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Thread: .. East African HG pops and insights into local adaptation (Scheinfeldt, 2019)

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    .. East African HG pops and insights into local adaptation (Scheinfeldt, 2019)

    Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation (Scheinfeldt, 2019)



    Abstract:

    Anatomically modern humans arose in Africa ∼300,000 years ago, but the demographic and adaptive histories of African populations are not well-characterized. Here, we have generated a genome-wide dataset from 840 Africans, residing in western, eastern, southern, and northern Africa, belonging to 50 ethnicities, and speaking languages belonging to four language families. In addition to agriculturalists and pastoralists, our study includes 16 populations that practice, or until recently have practiced, a hunting-gathering (HG) lifestyle. We observe that genetic structure in Africa is broadly correlated not only with geography, but to a lesser extent, with linguistic affiliation and subsistence strategy. Four East African HG (EHG) populations that are geographically distant from each other show evidence of common ancestry: the Hadza and Sandawe in Tanzania, who speak languages with clicks classified as Khoisan; the Dahalo in Kenya, whose language has remnant clicks; and the Sabue in Ethiopia, who speak an unclassified language. Additionally, we observed common ancestry between central African rainforest HGs and southern African San, the latter of whom speak languages with clicks classified as Khoisan. With the exception of the EHG, central African rainforest HGs, and San, other HG groups in Africa appear genetically similar to neighboring agriculturalist or pastoralist populations. We additionally demonstrate that infectious disease, immune response, and diet have played important roles in the adaptive landscape of African history. However, while the broad biological processes involved in recent human adaptation in Africa are often consistent across populations, the specific loci affected by selective pressures more often vary across populations.


    Supplement below is found here (courtesy of Lank ; )


    Figure S4. ADMIX results K2-K9:

     

    Figure S9. PCA:
     
    Last edited by NiloSaharan; 02-20-2019 at 05:08 PM.
    PuntDNAL K8
    Population: Hidden Content 46.16, Ubangian_Congo 9.56, W_Benue_Congo 24.21, Eastern_HG 2.09, E_Benue_Congo 12.94, Omotic 5.05
    Single Population Sharing: Hidden Content 14.17, Hidden Content 17.26, South_Sudanese 25.21, South_Sudan_Anuak 25.65, Cameroon_Mada 28.57, Ethiopian_Gumuz 33.91, Kenyan_Maasai 36.07, Kenyan_Bantu 38.05, Chad_Kaba 40.04, DRC_Hema 42.08, Kenyan_Luhya 46.64

    The truth is not for all men, but only for those who seek it - Hidden Content

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    Some thoughts so far... though mostly limited to ADMIXTURE:


    • I'm fascinated by the fuchsia component appearing at K8; it's present among the Fulani but negligible among fellow sahelian pops like the Maɗa (Chadic speakers) and Bulala (Central-Sudanic NS speakers)

      Could this horner-like component be a marker for pastoral migrations from the horn? The component peaks among the Sanye (aka Aweer, Boni) a former HG pop known to occupy southern Somalia down to coastal Kenya

      ...then again, maybe it's absence among Chadic and Central-Sudanic speakers should be expected:

      "The proposed migration of proto-Chadic Afroasiatic speakers ~7000 years ago from the central Sahara into the Lake Chad Basin may have resulted in a Nilo-Saharan to Afroasiatic language shift among Chadic speakers. However, our data suggest that this shift was not accompanied by large amounts of Afroasiatic gene flow ... the Afroasiatic Chadic–speaking populations from northern Cameroon cluster close to the Nilo-Saharan–speaking populations from Chad, rather than with East African Afroasiatic speakers , consistent with a language replacement among the Chadic populations." (Tishkoff, 2009)


    • It's great seeing such a wide breadth of ethnic groups I've honestly never heard of but it's a shame they didn't include Somali samples -- I'm extremely curious on how much they'd peak with this fuchsia component

    • The red K7 Nilo-Saharan component appears before the fuchsia Horner affinity K8 -- any significance here?

    • Would it be fair to say the green Mbuti affinity for the Luo isn't literally derived from the Mbuti pygmies of the Ituri rainforest but rather other Great-Lake HG pops? There's non-pygmy indigenous HGs like the Ik, Benet and Ogiek who'd fall within the path of Luo migrations towards the rift-valley.
      Between the Congo basin and Kenya, it'll be interesting to see if a clear regional delineation emerges between the Biaka/Mbuti and EHG affinity -- these Ugandan HGs should be of prime interest!

    • Would the teal ADMIXTURE from K4-K6 be reflective of "Ancient East-African"? It seems to be the source component for the subsequent K7-K9 Nilo-Saharan (red), Horner (fuchsia) and (teal) EHG affinities. I wonder if this would give more credence to remarks made earlier on a proposed SW-Ethiopia/South-Sudanese origin for "Proto-Nilosaharan"
    Last edited by NiloSaharan; 02-20-2019 at 05:08 PM. Reason: component colour correction - violet=fuchsia
    PuntDNAL K8
    Population: Hidden Content 46.16, Ubangian_Congo 9.56, W_Benue_Congo 24.21, Eastern_HG 2.09, E_Benue_Congo 12.94, Omotic 5.05
    Single Population Sharing: Hidden Content 14.17, Hidden Content 17.26, South_Sudanese 25.21, South_Sudan_Anuak 25.65, Cameroon_Mada 28.57, Ethiopian_Gumuz 33.91, Kenyan_Maasai 36.07, Kenyan_Bantu 38.05, Chad_Kaba 40.04, DRC_Hema 42.08, Kenyan_Luhya 46.64

    The truth is not for all men, but only for those who seek it - Hidden Content

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    So the Sabue are the Chabu/Shabo? Man, everyone needs to settle on one spelling.

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    This looks more or less like Tishkoff's 09 early K results, but with a few missing groups like Omotics.

    What kind of SNP chip did they use and can the data be used by genome hobbyists?

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    Quote Originally Posted by NiloSaharan View Post
    It's great seeing such a wide breadth of ethnic groups I've honestly never heard of but it's a shame they didn't include Somali samples -- I'm extremely curious on how much they'd peak with this violet component
    The Gurreh (Garre), Gabra, Rendille, Wata, Orma, Boni and Sanye are technically all Somaloid speakers or former speakers of that language group. Somaloid speakers have lived in North-Central Kenya significantly earlier than Oromoid groups (Borana Oromos). In recent centuries, the Gabra, Orma, Wata, and Sanye have language shifted to Oromoid languages. About the Boni, they were sampled near Lamu and likely have absorbed nearby Swahili Bantu populations explaining their orange NC component. In regards to the Sanye, their fuschia component at K=9 may be due to recent high levels of endogamy rather than a genuine ancient component. In Tishkoff '09, the Mbugwe similarly formed an endogamy-based uninformative component. Out of these groups, the Gurreh (Garre) are the closest to most Somalis overall, although they are more SW Ethiopian-shifted autosomally.

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    Quote Originally Posted by NetNomad View Post
    The Gurreh (Garre), Gabra, Rendille, Wata, Orma, Boni and Sanye are technically all Somaloid speakers or former speakers of that language group. Somaloid speakers have lived in North-Central Kenya significantly earlier than Oromoid groups (Borana Oromos). In recent centuries, the Gabra, Orma, Wata, and Sanye have language shifted to Oromoid languages. About the Boni, they were sampled near Lamu and likely have absorbed nearby Swahili Bantu populations explaining their orange NC component. In regards to the Sanye, their fuschia component at K=9 may be due to recent high levels of endogamy rather than a genuine ancient component. In Tishkoff '09, the Mbugwe similarly formed an endogamy-based uninformative component. Out of these groups, the Gurreh (Garre) are the closest to most Somalis overall, although they are more SW Ethiopian-shifted autosomally.
    Agreed, the Sanye component does not look informative. Sanye, along with most of the Kenyan/Tanzanian HG groups, seem to have quite significant Cushitic ancestry. Looking at K=4, the component peaking in Mozabites is a proxy for Eurasian admixture, which in turn is a proxy for Cushitic admixture in East Africa, and it's quite significant in most of the HGs. This component is only minor in Hadza, and absent in Shabu. Incidentally, the K=4 East African component peaks in Shabu, followed by the Hadza, then come the Ari/Hamer/Dinka. The Burji are quite similar to the Ari, despite speaking a Cushitic language.

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    For anyone who didn't know, one of the authors (J Hirbo) studied the uniparental markers of these populations (not including the Shabo) for his thesis back in 2011: Complex genetic history of East African populations. There are some errors in it and it's not full sequences (though decent set of SNPs), but still worth checking out. The results were nicely put together by Ethio Helix back in the day, his Y DNA charts are still up, though the mtDNA page is broken.

    The Burji language is basal Highland East Cushitic according to Glottolog, so they may have originated a good bit further north and higher up. They have 35% E1b1* (presumably E-M329) and 29% L3x which looks pretty Omotic (only n=23 and n=21 though). They also have Y hgs J2 and R (!?).

    The Boni (Aweer) have 43% E-M2 which together with their irregular levels of West African fits Bantu admixture as NetNomad pointed out; other than that they aren't so different from other Kenyan Cushitic speakers. Next highest is 19% E-M293. mtDNA includes 23% L0f, which otherwise seems to peak in South Cushitic speakers in this study, and 1 L0d2, which is rarely seen so far north.

    As was mentioned in another thread there is quite a bit of B2a in the hunter-gatherer-ish groups around here: 50% in Yaaku (n=24), 41% in Sanye (n=12), and 21% in Elmolo (n=15), and surprisingly little B2b (only 1/21 Boni). The other most common hgs are E-M293 and E-V32, as you'd expect. For mtDNA you find a little of practically every kind of East African L3, with L3a peaking in these groups, in addition to moderate amounts of L0a, L2a1, L4b, L5, M1a, N, etc typical of East Africa.
    Last edited by Megalophias; 02-21-2019 at 09:31 PM.

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    Quote Originally Posted by Megalophias View Post
    The Burji language is basal Highland East Cushitic according to Glottolog, so they may have originated a good bit further north and higher up. They have 35% E1b1* (presumably E-M329) and 29% L3x which looks pretty Omotic (only n=23 and n=21 though). They also have Y hgs J2 and R (!?).
    The Burji mostly live near Lake Chamo, Southwest Ethiopia and with small communities in Kenya due to migration. The ones in Kenya are of recent SW Ethiopian-origin mostly.

    I suspect that most Cushitic speaking groups from Southwest Ethiopia are more or less like this, i.e. a mixture of Omotics and something more akin to Somalis (Cushites).

    PS. The co-author of this paper is Burji (Mr. Hirbo), perhaps explaining why he added them in. This is him:

     
    Last edited by NetNomad; 02-22-2019 at 03:21 PM.

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