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Thread: Reconstructing Prehistoric African Population Structure

  1. #21
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    Nice to see the mixture models being tested in nMonte. We know there is some sort of relationship between the Mota-related Ethiopian highland ancestry, and hunter-gatherers farther south, so it's not surprising that both groups can be used in the models. Although I think it's notable that it prefers the Khoisan populations for the Tanzanian pastoralist.

    As you have noted in the past, there is some diffuse "San" affinity that is associated with Mota/Omotic-related ancestry. The authors of this paper even manage to fit some Hadza, as well as the Kenya 400BP and Tanzania Pemba 1400BP samples, as 100% Mota-related. These models look rather crude though, and Mota-related populations have vastly different uniparental markers from East African HGs sampled by Hirbo (e.g. the latter have lot of mtDNA L0f, also common in modern South Cushites, and interestingly found in 1 ancient Malawian). I would bet that with some new aDNA from East African HGs south of Ethiopia, or perhaps even the modern East African HGs sampled by Hirbo, they would be a much better fit for the HG ancestry in South Cushites, as well as the "Mota-related" ancient Kenyan/Tanzanian samples.
    Last edited by Lank; 09-26-2017 at 09:16 AM.

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  3. #22
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    Quote Originally Posted by Lank View Post
    As you have noted in the past, there is some diffuse "San" affinity that is associated with Mota/Omotic-related ancestry. The authors of this paper even manage to fit some Hadza, as well as the Kenya 400BP and Tanzania Pemba 1400BP samples, as 100% Mota-related. These models look rather crude though, and Mota-related populations have vastly different uniparental markers from East African HGs sampled by Hirbo (e.g. the latter have lot of mtDNA L0f, also common in modern South Cushites, and interestingly found in 1 ancient Malawian). I would bet that with some new aDNA from East African HGs south of Ethiopia, or perhaps even the modern East African HGs sampled by Hirbo, they would be a much better fit for the HG ancestry in South Cushites, as well as the "Mota-related" ancient Kenyan/Tanzanian samples.
    I totally agree. Modelling the South-Erythraean as part South-Africa 1,300ybp fits better and makes more sense with other data than Omotic-speaker related ancestry. Also, the Maasai_Kinyawa actually fit quite well as Luxmanda + Dinka:

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

    Masai_Kinyawa

    Tanzania_Luxmanda_3000BP 50.7
    Dinka 49.3

    Interestingly, however, when I added Somalis in, they shook up the results:

    [1] "distance%=0.1731 / distance=0.001731"

    Masai_Kinyawa

    Dinka 47.1
    Tanzania_Luxmanda_3000BP 26.9
    Somali 25.9

    Wonder if this points to these Masais having admixture from later East-Erythraeic speakers. Idk... Great comments as always, by the way.

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  5. #23
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    Quote Originally Posted by Awale View Post
    I totally agree. Modelling the South-Erythraean as part South-Africa 1,300ybp fits better and makes more sense with other data than Omotic-speaker related ancestry. Also, the Maasai_Kinyawa actually fit quite well as Luxmanda + Dinka:

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

    Masai_Kinyawa

    Tanzania_Luxmanda_3000BP 50.7
    Dinka 49.3

    Interestingly, however, when I added Somalis in, they shook up the results:

    [1] "distance%=0.1731 / distance=0.001731"

    Masai_Kinyawa

    Dinka 47.1
    Tanzania_Luxmanda_3000BP 26.9
    Somali 25.9

    Wonder if this points to these Masais having admixture from later East-Erythraeic speakers. Idk... Great comments as always, by the way.
    Truth be told I envision Massai as having 3 successive waves of northern admixture. The last 2 being post Ethnogenisis. V32, V22, M293, and T2 IMO didn’t all travel in tandem into the Rift Valley and Great Lakes / Nile Basin.

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  7. #24
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    Well, my fellows, it seems like we have some new developments. I don't know what's changed about nMonte's results all of a sudden (if this is indeed a change) but my conversation with Agamemnon below should get everyone up to speed:

     


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    But yeah, it seems to me like every current day Erythræic and Ethiosemitic speaking group has seemingly post Bronze-Age, pre-historic Zagrosian ancestry carrying admixture (with Somalis having the least):

    Code:
    [1] "distance%=0.5453 / distance=0.005453"
    
             Somali
                                  
    Dinka                    54.35
    Natufian                 34.40
    Yemenite-Jew             9.80
    Ari-Blacksmith           1.45
    
    --
    
    [1] "distance%=0.6277 / distance=0.006277"
    
             Xamtanga-Agaw ("Ethiopian-Afar")
                                  
    Dinka                    39.80
    Natufian                 31.85
    Yemenite-Jew             22.40
    Ari-Blacksmith           5.95
    
    --
    
    [1] "distance%=0.7816 / distance=0.007816"
    
             Amhara
                                  
    Dinka                    39.20
    Natufian                 34.70
    Yemenite-Jew             20.15
    Ari-Blacksmith           5.95
    
    --
    
    [1] "distance%=0.958 / distance=0.00958"
    
             Tigray-Tigrinya
                                 
    Dinka                    33.8
    Natufian                 32.6
    Yemenite-Jew             20.1
    Ari-Blacksmith           13.5
    Whilst, like in the paper, and unlike before, the Luxmanda sample lacks this affinity and mostly just comes off as "Natufian-like + Dinka-like + South-African HG":

    [1] "distance%=0.8087 / distance=0.008087"

    Tanzania-Luxmanda-3000BP

    Dinka 44.70
    Natufian 42.45
    South-Africa-1300BP 12.50
    Yemenite-Jew 0.35

    There are some oddities here other than me not recalling being able to get these results in the past like how the Agaw/"Afar" samples seem about as later West-Asian admixed as Habeshas when I recall them usually showing less (though they show somewhat less than Tigrinyas and Amharas when you use Negev Bedouin Bs instead of YJs). The higher Ari-like ancestry in Tigrinyas over Amharas is odd too but that might be skewed by an outlier among the Amharas and, as Lank in particular will remember, nMonte's had a hard time getting really decent Ari-like estimates for any group beyond Oromos, as far as I've seen. There's also the odd fact that even Aris are now showing some of this later admixture:

    [1] "distance%=0.5979 / distance=0.005979"

    Ari-Blacksmith

    Dinka 52.2
    South-Africa-1300BP 25.6
    Natufian 13.4
    Yemenite-Jew 8.8

    -

    [1] "distance%=0.896 / distance=0.00896"

    Ari-Cultivator

    Dinka 53.65
    South-Africa-1300BP 23.60
    Natufian 13.80
    Yemenite-Jew 8.95

    Has me surprised (but I guess it makes vague sense of all the Y-DNA J they have and even some of their mtDNA lineages?). I'm still thinking that something odd's amok but if this is legit; Somalis indeed do have some later West-Asian ancestry but, like I said to Agamemnon, these estimates are more acceptable to me than the ones gained via qpAdm. There is another difference as well in that nMonte clearly favors Natufians over Levant_N as the deeper, and older, layer of West-Asian ancestry in the region.

    And, finally, it does make sense that the Luxmanda sample would lack such ancestry and clearly points to how it's a later, post ~3kya addition into the horn.

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  9. #25
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    I have a thread that may be of interest in Autosomal DNA.. I am looking for feedback on a project.

  10. #26
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    Is it possible this Yemenite-Jew like admixture (in Somalis,Afars etc) arrived at the same time camels where introduced to the Horn considering majority of experts claim that camels were domesticated in SE Arabia?

    Or do you think it was similar to what happened in the Ethiopian highlands with Semitic speakers entering the Djibouti/Somaliland area but they weren't as successful as they did in the highlands of Ethiopia?


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  12. #27
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    Made sense of why the Luxmanda sample was showing Negev-Bedouin-B before as well:

    [1] "distance%=0.5565 / distance=0.005565"

    Tanzania-Luxmanda-3000bp

    Somali 79.4
    South-Africa-1300bp 12.3
    Natufian 8.3
    Negev-Bedouin-B 0.0

    -

    [1] "distance%=0.7378 / distance=0.007378"

    Tanzania-Luxmanda-3000bp

    Somali 83.50
    South-Africa-1300bp 11.45
    Negev-Bedouin-B 5.05

    I noticed a while ago that, somewhat differently from some other Arabian-Southern_Levantine groups, Negev Bedouin Bs seem very Natufian-shifted:

    Code:
    [1] "distance%=2.1982 / distance=0.021982"
    
             Negev-Bedouin-B
                 
    Natufian 72.8
    Iran_ChL 27.2
    Levant_N  0.0
    Dinka     0.0
    Yoruba    0.0
    
    -
    
    [1] "distance%=0.8847 / distance=0.008847"
    
             Yemenite_Jew
                 
    Natufian 49.5
    Iran_ChL 40.4
    Levant_N 10.1
    Dinka     0.0
    Yoruba    0.0
    
    
    
    Notice the very poor fit for the Negevians, though. I'm reminded of North-Africans, actually. I think they may have something perhaps even more basal than Natufian in them or just some pre-historic element we don't have yet in the aDNA record that we'll need to improve their fits. But nevertheless, you can still see how Natufian-like much of their ancestry looks when compared to Yemenite Jews. In fact I bet this is why they often provide better fits for Horn-Africans in comparison to Yemenite Jews (given that we have a lot of Natufian-like ancestry as well based on nMonte).
    So the reason the South-Erythraean was turning up as part Bedouin-B seems to be because they were standing in for the extra Natufian-like ancestry she has in comparison to Somalis. This is probably also why these Bedouin samples often provide better fits for Horners than Yemenite Jews do given that we too seem rather Natufian-shifted in these models. But, for the record, they're not actually as good an explanation for the levels of Zagros-Chl these groups are showing as Yemenite Jews are:

     
    [1] "distance%=0.8847 / distance=0.008847"

    Yemenite-Jew

    Natufian 49.5
    Iran_ChL 40.4
    Levant_N 10.1
    Dinka 0.0
    Yoruba 0.0

    According to the above, Yemenite Jews are about ~40% Zagros-Chal so for Somalis to be about ~10% Yemenite-Jew; they'd need to be about ~4% Zagros-Chl and that roughly is the case:

    [1] "distance%=0.5261 / distance=0.005261"

    Somali

    Dinka 54.1
    Natufian 40.2
    Iran_ChL 4.4
    Mota 1.3

    In contrast, they'd need to be about >or=15% Negev-Bedouin-B to explain 4-5% Zagros-Chl but >or=15% is not actually what they end up with:

    [1] "distance%=2.1982 / distance=0.021982"

    Negev-Bedouin-B

    Natufian 72.8
    Iran_ChL 27.2
    Levant_N 0.0
    Dinka 0.0
    Yoruba 0.0

    [1] "distance%=0.5549 / distance=0.005549"

    Somali

    Dinka 53.20
    Natufian 32.40
    Negev-Bedouin-B 11.05
    Mota 3.35

    It's the same for other groups like Tigrinyas. ~20% Yemenite-Jew makes sense with their 8-9% Zagros-Chalcolithic:

    [1] "distance%=0.9658 / distance=0.009658"

    Tigray-Tigrinya

    Natufian 46.65
    Dinka 35.30
    Mota 9.35
    Iran_ChL 8.70

    Doesn't necessarily mean the population had to be exactly like Yemenite Jews but something very similar is likely. Although, there is one weird issue in that none of these Horn-African groups are showing any Levant_N... Sure, there's some in the Zagros-related ancestry:

    [1] "distance%=0.5399 / distance=0.005399"

    Iran_Chl

    Iran_N 37.1
    Levant_N 31.6
    CHG 31.3

    But Yemenite Jews are seemingly north of 5% Levant_N even when you account for their Zagros-related ancestry so it's odd that both Somalis and Tigrinyas don't show any Levant_N until you remove Iran_Chl:

    [1] "distance%=1.3007 / distance=0.013007"

    Tigray-Tigrinya

    Natufian 47.1
    Dinka 33.1
    Mota 14.8
    Levant_N 4.9

    But ehhh, I don't know how much you can really read into that.


    Quote Originally Posted by Drobbah View Post
    Image 1
    Hmm, I wouldn't connect this admixture to those particular medieval to sometimes late classical settlements in the interior of areas like Awdal. Those are unlikely to have ever been inhabited by actual South-Arabians and seem more like they were likely, to some degree, inhabited by Southern-Ethiosemitic speakers (i.e. speaking languages related to modern Harari, most likely) who seemingly did leave a linguistic impression on Somalis (loan words) who probably assimilated them as time went by. I say they're not a likely source of this admixture because I've seen at least two Hararis' autosomal results and they probably have significant Ari/Mota-related ancestry like Habeshas do, too much to have passed ~10% Yemenite-Jewish-like ancestry onto Somalis and then have Somalis turn up as 1-3% Ari/Mota-like at best.

    Besides, those settlements only seem to have existed in stride along the northwest of the Peninsula, as far as I know; but, given Somalis' relative homogeneity (and even the fact that these samples I've used are from the northeast), this admixture, if it's real, is probably something much older.

    Quote Originally Posted by Drobbah
    Or do you think it was similar to what happened in the Ethiopian highlands with Semitic speakers entering the Djibouti/Somaliland area but they weren't as successful as they did in the highlands of Ethiopia?
    This makes somewhat more sense at least. But yeah, I'm still real weirded and intrigued by all of this.

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  14. #28
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    Tanzania underwent many changes in ethnic makeup in such a short period of time. From HG to S-Cushitic to Nilotic to Bantu. Interesting.

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    Quote Originally Posted by NetNomad View Post
    Tanzania underwent many changes in ethnic makeup in such a short period of time. From HG to S-Cushitic to Nilotic to Bantu. Interesting.
    Good observation.

    A slight correction in chronology though. Wouldn't the major waves of migration be HG to S-Cushitic to Bantu then to Nilotic?
    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

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    Quote Originally Posted by NiloSaharan View Post
    Good observation.

    A slight correction in chronology though. Wouldn't the major waves of migration be HG to S-Cushitic to Bantu then to Nilotic?
    I'm not too sure when Nilotes got to TZ. Just a hunch.

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