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Thread: Modern Nilotic Dinka wrong proxy for ancient African admixture in East Africans?

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    Modern Nilotic Dinka wrong proxy for ancient African admixture in East Africans?

    I was reading this one blog post about Ancient DNA in Ethiopia and i found what the author put down about how Modern Nilo-saharan speakers like the Dinka, Nuer, Shuluk and so on are wrong proxies for ancient African ancestry in East Africans interesting. Especially since we see so many on this forum emphasize Dinka related ancestry in East Africans and express it as ''Dinka like''

    Thoughts on this?

    African admixture component


    When the Mota man was excavated in Ethiopia, some scholars wondered if the population to which he belonged might represent the native hunter-gatherers whom the Afro-Asiatic-speaking agropastoralists encountered and possibly mixed with when the latter first settled in the Horn. More extensive DNA analysis has, however, shown that gene flow between the two communities, although present, was minimal (Lipson et al. (2020) places Mota-related admixture in the Cushitic-speaking Agaw at 8%; no other hunter-gatherer-related admixture has been detected in the Horn). Due to this apparent lack of a suitable ancient proxy sample, researchers have formulated alternative admixture scenarios using various modern populations. In qpAdm and other genomic programs, these contemporary reference groups have served as stand-ins for the elusive ancient African contact population(s). The Dinka, Nuer and other northern Nilotic communities have often been the go-to populations utilized as the African proxies. The problem is that all of these groups have proven to be even less reliable surrogates than Mota.

    Let us examine why that is:

    The Dinka, Nuer, Shilluk and other northern Nilotes are not ‘purely’ African populations to begin with. Like the Nilote groups to their south in the Horn (e.g. Kunama, Nara, Gumuz and Mursi) and Great Lakes (such as the Maasai, Kalenjin, Samburu and Turkana), the northern Nilotes also have considerable non-African admixture. This was already suggested by the uniparental lineages that they carry. Hassan et al. (2008) observed that around 20% of Shilluk and 15% of Dinka individuals bear the E1b1b/E3b haplogroup, a paternal clade that is most common among Afro-Asiatic speakers. Most strikingly, Balemi (2018) reports that 51.62% of his Nuer sample from southwestern Ethiopia carry the E1b1b-M78 haplogroup, compared to 16.67% of Hassan et al. (2008)’s Nuer sample from Sudan. Furthermore, 55.55% and 33.33% of Balemi (2018)’s Berta and Gumuz samples, respectively, bear the Eurasian F-M89 clade. Non (2010) likewise notes that over 40% of her Sudanese Nuer sample belongs to the mtDNA haplogroups M and N, including around 18% M1 carriers (cf. Table 3-3). The M1 subclade has been found in ancient Maghreban, Egyptian and South Cushitic specimens, and still remains a signature maternal lineage among the modern Afro-Asiatic-speaking populations in Northeast Africa. In short, uniparental markers indicate that there was significant gene flow from Afro-Asiatic-speaking groups (especially Cushitic speakers) into neighboring Nilote communities.
    By contrast, in various autosomal DNA studies, the northern Nilotes have appeared to be almost completely of African ancestry. For example, in the African Genome Variation Project’s analysis, the Dinka sample showed no extraneous influence at K=2 (cf. Gurdasani et al. (2015)). This apparent lack of non-African affinities is why the Dinka, Nuer and other northern Nilotes have often been used by researchers as proxies for the African component. In 2017, Skoglund et al. compared the same AGVP Dinka sample to that of an ancient South Cushitic pastoralist (Luxmanda), the first such specimen to be genetically analyzed. In their admixture analysis, the Dinka individuals now all of a sudden showed almost 30% non-African ancestry at the K=2 level. Judging by the existing uniparental marker data, it’s pretty clear why that is: there was non-African ancestry buried within the northern Nilote gene pool, and that ancestry was specifically derived from earlier Cushitic peoples such as Luxmanda.


    Genome analysis detecting almost 30% non-African ancestry in a sample of Dinka. This Nilotic population was previously assumed to have little-to-no non-African ancestry, and was therefore often used as a proxy for inferring African ancestry (Skoglund et al. (2017)).

    This, in a nutshell, explains why the Dinka, Nuer and other northern Nilotes often fit well as proxies for the African component in admixture testing models. However, the problem with using such admixed groups in these analyses is that doing so leads to highly distorted estimates of ancestry proportions. For example, let’s say a researcher is testing admixture models on qpAdm and finds that his modern Cushitic or Ethiosemitic-speaking population is best modeled as 50% Neolithic Levantine + 50% Dinka. What that program is really telling him is that his sample is best modeled as 50% Neolithic Levantine + X% ancient Nilotic + X% ancient Cushitic. This again stems from the fact that the Dinka are not a purely African population, but rather a Nilote-descended community with significant Cushitic admixture (whence was derived their non-African ancestry). When factoring in the ~30% of non-African ancestry that Skoglund et al. (2017) detected in their Dinka reference sample, the estimated whole genome ancestry apportionment then actually becomes 50% Neolithic Levantine + 35% African + 15% unclassified Eurasian. This necessary adjustment therefore brings the non-African total to around 65%. The same corrective adjustment would have to be made if the African reference sample were a southern Nilotic group, such as the Maasai Nilotes (e.g. when the ~30% of West Eurasian admixture in Ali et al. (2020)‘s East African proxy sample (Maasai) is taken into account, the estimated non-African ancestry for their northeastern Somali sample rises to 70%; this more accurate total is close to Hodgson et al.’s 66% average for their general ethnic Somali sample). That’s also before correcting for linkage disequilibrium bias, which, as Hodgson et al. (2014) observed and Choudhury et al. (2020) also demonstrated, would increase the Cushitic speakers’ Eurasian total even further. Put simply, there is considerable extra non-African ancestry in the genome of the Afro-Asiatic-speaking sample which is not being counted. This results in an inaccurate overall estimation of ancestry proportions. It also conflicts with scientific data gathered through other means (viz. craniometric analysis, anthropometric analysis, linguistics).
    Last edited by Mirix; 02-02-2021 at 12:29 PM.

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    Principal Component Analysis indicates that the ancient Cushitic pastoralists of the Great Lakes and modern Afro-Asiatic-speaking populations of the Horn of Africa genetically cluster with Epipaleolithic Iberomaurusian specimens excavated at Taforalt and early Neolithic individuals buried at Ifri n’Amr or Moussa, both situated in Morocco. These samples also plot near the Levant Chalcolithic cohort. This is consistent with Wang et al. (2020)’s admixture analysis and genome modeling, which both suggest that the oldest Cushitic settlers in East Africa were almost entirely of non-African ancestry (~90%) at the time of their arrival in the region (Wang et al. (2020), Supplementary Material).



    Genetic research has found that a significant portion of the core Sub-Saharan ancestry of the northern Nilotes (Dinka, Nuer, Shilluk, etc.) is related to West African populations (e.g. Skoglund et al. (2017)). However, Prendergast et al. (2008) remark that there was “no evidence of western African-related ancestry” in the ancient Cushitic individuals that they examined. Skoglund et al. (2017) and Wang et al. (2020) likewise did not detect any West African affinity in the early Cushitic specimens that they analyzed. This is hardly surprising since West African-related ancestry appears to have arrived in East Africa much later, during the Iron Age with the first Bantu settlers of the Great Lakes region. A specimen excavated at the Deloraine Farm in Kenya, the Rift Valley’s oldest agricultural site, is the earliest individual found to carry such West African-related ancestry (dated ca. 1170-970 BP; cf. Prendergast et al. (2008)). This makes modern Nilotic individuals unrealistic proxies for inferring an African admixture component among the ancient Cushitic settlers of the Pastoral Neolithic.

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    Last edited by Keneki20; 02-02-2021 at 08:40 PM. Reason: Deleted due to the post being based on a misunderstanding of the information in the initial post of the thread.

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    I actually agree with the premise that the Dinka and other Nilotic speakers aren’t a perfect stand in for the African ancestry in Cushitic speakers and related group, but not for the same reasons as the author of this blog post. This blog post sounds like it was written by the author of the “Land of Punt”, who seems to harbor some sort of agenda and doesn’t appear to have a very strong grasp on population genetics. How else could s/he take the cited ADMIXTURE analysis as evidence for substantial Eurasian gene-flow (30%) into Dinka? It’s as if African population substructure doesn’t exist.

    We can use Dinka to model the African ancestry in Cushites because the two groups - Nilotic and Cushitic speakers respectively - probably share common descent from an ancient population - Ancient East African - that contributed to both groups separately. This doesn’t mean that we can equate Dinka with AEA. It’s been suspected for years that Nilotes have elevated West African-related ancestry, which is generally absent in Cushitic speakers. This suggests that the African ancestors of Cushitic speakers were related but distinct from Dinka and other Nilotic speakers in the present day.

    That being said, I do suspect that Cushitic speakers have some direct Dinka-like ancestry, based on linguistic evidence and presence of certain uniparental lineages across NE Africa, but the genesis of Cushitic-related ancestry is probably a bit more complicated than population A + population B.
    Last edited by gihanga.rwanda; 02-02-2021 at 02:51 PM.

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    Dinka has too much Central African related admixture to be a direct proxy for the AEA ancestry in North Africa and the Horn but it's still mostly the same stuff.

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    The analysis is correct. The obvious bias just throws the whole thing left.
    The E1b uniparental makers in Nilotics are not Eurasian.
    Nilotes ARE a composite, but i would argue mostly a composite of North African and equatorial ancestry....in fact I personally would take it a step further and argue they are mostly North African as far as recent ancestry and migration patterns.

    Once a genetic analysis of any African populations goes down that road that North Africans dont exist and there is a clean distinction between Eurasians and Sub Saharan Africans you might as well just discard it.
    The same type of analysis used to show Nilotes as partially Eurasian or Ancient East Africa pastoralists predominantly Eurasian could be better put to use in showing how north African ancestry is ubiquitous among geographically African adjacent populations carrying African derived lineages of E, M,N, and U. IMO....This could have been good scholarship.

    2 cents.

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    Quote Originally Posted by Mnemonics View Post
    Dinka has too much Central African related admixture to be a direct proxy for the AEA ancestry in North Africa and the Horn but it's still mostly the same stuff.
    Discount any overt Central-African related ancestry, the bidirectional sahelian W-African admixture in Dinka (*exempt in Horners) would likely make it a more appropriate proxy for the bulk of AEA ancestry in North-(West) Africans.

    Curious, what kind of "Central-African" related admixture are you referring to in Dinka: are you noticing KEN_LSA/Mota type affinities in qpadm?

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    Quote Originally Posted by gihanga.rwanda View Post
    I actually agree with the premise that the Dinka and other Nilotic speakers aren’t a perfect stand in for the African ancestry in Cushitic speakers and related group, but not for the same reasons as the author of this blog post. This blog post sounds like it was written by the author of the “Land of Punt”, who seems to harbor some sort of agenda and doesn’t appear to have a very strong grasp on population genetics. How else could s/he take the cited ADMIXTURE analysis as evidence for substantial Eurasian gene-flow (30%) into Dinka? It’s as if African population substructure doesn’t exist.

    We can use Dinka to model the African ancestry in Cushites because the two groups - Nilotic and Cushitic speakers respectively - probably share common descent from an ancient population - Ancient East African - that contributed to both groups separately. This doesn’t mean that we can equate Dinka with AEA. It’s been suspected for years that Nilotes have elevated West African-related ancestry, which is generally absent in Cushitic speakers. This suggests that the African ancestors of Cushitic speakers were related but distinct from Dinka and other Nilotic speakers in the present day.

    That being said, I do suspect that Cushitic speakers have some direct Dinka-like ancestry, based on linguistic evidence and presence of certain uniparental lineages across NE Africa, but the genesis of Cushitic-related ancestry is probably a bit more complicated than population A + population B.
    The author argues that nilotic speakers have Ancient Cushitic admixture. According to him this is why they fit so well as a proxy.


    In 2017, Skoglund et al. compared the same AGVP Dinka sample to that of an ancient South Cushitic pastoralist (Luxmanda), the first such specimen to be genetically analyzed. In their admixture analysis, the Dinka individuals now all of a sudden showed almost 30% non-African ancestry at the K=2 level. Judging by the existing uniparental marker data, it’s pretty clear why that is: there was non-African ancestry buried within the northern Nilote gene pool, and that ancestry was specifically derived from earlier Cushitic peoples such as Luxmanda.

    But your explanation makes sense too , a related common yet distinct ancient descent can be an explanation for the absence of West African in Cushitic speakers and why they might share similar non African ancestry with ancient cushites. But on the flipside failing to take account for the non-African related ancestry in these populations don't they give you distorted African ancestry proportions?

    Anyways i sent him a message to come debate and discuss his points, i think he probably has a decent grasp of genetics seems to have been writing about it for some time and but yeah he probably is ideologically driven which is why i made this thread asking for peoples in put and perspective on this. Don't particularly agree with many of his points and some of his terminological usages is outdated.
    Last edited by Mirix; 02-02-2021 at 09:20 PM.

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    Quote Originally Posted by Angoliga View Post
    Discount any overt Central-African related ancestry, the bidirectional sahelian W-African admixture in Dinka (*exempt in Horners) would likely make it a more appropriate proxy for the bulk of AEA ancestry in North-(West) Africans.

    Curious, what kind of "Central-African" related admixture are you referring to in Dinka: are you noticing KEN_LSA/Mota type affinities in qpadm?
    The Z-scores for Shum Laka or Mbuti (when I use a modern right pop list)
    seem to push plausible qpAdm models into the implausible range which indicates that Dinka has an excess of something present in both.

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