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Thread: Ancient genomes reveal complex patterns of population movement, interaction, and repl

  1. #51
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    Quote Originally Posted by sum1 View Post
    Target: BWA_Xaro_1400BP:XAR002
    Distance: 2.4342% / 0.02434244
    44.4 Yoruba
    26.0 ZAF_2100BP
    13.2 Dinka
    6.8 KEN_LSA
    4.6 Levant_Natufian
    4.2 CMR_Shum_Laka_8000BP
    0.8 MAR_EN

    Target: BWA_Xaro_1400BP:XAR001
    Distance: 2.3741% / 0.02374073
    48.2 Yoruba
    18.4 ZAF_2100BP
    18.0 CMR_Shum_Laka_8000BP
    5.4 KEN_Nyarindi_3500BP
    4.6 Levant_Natufian
    3.4 Dinka
    2.0 KEN_LSA

    Target: BWA_Taukome_1100BP:TAU001
    Distance: 4.8229% / 0.04822897
    77.0 Yoruba
    15.2 ZAF_2100BP
    4.4 Dinka
    3.4 Mbuti
    According to the supplement, Taukome and Nqoma pottery types descend culturally from different major Bantu traditions - Nkope and Kalundu, respectively (but according to other sources, the Xaro pottery should be Naviundu - IDK). It'd be interesting to see whether any difference appears in their non-Khoisan-related ancestry. At Xaro people seem to have ate mostly fish and turtles, with no sign of livestock, while at Taukome they had a cattle kraal and grain storage pits and lived mainly on livestock.

    Kindoki 230BP works better than Pemba 600BP for Xaro 1400BP, which suggest a western affinity, but that doesn't help much (might not mean anything).
    Xaro 1400BP - 67% Pemba 600BP, 23% ZAF 2000BP, 10% Tanzania PN O - distance 2.06%; 64% Kindoki 230BP, 23% ZAF 2000BP, 13% Luxmanda - distance 1.19%.

    We have quite a lot of ancient Bantu-related DNA now, but none of it seems to be from the right times or places to address the big questions.

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  3. #52
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    The paper about the sites in Senegal is quite interesting. Too bad they could not retrieve a DNA sample, because the transition to the Iron Age in West Africa was probably the single most important event in all of Subsaharan more recent prehistory and we know very little about the people involved.

    Occupation at Walaldé began in the period 800-550 cal BC and continued until ca 200 cal BC. The sequence appears to document the transi-tion from stone- to iron-based technology, with the use of iron objects and stone initially, followed by evidence for iron smelting and forging from 500-200 cal BC. Copper with the distinctive chemical signature of the Akjoujt mines in Mauritania was also present after 500 cal BC, attesting to interaction over long distances.
    The 1999 Walaldé excavations cast considerable new light on our understanding of the initial coloniza tion of the MSV, pushing back the date by 700-1000 years, and linking the early colonists to both Neolithic and copper-using groups farther west and north.The Walaldé agropastoralists used and smelted iron, and wore jewelry crafted from imported copper.
    Most of the slag and 46 of the tuyere pieces came from Walaldé Unit W1, which clearly was the locus of significant metallurgical activity during the later phase of occupation -i.e., after 500 cal BC.
    Most of the identifiable remains are domestic stock. Over half were cattle, and approximately 10 % were ovi-caprines
    Agropastoralists with millet and cattle, plus a few sheep and goat, first occupied Walaldé sometime between 800 and 550 cal BC.
    Comparative multivariate craniometric analysis by Isabelle RIBOT (2003) of the Feature 9 skull indicated that it was more similar to present-day West African groups such as Ashanti than to North Africans and modern Serer.
    The vault appears to be long and broad, the face is high and prognathic with long zygomatics, the nose is moderately high and wide, and the mandible is relatively large.
    The affinities of this early assemblage are sug-gested by the pottery, which shares some similari-ties in vessel rim form and decoration with pottery to the west and north. Ceramics collected from the surface by R. Vernet (pers. comm.) in the Lac Rkiz area show close affinities, as do ceramics excavated by M.A. MBOW (1997) from the oyster shell middens at Poudioum and Bole de Mengueye near St. Louis on the Senegal River delta.
    First, at Walaldé, as at other first millennium BC smelt-ing locales in the Sahel (Jenne-jeno, Do Dimmi, Bou Khzama (pending 14C dating)), early iron appears to arrive with pastoral or agropastoral peoples who tran-shume and have wide-reaching networks for movement and exchange.Copper artifacts from Akjoujt ores testify to the circulation of pastoralists/agropastoralists and objects in western Mauritania ca 2600-2200 bp.
    https://www.academia.edu/5846186/Exc...-using_peoples

    It seems to me that we deal with a similar situation as in the North Pontic steppe, that indigenous foragers and semi-Neolithicised people adopted advanced technologies from newcomers and were, probably because of the favourable habitat and already large numbers, as well as ecological barriers for the newcomers, able to keep their independence. It seems to be the root of the Niger-Kordofan expansion, whether its exactly this people (likely), or a related group from the same wider region. A sufficient DNA sample could have helped a big deal to resolve this. Its unfortunate.
    Last edited by Riverman; 06-16-2020 at 08:54 AM. Reason: Missing part of a quotation

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  5. #53
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    Quote Originally Posted by drobbah View Post
    G25 results of the Cushitic pastoralists samples:

    Target: KEN_MoloCave_1500BP:MOL003
    Distance: 8.1557% / 0.08155669
    42.0 Levant_Natufian
    40.8 Dinka
    17.2 ETH_4500BP
    What is your method for managing rows? Like what rows do you start with, what rows do you end with and why?
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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    Quote Originally Posted by VytautusofAukstaitija View Post
    Most interestingly the 1400 Xaro duo show us that a group like South Africa 1200 deriving close to around of their ancestry from Cushitic groups once ranged in southern African upland plataeu. This can give us hints as to where the collision between early Cushitic groups and aboriginal Southern African populations occured. The almost absolute lack of linguistic influence as ever still remains as mystifying as it were. Some useful information is expected from a Bantu Tswana E-M293 uploaded on yfull recently, and he shares a ~4kya mrca with Luhyas and Tutsis, and he may share an even more recent ancestor with a lone Masai. the time window will be greatly informative in efforts to find canidate sites of early contact between Cushitic immigrants and southern African populations. It is telling they do not have to be modelled with the Chenchere ancients, and the sequence of admixture events favoring one between a Pastoral Neolithic group, and aboroginal souther African populations.
    If I had to bet, this admixture event probably took place in the vicinity of Tanzania. If I am not mistaken, we have evidence of ZAF-2100BP-like admixture in PN samples like Luxmanda, which suggests that groups with that sort of ancestry once spanned a larger geographic area than they currently do today. We also have to remember that contemporary non-Bantu Southern Africans generally fall into two distinct linguistic groups, one being the Khoe-Kwadi who are traditionally pastoralists and carry substantially more Cushitic ancestry than their HG neighbors. Khoe-Kwadi is thought to be “intrusive” to Southern Africa and we have plenty of reason to believe that Sandawe in Tanzania is a distant relative. I have no doubt in my mind that ZAF-1200BP spoke a Khoe-Kwadi language and that these likely Bantu speakers from Botswana also descended in part from Khoe-Kwadi speakers.

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    Quote Originally Posted by Espoir View Post
    I can’t ignore these two samples from Mangatai Turu, especially one with very high Luxmanda ancestry.
    That individual dates to a period of states formation in regions East(inter-lacustrine region) of her. This reminds me of oral history that says my ancestors moved from Uganda to Eastern Congo(Rutchuru/Goma) and expanded later in Western Rwanda and many staying behind. However, my ancestors left before 1200s.
    This could mean that it was a common occurrence for pastoralists to move west.
    Banyamulenge are living testimony to that, though, we expanded southwest as far as Kasai(South-Central Congo)

    Oral accounts say that Bachwezi(founders of Bunyoro-kitara) moved west when Luos took over Bunyoro.

    Looking forward to seeing someone work on this. Since we even have a present day cushitic admixed population leaving there(pastoralists Hema).
    And here I thought that the Hema in Ituri were relatively recent migrants from Nkore. The presence of a sample like Mangatai Turu at that specific time and place proves what we’ve already known for a long time, Tutsi-like pastoralists were hanging around the Virunga Mts for quite awhile.

    What’s up with her significant Mbuti ancestry though and does she completely lack any Dinka or Yoruba-like ancestry? We have samples from the Hema in Ituri, can anybody confirm if they possess any significant Mbuti ancestry? And why I am I seeing her twice in the Admixture Chart but not in the other charts?

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  10. #56
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    Quote Originally Posted by gihanga.rwanda View Post
    WhatÂ’s up with her significant Mbuti ancestry though and does she completely lack any Dinka or Yoruba-like ancestry?
    Now that you mention it, something does seem rather wonky with some of the paper's ADMIXTURE results.

    e.g. the paper's renderings show KEN_Kakapel_300BP as shown as 100% Dinka but these (rudimentary) G25 results show her completely different:

     



    Regarding the Mbuti affinity in the paper's runs, maybe it should be taken with a grain of salt. For Ugandan Central-Sudanics in the adjacent West-Nile region, it's wasn't uncommon for their ancient HG-affinity to show as entirely Mbuti (~10%) in ADMIXTURE. Though when using G25, it's more of a variation between mostly KEN_LSA, followed by Mbuti and some South_African related ancestry -- I think ADMIXUTRE might have some difficulties capturing these archaic splits



    Quote Originally Posted by gihanga.rwanda View Post
    We have samples from the Hema in Ituri, can anybody confirm if they possess any significant Mbuti ancestry?
    For what they're worth, not seeing any significant Mbuti in these Hema (~ < 3%) *can't confirm their region in DRC:

     







    Quote Originally Posted by gihanga.rwanda View Post
    ... And why I am I seeing her twice in the Admixture Chart but not in the other charts?
    Maybe Generalissimo can confirm, perhaps the Mangatai Turu samples were among those that didn't make the cut (low quality/resolution)?

    - they're not on the posted list from earlier
    Last edited by Angoliga; 06-27-2020 at 12:40 AM.
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    Quote Originally Posted by Angoliga View Post
    Now that you mention it, something does seem rather wonky with some of the paper's ADMIXTURE results.
    [INDENT]e.g. the paper's renderings show KEN_Kakapel_300BP as shown as 100% Dinka but these (rudimentary) G25 results show her completely different
    It's not ADMIXTURE but qpAdm; different models for Kakapel 300BP are in Table S4. The 100% Dinka mode gets p=0.241, while 100% Luhya (the closest pop in G25) gets p=0.058. Dinka is normally in the outgroups, in this it's moved to sources so there's no East African outgroup, but even so I'm surprised it works. Most of the qpAdm models though involve Bantu, e.g. 73% Ovambo + 27% Maasai, p=0.234.

    So yeah, I think they just put the best-fitting simplest model in Figure 3, even though it was actually not a good model. Kakapel 300BP seems very close to modern Luhya.
    Last edited by Megalophias; 06-27-2020 at 11:34 AM.

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    Quote Originally Posted by Megalophias View Post
    It's not ADMIXTURE but qpAdm; different models for Kakapel 300BP are in Table S4. The 100% Dinka mode gets p=0.241, while 100% Luhya (the closest pop in G25) gets p=0.058. Dinka is normally in the outgroups, in this it's moved to sources so there's no East African outgroup, but even so I'm surprised it works. Most of the qpAdm models though involve Bantu, e.g. 73% Ovambo + 27% Maasai, p=0.234.
    Ohhh!! didn't notice we were looking at qpAdm models here lol -- seemed misleading how they've displayed the qpAdm models in fig 3.

    Quote Originally Posted by Megalophias View Post
    So yeah, I think they just put the best-fitting simplest model in Figure 3, even though it was actually not a good model. Kakapel 300BP seems very close to modern Luhya.
    Wow! They actually really do seem close:

    Target: KEN_Kakapel_300BP
    Distance: 7.8324% / 0.07832413
    53.2 Yoruba
    25.4 Dinka
    19.4 KEN_LSA
    1.2 Yamnaya_UKR
    0.8 IRN_Wezmeh_N

    Target: Luhya_Kenya
    Distance: 7.7444% / 0.07744406
    55.2 Yoruba
    26.2 Dinka
    18.2 KEN_LSA
    0.4 Anatolia_Barcin_N
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    Quote Originally Posted by Angoliga View Post


    For what they're worth, not seeing any significant Mbuti in these Hema (~ < 3%) *can't confirm their region in DRC:

     





    Intersting @Angoliga, this calculator Ethiohelix K10 Africa gives me 4.5% Mbuti

    Nilosaharan 29.9%
    EastAfrica2 26%
    Mbuti 4.5%
    EastAfrica1 9%
    West Africa 17.83%
    North Africa 2.93%
    Omotic 8%

    may be missing some decimal points here and there

    PuntDNAL K8 Africa also gives me "Ubangian congo" ~4% as well. So maybe there is something there.

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