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Thread: PCA G25_scaled - Africans only (Users & Ancients/Modern Avgs)

  1. #991
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    Quote Originally Posted by Cabaon View Post
    I think you misunderstood, I was pointing out the fact that the modern borders of north african countries (established during the colonial era) were recently established and were simply not the same in the past.
    I agree, modern borders of African countries in general are recently established and can be quite different going further back in time before the colonial area. I'm only hesitant with redefining broad regions- that is to say, changing what we mean when we say West, East or indeed North of an area. Piye was pointing out interactions between different regions and I now think you meant to caution against going by modern national borders when talking about the past when they didn't exist. However, I don't believe this was the point Piye was making in saying that people of different African regions (North and West) had relations beyond that of slavery.
    I believe I see what you mean, and agree, but as I was referring to regions in general as opposed to national borders, I can't say that I would agree that a city in a random area of North Africa today would not be called North Africa back then just because it happened to be governed by a power centred further south. To illustrate what I mean more clearly, in a hypothetical example where Egypt (which everyone agrees is a part of North Africa) and Sudan (largely considered to be part of Sub-Saharan Africa) in a pre-2011 situation were joined together and governed by the former tomorrow, I don't think that would make Juba a North African city overnight. To me, at least, it would still remain a part of East Central Africa. I don't mean to talk around in circles or aggravate anyone by pursuing a point as small as this for ages, so I'll try to leave it here and hope you've caught my meaning.

    Anyway, you listed a plethora of sources that I'm happy to add to my collection and your addition of them is appreciated .
    Last edited by Atlas; 01-26-2021 at 09:17 PM.

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  3. #992
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    Quote Originally Posted by Atlas View Post
    I agree, modern borders of African countries in general are recently established and can be quite different going further back in time before the colonial area. I'm only hesitant with redefining broad regions- that is to say, changing what we mean when we say West, East or indeed North of an area. Piye was pointing out interactions between different regions and I now think you meant to caution against going by modern national borders when talking about the past when they didn't exist. However, I don't believe this was the point Piye was making in saying that people of different African regions (North and West) had relations beyond that of slavery.
    I believe I see what you mean, and agree, but as I was referring to regions in general as opposed to national borders, I can't say that I would agree that a city in a random area of North Africa today would not be called North Africa back then just because it happened to be governed by a power centred further south. To illustrate what I mean more clearly, in a hypothetical example where Egypt (which everyone agrees is a part of North Africa) and Sudan (largely considered to be part of Sub-Saharan Africa) in a pre-2011 situation were joined together and governed by the former tomorrow, I don't think that would make Juba a North African city overnight. To me, at least, it would still remain a part of East Central Africa. I don't mean to talk around in circles or aggravate anyone by pursuing a point as small as this for ages, so I'll try to leave it here and hope you've caught my meaning.

    Anyway, you listed a plethora of sources that I'm happy to add to my collection and your addition of them is appreciated .
    I get what you mean but I still don't think you understood quite well : for instance Tamanrasset today is a city in the far south of Algeria (https://fr.wikipedia.org/wiki/Tamanrasset), today this city is considered as being part of North Africa because it's located in Algeria but if this city had existed 500 years ago it wouldn't have been seen as "north africa" nor its inhabitants seen as Berbers or Arabs. "North Africa" as we know it today is a recent geopolitical concept, in the past, it was quite different.

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    Quote Originally Posted by Cabaon View Post
    I get what you mean but I still don't think you understood quite well : for instance Tamanrasset today is a city in the far south of Algeria (https://fr.wikipedia.org/wiki/Tamanrasset), today this city is considered as being part of North Africa because it's located in Algeria but if this city had existed 500 years ago it wouldn't have been seen as "north africa" nor its inhabitants seen as Berbers or Arabs. "North Africa" as we know it today is a recent geopolitical concept, in the past, it was quite different.
    I'll PM you from now on so we don't fill up the thread on this.

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    Quote Originally Posted by Cabaon View Post
    I get what you mean but I still don't think you understood quite well : for instance Tamanrasset today is a city in the far south of Algeria (https://fr.wikipedia.org/wiki/Tamanrasset), today this city is considered as being part of North Africa because it's located in Algeria but if this city had existed 500 years ago it wouldn't have been seen as "north africa" nor its inhabitants seen as Berbers or Arabs. "North Africa" as we know it today is a recent geopolitical concept, in the past, it was quite different.
    What would more accurate borders be?

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    Quote Originally Posted by davit View Post
    What would more accurate borders be?
    depends on the era, not all kingdoms,emirates, empires had the same borders but what is sure is that the modern algerian sahara has never really been part and unified by one political entity

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  9. #996
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    Here are 1552 high quality samples from the Malaria Gen project. Massive thanks to David Bush and teepean for kickstarting me into action and running the preliminary conversion from a tricky format and my brother for converting/annotating/merging the files and ofc Davidski for being a top bloke.

    The following data-set contains individuals from the following:

    Code:
    Burkina Faso: 
    
    - Mossi [Gur peoples]
    
    Cameroon: 
    
    - Bantu [most likely Beti speaking  peoples like Fang etc very different from the NW-Cameroonians currently in the g25]
    - Semi-Bantu [essentially the same as the current Bantoid/NW Cameroonians]
    
    Gambia: 
    
    - Fula1
    - Fula2 
    - Mandenka1
    - Mandenka2
    - Jola
    - Wolof
    - Manjago 
    - Serer
    - Serehule (Soninke)
    
    Ghana:
    
    - Akan
    - Kasem [Kassena]
    - Namkam [a Kessena group]
    
    Kenya [Mijikenda]:
    
    - Kauma
    - Chonyi
    - Kambe
    - Giriama
    
    Malawi:
    
    - Malawian Bantu
    
    
    Mali:
    
    - Malinke
    - Bambara
    
    Tanzania:
    
    - Wabondei
    - Wasambaa
    - Mzigua
    There are also samples from the Gambian Genome Project thrown in there. Herero/Zulu/Xhosa/Afram/Caribbean samples I'll work on shortly and hopefully get them uploaded, I think Michalis said he's interested in those, their formatting is strange and requires more work. Enjoy.

    https://www.mediafire.com/folder/66f.../MalariaGenPop


    Some notes: alot of the Kenya and Tanzania samples are quite significantly admixed. The Jola enhance the Africa PCAs greatly by anchoring a true Atlantic-West African component plotting west of the current Yoruba/Esan contingent.
    Last edited by ThaYamamoto; 01-27-2021 at 04:30 PM.

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    Can someone enlighten me about the Kamba people? How does an outlier like this exist?

    Target: Kenya_KAMBE:per205
    Distance: 4.1239% / 0.04123943
    36.4 Yoruba
    24.4 Levant_PPNB
    23.2 Bantu_S.E.
    16.0 SUDANESE7

  12. #998
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    Quote Originally Posted by drobbah View Post
    Can someone enlighten me about the Kamba people? How does an outlier like this exist?

    Target: Kenya_KAMBE:per205
    Distance: 4.1239% / 0.04123943
    36.4 Yoruba
    24.4 Levant_PPNB
    23.2 Bantu_S.E.
    16.0 SUDANESE7
    These are all coastal Bantu, this is a Kambe Mijikenda person as opposed to Akamba. Some are quite mixed with MENA and peripheral South Asians i.e. Baloch. The Busby paper observed some significant non-African introgression into all these groups. Some say that the Mijikenda languages are the base language of Kiswahili.

    Target: Kenya_KAMBE:per205
    Distance: 0.8915% / 0.00891516
    37.0 Luhya_Kenya
    22.0 Cameroon_Mbo
    16.4 Palestinian_Beit_Sahour
    6.0 Tunisian_Rbaya

    5.0 Kongo
    4.4 Manyika
    2.8 Igbo
    1.4 Kikuyu
    1.4 Macedonian
    1.2 BedouinB

    0.8 Biaka
    0.6 Mada
    0.6 Yukpa
    0.4 Nyanja
    Last edited by ThaYamamoto; 01-27-2021 at 04:32 PM.

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  14. #999
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    Quote Originally Posted by ThaYamamoto View Post
    Here are 1552 high quality samples from the Malaria Gen project. Massive thanks to David Bush and teepean for kickstarting me into action and running the preliminary conversion from a tricky format and my brother for converting/annotating/merging the files and ofc Davidski for being a top bloke.

    The following data-set contains individuals from the following:

    Code:
    Burkina Faso: 
    
    - Mossi [Gur peoples]
    
    Cameroon: 
    
    - Bantu [most likely Beti speaking  peoples like Fang etc very different from the NW-Cameroonians currently in the g25]
    - Semi-Bantu [essentially the same as the current Bantoid/NW Cameroonians]
    
    Gambia: 
    
    - Fula1
    - Fula2 
    - Mandenka1
    - Mandenka2
    - Jola
    - Wolof
    - Manjago 
    - Serer
    - Serehule (Soninke)
    
    Ghana:
    
    - Akan
    - Kasem [Kassena]
    - Namkam [a Kessena group]
    
    Kenya:
    
    - Kauma
    - Chonyi
    - Kamba
    - Giriama
    
    Malawi:
    
    - Malawian Bantu
    
    
    Mali:
    
    - Malinke
    - Bambara
    
    Tanzania:
    
    - Wabondei
    - Wasambaa
    - Mzigua
    There are also samples from the Gambian Genome Project thrown in there. Herero/Zulu/Xhosa/Afram/Caribbean samples I'll work on shortly and hopefully get them uploaded, I think Michalis said he's interested in those, their formatting is strange and requires more work. Enjoy.

    https://www.mediafire.com/folder/66f.../MalariaGenPop


    Some notes: a lot of the Kenya and Tanzania samples are quite significantly admixed. The Jola enhance the Africa PCAs greatly by anchoring a true Atlantic-West African component plotting west of the current Yoruba/Esan contingent.
    Could you clarify what you mean here? Here are my predictions.

    I expect the Kamba to be very similar to the Kikuyu, so essentially predominantly Bantu with significant Cushitic and Nilotic-related admixture.

    The remaining groups from Kenya (e.g. Kauma, Chonyi, Giriama) speak a variety of Mijikenda dialects. Since Mijikenda is a Sabaki language, I suspect that these samples can be used to model the SE African ancestry in Swahili, Malagasy, and related groups. Furthermore, according to oral tradition, the Mijikenda were once found north of the Tana river but were later pushed to their present location by pastoralists who are assumed to have spoken Oromo. Swahili speakers don’t appear to have significant Cushitic admixture, but I wonder if these samples contain any evidence for early contact between the Mijikenda and Oromo?

    The three Tanzanian groups belong to a single dialect cluster called “Seuta” found in NE Tanzania. The Seuta are closely related to the Pare and Mbugu, and live alongside the Masai, so I am expecting significant Cushitic admixture in these samples.

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  16. #1000
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    Quote Originally Posted by ThaYamamoto View Post
    These are all coastal Bantu, this is a Kambe Mijikenda person as opposed to Akamba. Some are quite mixed with MENA and peripheral South Asians i.e. Baloch. The Busby paper observed some significant non-African introgression into all these groups. Some say that the Mijikenda languages are the base language of Kiswahili.

    Target: Kenya_KAMBE:per205
    Distance: 0.8915% / 0.00891516
    37.0 Luhya_Kenya
    22.0 Cameroon_Mbo
    16.4 Palestinian_Beit_Sahour
    6.0 Tunisian_Rbaya

    5.0 Kongo
    4.4 Manyika
    2.8 Igbo
    1.4 Kikuyu
    1.4 Macedonian
    1.2 BedouinB

    0.8 Biaka
    0.6 Mada
    0.6 Yukpa
    0.4 Nyanja
    Thanks for clarifying that this sample is Kambe and not Kamba, and that these samples are from Busby et al. 2016. It looks like I was right about Cushitic admixture in the Saute samples from Tanzania.

    https://elifesciences.org/articles/15266

    In Tanzanian groups from the same ancestry region, we infer admixture during the same period, this time involving minor admixture sources with Afroasiatic ancestry: in the Giriama (1196CE: 1138-1254CE), Wasambaa (1312CE: 1254-1341CE), and Mzigua (1080: 1007-1138CE). Although the proportions of admixture from these minor sources differ, the major sources of admixture in East African Niger-Congo speakers are similar, containing a mix of Southern Niger-Congo (Malawi), Central West African, Afroasiatic, and Nilo-Saharan ancestries.
    Last edited by gihanga.rwanda; 01-27-2021 at 04:49 PM.

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