414 0.548051562 0.049833024
    std. errors: 0.010 0.036 0.037

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  17. #9
    Can anyone use Chabu and Bari samples instead of Mota and Dinka? those two groups get at more of what we want, i.e SW Paleolithic Ethiopian HG ancestry and aEA.

    Did Mota have any legit Eurasian ancestry? what exactly differentiated him from the Chabu? perhaps these folks?

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    Quote Originally Posted by blackflash16 View Post
    Using the same outgroups for qpAdm from the paper:

    Kenya_Early_Pastoral_N (~4000BP):

    50.0% (+/- 0.9%) Levant_N
    22.6% (+/- 3.4%) Dinka
    26.7% (+/- 3.6%) Mota

    qpAdm output:
     

    left pops:
    Kenya_Early_Pastoral_N
    Levant_N
    Dinka.DG
    Ethiopia_4500BP.SG

    right pops:
    South_Africa_2000BP.SG
    Yoruba.DG
    Luxembourg_Loschbour.DG
    Mbuti.DG
    Biaka.DG
    Iranian.DG
    French.DG

    0 Kenya_Early_Pastoral_N 2
    1 Levant_N 12
    2 Dinka.DG 4
    3 Ethiopia_4500BP.SG 1
    4 South_Africa_2000BP.SG 3
    5 Yoruba.DG 4
    6 Luxembourg_Loschbour.DG 1
    7 Mbuti.DG 5
    8 Biaka.DG 2
    9 Iranian.DG 2
    10 French.DG 4
    jackknife block size: 0.050
    snps: 1135527 indivs: 40
    number of blocks for block jackknife: 714
    ## ncols: 1135527
    coverage: Kenya_Early_Pastoral_N 765633
    coverage: Levant_N 839184
    coverage: Dinka.DG 1135405
    coverage: Ethiopia_4500BP.SG 1134612
    coverage: South_Africa_2000BP.SG 1135087
    coverage: Yoruba.DG 1135401
    coverage: Luxembourg_Loschbour.DG 1048865
    coverage: Mbuti.DG 1135367
    coverage: Biaka.DG 1106999
    coverage: Iranian.DG 1107130
    coverage: French.DG 1135340
    dof (jackknife): 620.693
    numsnps used: 634874
    codimension 1
    f4info:
    f4rank: 2 dof: 4 chisq: 5.940 tail: 0.203638453 dofdiff: 6 chisqdiff: -5.940 taildiff: 1
    B:
    scale 1.000 1.000
    Yoruba.DG 0.046 1.766
    Luxembourg_Loschbour.DG 1.396 -0.607
    Mbuti.DG 0.001 0.931
    Biaka.DG 0.020 1.042
    Iranian.DG 1.380 -0.508
    French.DG 1.464 -0.549
    A:
    scale 79.955 730.950
    Levant_N 0.984 0.266
    Dinka.DG -0.908 1.024
    Ethiopia_4500BP.SG -1.099 -1.371


    full rank
    f4info:
    f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 4 chisqdiff: 5.940 taildiff: 0.203638453
    B:
    scale 1.000 1.000 1.000
    Yoruba.DG 0.075 1.725 -1.578
    Luxembourg_Loschbour.DG 1.396 -0.661 0.877
    Mbuti.DG 0.016 0.914 1.377
    Biaka.DG 0.038 1.023 0.422
    Iranian.DG 1.379 -0.571 -0.777
    French.DG 1.464 -0.614 -0.252
    A:
    scale 81.442 736.284 8396.106
    Levant_N 1.015 0.230 1.028
    Dinka.DG -0.885 1.306 0.945
    Ethiopia_4500BP.SG -1.090 -1.114 1.024


    best coefficients: 0.507 0.226 0.267
    Jackknife mean: 0.506807208 0.226173867 0.267018925
    std. errors: 0.009 0.034 0.036


    Somali (Single individual from Garissa, Kenya):

    40.2% (+/- 1%) Levant_N
    54.8% (+/- 3.6%) Dinka
    5.0% (+/- 3.7%) Mota


    qpAdm output:
     

    left pops:
    Somali.DG
    Levant_N
    Dinka.DG
    Ethiopia_4500BP.SG

    right pops:
    South_Africa_2000BP.SG
    Yoruba.DG
    Luxembourg_Loschbour.DG
    Mbuti.DG
    Biaka.DG
    Iranian.DG
    French.DG

    0 Somali.DG 1
    1 Levant_N 12
    2 Dinka.DG 4
    3 Ethiopia_4500BP.SG 1
    4 South_Africa_2000BP.SG 3
    5 Yoruba.DG 4
    6 Luxembourg_Loschbour.DG 1
    7 Mbuti.DG 5
    8 Biaka.DG 2
    9 Iranian.DG 2
    10 French.DG 4
    jackknife block size: 0.050
    snps: 1135527 indivs: 39
    number of blocks for block jackknife: 714
    ## ncols: 1135527
    coverage: Somali.DG 1104854
    coverage: Levant_N 839184
    coverage: Dinka.DG 1135405
    coverage: Ethiopia_4500BP.SG 1134612
    coverage: South_Africa_2000BP.SG 1135087
    coverage: Yoruba.DG 1135401
    coverage: Luxembourg_Loschbour.DG 1048865
    coverage: Mbuti.DG 1135367
    coverage: Biaka.DG 1106999
    coverage: Iranian.DG 1107130
    coverage: French.DG 1135340
    dof (jackknife): 621.987
    numsnps used: 804292
    codimension 1
    f4info:
    f4rank: 2 dof: 4 chisq: 4.187 tail: 0.381342398 dofdiff: 6 chisqdiff: -4.187 taildiff: 1
    B:
    scale 1.000 1.000
    Yoruba.DG 0.060 1.757
    Luxembourg_Loschbour.DG 1.396 -0.641
    Mbuti.DG 0.007 0.932
    Biaka.DG 0.027 1.042
    Iranian.DG 1.379 -0.482
    French.DG 1.465 -0.561
    A:
    scale 80.416 603.495
    Levant_N 1.189 -0.358
    Dinka.DG -0.783 0.412
    Ethiopia_4500BP.SG -0.986 -1.644


    full rank
    f4info:
    f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 4 chisqdiff: 4.187 taildiff: 0.381342398
    B:
    scale 1.000 1.000 1.000
    Yoruba.DG 0.079 1.789 -0.320
    Luxembourg_Loschbour.DG 1.395 -0.592 0.571
    Mbuti.DG 0.017 0.944 -0.502
    Biaka.DG 0.038 1.057 1.246
    Iranian.DG 1.379 -0.432 -1.760
    French.DG 1.465 -0.505 0.820
    A:
    scale 81.353 638.351 9431.717
    Levant_N 1.204 -0.457 1.062
    Dinka.DG -0.781 0.519 1.057
    Ethiopia_4500BP.SG -0.969 -1.588 0.868


    best coefficients: 0.402 0.548 0.050
    Jackknife mean: 0.402115414 0.548051562 0.049833024
    std. errors: 0.010 0.036 0.037
    What are the p-values for the models?
    Quoted from this Forum:

    "Which superman haplogroup is the toughest - R1a or R1b? And which SNP mutation spoke Indo-European first? There's only one way for us to find out ... fight!"

  19. The Following 5 Users Say Thank You to Ryukendo For This Useful Post:

     Agamemnon (06-01-2019),  Inigo Montoya (06-01-2019),  palamede (05-31-2019),  Power77 (06-01-2019),  VytautusofAukstaitija (05-31-2019)

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