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Thread: G25 nMonte - Inferring ANA/Eurasian layers in SSA pops

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    G25 nMonte - Inferring ANA/Eurasian layers in SSA pops

    We're limited on available aDNA but thought we could speculate using nMonte on these interrelated topics:






    After playing with some runs, I found "MWI_Fingira_6100BP" worked as a good crude proxy for SSA -- that includes West-African as well as the Ancient-East-African (Nilotic) component.
    Moreover, the sample "MWI_Fingira_2500BP" seemed to correlate nicely as a layer of archaic SSA ancestry (Pygmy/South HG).


    MWI_Fingira_6100BP = SSA
    MWI_Fingira_2500BP = Arachaic SSA


    Using this a basis to tease out deep Eurasian layers, I removed all modern and ancient SSA pops along with modern Saharans while leaving all other G25 pops to see what happens:

    Code:
    [1] "distance%=31.2193"
    
             Yoruba
    
    MWI_Fingira_6100BP,70.6
    MAR_Iberomaurusian,15.8
    MWI_Fingira_2500BP,8.5
    MAR_EN,4.7
    BLZ_SakiTzul_7400BP,0.2
    CHL_LosRieles_5100BP,0.1
    Anatolia_N_Kumtepe_low_res,0.1
    
    
    [1] "distance%=28.1667"
    
             Gambian
    
    MWI_Fingira_6100BP,68.7
    MAR_Iberomaurusian,19
    MWI_Fingira_2500BP,7.3
    MAR_EN,4.6
    Anatolia_N_Kumtepe_low_res,0.3
    
    
    [1] "distance%=25.7217"
    
             Dinka
    
    MWI_Fingira_6100BP,72.5
    MAR_Iberomaurusian,20.7
    MAR_EN,4.5
    MWI_Fingira_2500BP,2
    Eskimo_Sireniki,0.1
    BRA_Laranjal_6700BP,0.1
    PER_Lauricocha_3500BP,0.1
    
    
    [1] "distance%=28.2958"
    
             Mandenka
    
    MWI_Fingira_6100BP,69.6
    MAR_Iberomaurusian,19.6
    MWI_Fingira_2500BP,6.4
    MAR_EN,4
    Anatolia_N_Kumtepe_low_res,0.2
    BLZ_SakiTzul_7400BP,0.1
    PER_Laramate_900BP,0.1
    
    [1] "distance%=29.943"
    
             Igbo
    
    MWI_Fingira_6100BP,69.5
    MAR_Iberomaurusian,16
    MWI_Fingira_2500BP,10.9
    MAR_EN,3.3
    Anatolia_N_Kumtepe_low_res,0.3
    
    
    [1] "distance%=23.0629"
    
             UG_CentralSudanic
    
    MWI_Fingira_6100BP,72.3
    MAR_Iberomaurusian,16.6
    MWI_Fingira_2500BP,7
    MAR_EN,3.1
    PER_Lauricocha_3500BP,0.4
    CHL_LosRieles_5100BP,0.2
    USA_Spirit_Cave_11000BP,0.2
    BRA_Laranjal_6700BP,0.1
    PER_Laramate_900BP,0.1
    
    
    [1] "distance%=27.867"
    
             Kongo
    
    MWI_Fingira_6100BP,67.8
    MAR_Iberomaurusian,16.9
    MWI_Fingira_2500BP,14.1
    MAR_EN,1
    Anatolia_N_Kumtepe_low_res,0.2
    
    
    [1] "distance%=23.1196"
    
             Biaka
    
    MWI_Fingira_2500BP,74.7
    MWI_Fingira_6100BP,20.6
    Anatolia_N_Kumtepe_low_res,2
    MAR_Iberomaurusian,1.9
    MAR_EN,0.7
    IRN_Wezmeh_N,0.1
    
    
    [1] "distance%=11.342"
    
             Ethiopian_Tigray
    
    Levant_Natufian,45.6
    MWI_Fingira_6100BP,29.8
    MAR_Iberomaurusian,14.9
    IRN_Tepe_Abdul_Hosein_N,7.4
    IRN_Wezmeh_N,2
    MAR_EN,0.3
    
    
    [1] "distance%=15.1951"
     
            Somali
    
    MWI_Fingira_6100BP,40.1
    Levant_Natufian,29
    MAR_Iberomaurusian,24.1
    IRN_Tepe_Abdul_Hosein_N,5.2
    IRN_Wezmeh_N,1.2
    Canary_Islands_Guanche,0.3
    MAR_EN,0.1
    
    
    
    [1] "distance%=1.3255"
    
             MWI_Hora_9000BP
    
    MWI_Fingira_2500BP,66.5
    MWI_Fingira_6100BP,26.7
    CZE_N,0.9
    Scotland_N_o,0.9
    IRN_Wezmeh_N,0.6
    Koinanbe,0.4
    Kosipe,0.4
    IRN_Ganj_Dareh_N,0.4
    IRN_Tepe_Abdul_Hosein_N,0.3
    Iberia_Southwest_EN,0.3
    IRN_Seh_Gabi_LN,0.2
    ITA_Remedello_BA,0.2
    Corded_Ware_CZE_o,0.2
    UKR_Globular_Amphora,0.2
    Bell_Beaker_HUN_EBA_o,0.2
    WHG,0.2
    Iberia_Northeast_CA,0.2
    Levant_Natufian,0.1
    Kurumba,0.1
    IRN_Seh_Gabi_C,0.1
    Levant_LBN_MA_NE,0.1
    IRN_Hajji_Firuz_IA,0.1
    Anatolia_Kumtepe_N,0.1
    IRL_MN,0.1
    Iberia_Southwest_MLN,0.1
    Iberia_Southeast_MLN,0.1
    DEU_Baalberge_MN,0.1
    HUN_Baden_LCA,0.1
    HRV_Vucedol,0.1
    MAR_Iberomaurusian,0
    
    
    [1] "distance%=2.0847"
    
             EGY_Late_Period
    
    Levant_ISR_MLBA,26.2
    Levant_PPNC,22
    Levant_ISR_C,16.6
    Levant_Natufian,15.9
    TKM_Parkhai_MBA,7.1
    MAR_Iberomaurusian,5.5
    Anatolia_Kaman-Kalehoyuk_MLBA_low_res,3.2
    GEO_CHG,2.4
    Syrian,0.5
    MWI_Fingira_6100BP,0.4
    Nganassan,0.2
    
    
    
    1st Modern North-African Attempted:
    
    [1] "distance%=2.2003"
    
             Mozabite
    
    Canary_Islands_Guanche,72.5
    MAR_Iberomaurusian,9.5
    Anatolia_Kumtepe_N,4.3
    MWI_Fingira_6100BP,4.2
    Anatolia_Tepecik_Ciftlik_N,2.8
    Anatolia_N_Kumtepe_low_res,2.4
    Anatolia_Kaman-Kalehoyuk_MLBA_low_res,1.6
    HRV_Vucedol,0.9
    DEU_MA_o,0.7
    TKM_Parkhai_MBA,0.4
    MAR_EN,0.4
    Levant_ISR_MLBA,0.1
    Levant_LBN_MA_NE,0.1
    GRC_Peloponnese_N,0.1
    
    
    ...results with Guanche removed:
    
    
    [1] "distance%=2.937"
    
             Mozabite
    
    MAR_Iberomaurusian,33.6
    Anatolia_Kumtepe_N,16
    HRV_Vucedol,11.7
    MWI_Fingira_6100BP,7.7
    Levant_ISR_MLBA,6.3
    TZA_Zanzibar_First_Millenium,6
    Anatolia_N_Kumtepe_low_res,5.1
    HUN_Tisza_LN,4.5
    MAR_EN,3.7
    DEU_MA_o,3.3
    Anatolia_Kaman-Kalehoyuk_MLBA_low_res,1.9
    Wales_CA_EBA,0.2
    
    ...relatively low "MAR_EN" due to multiple intrusive migrations?

    MAR_Iberomaurusian = ANA\BE
    MAR_EN = EEF? R1B Carriers?




    Observations:


    MWI_Fingira_2500BP:

    • These levels looks out of place for these West-African pops (Gambian, Igbo, Mandenka ...) -- could this be traces of an archaic West-Central African HG?



    MAR_Iberomaurusian:

    • Both West-African and Nilotic pops are getting significant ANA\BE-like ancestry, with the Dinka only slightly higher.

      I was expecting the Dinka to have substantially more based on lower ks showing them having ~20% Eurasian ancestry and negligible amounts for YRI -- maybe this will get corrected after we get more aDNA... after all we now know Yourba are ~12% Eurasian but we have yet to see this with ADMIXTURE runs. Since there's not much difference between WAs and Nilotes on pretty much all PCA plots, I suppose the similar ratio of Eurasian ancestry should be expected?
       

      Very marginal pull to Eurasians when WAs and Nilotic pops are compared:



      Would this reinforce the idea that West-Africans are direct offshoots of AEAs?
      Could it be an archaic West-Central African HG missing in the puzzle? I wonder if this would account for the embedded West-African ADMIXTURE in the Dinka.

    • The fits are horrible as expected but it's the ratio of SSA to Eurasian that might give the results some credence. When broken down, these results are holding the ~80/20 (EUR/SSA) split on lower ks for Nilotes.
    • @K33, based on these numbers -- the Basal ancestry does look skewed for West-Africans having more recent ANA "MAR_EN" and Nilotes having more




    MAR_EN:

    • this appears to be omnipresent in SSA pops except Horners and ancient South-Africans (MWI_Hora_9000BP).

    • Would this imply, Nilotes like the Dinka acquired MAR_EN during the green sahara period? This theory might have some merit if we agree the origin of Nilotes was in a more West/Central region of the southern-Sahara; @Beyoku I recall you proposing this here

    • @ChadRohlfsen, would this validate your theory of European farmer ancestry entering North Africa? The abstract from the Fregel 18' paper seems to confirm it "Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE).".

    • It's exclusion among Horners might explain why Nilotes/Central-Sudanics get ~5% "Farmer" ancestry on FTDNA's ancient origins and "Natufian" on calcs like Ancient Eurasia K6 yet fail to get any non-negligible "Western-Semitic"-like ancestry on modern calc's like puntDNAL k8, ancestry, 23andme etc.
      For lack of a MAR_EN reference, these calcs are forcing the minor Mediterranean-EEF ancestry of Central-Sudanics (and other nilotes) into "Natufian".
      Some more reference to this ~5% Eurasian affinity mentioned here

    • Here's GEDmatch Archaic results for UG_CentralSudanic (T068690), the Eurasian traces are minor but clearly present (0.5cm) for LBK, HN_BR2/NE1 -- as well as a handful of other Eurasian ancients (Usht-Ism, Loschbur...):
       

      Same goes for the Dinka (#Z022730):
       

    • I tried running modern North-Africans and Berbers to validate a plausible E-W cline for MAR_EN but ran into some trouble, their similar NW-African ancestry had Canary_Island_Guanche eating up "MAR_EN" so I removed it -- and things got complex... wayy too many reference samples for their ADMIXTURE breakdown. I'll have to revisit later -- their results are at the bottom of the code.
    PuntDNAL K8
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    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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  3. #2
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    If Lazardis' model is correct regarding the ANA-like affinity in the Yoruba (12.5%±1.1%), then these nMonte runs seem to hold some merit.


    Moreover, our model predicts that West Africans (represented by Yoruba) had 12.5%±1.1% ancestry from a Taforalt related group rather than Taforalt having ancestry from an unknown Sub-Saharan African source; this may have mediated the limited Neanderthal admixture present in West Africans. (Lazaridis, 2018)




    Based on ADMIXTURE, Taforalt and IAM samples (MAR_Iberomaurusian, MAR_EN) have ~about a third SSA-like affinity:



    Quote Originally Posted by NiloSaharan View Post
    Code:
             Yoruba
    
    MWI_Fingira_6100BP,70.6
    MAR_Iberomaurusian,15.8
    MWI_Fingira_2500BP,8.5
    MAR_EN,4.7
    BLZ_SakiTzul_7400BP,0.2
    CHL_LosRieles_5100BP,0.1
    Anatolia_N_Kumtepe_low_res,0.1
    15.8 + 4.7 = 20.5
    20.5 x .66 = 13.53 vs. 12.5%±1.1%



    Graph model from the afmd Lazardis' paper:
     
    Last edited by NiloSaharan; 06-26-2019 at 06:50 PM. Reason: Fregel et al., PNAS (2018) added
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    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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    "YRI -- maybe this will get corrected after we get more aDNA... after all we now know Yourba are ~12% Eurasian"

    According to Lazaridis the Yoruba (or at least those sampled) are about 12% Iberomaurusian-like/Taforalt-like, and he models Taforalt (the Iberomaurusians from Northern Morocco) as about half (45-50%) ANA and about half (50-55%) Eurasian. The ANA (Ancient North African) population is an African one (albeit one native to North Africa and distinct from other populations) rather than an OOA/Eurasian population, and is more basal than BE/Basal Eurasian. So the Yoruba, according to Lazaridis would seem to be about 6-7% Eurasian (rather than 12%).

    It also seems likely that, if Taforalt from northern Morocco was about 50% ANA and half Eurasian, more southerly Iberomaurusian groups (e.g. in parts of North Africa significantly south of the Mediterranean coast region) would likely have had considerably more ANA (and perhaps sometimes other African) ancestry. It would be interesting too see the autosomal and uni-parental results for (from the remains of) a range of Iberomaurusian and putatively Iberomaurusian-related populations from around North Africa and nearby.
    Last edited by Jm8; 06-26-2019 at 10:24 PM.

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    Quote Originally Posted by Jm8 View Post
    "YRI -- maybe this will get corrected after we get more aDNA... after all we now know Yourba are ~12% Eurasian"

    According to Lazaridis the Yoruba (or at least those sampled) are about 12% Iberomaurusian-like/Taforalt-like, and he models Taforalt (the Iberomaurusians from Northern Morocco) as about half (45-50%) ANA and about half (50-55%) Eurasian. The ANA (Ancient North African) population is an African one (albeit one native to North Africa and distinct from other populations) rather than an OOA/Eurasian population, and is more basal than BE/Basal Eurasian. So the Yoruba, according to Lazaridis would seem to be about 6-7% Eurasian (rather than 12%).

    It also seems likely that, if Taforalt from northern Morocco was about 50% ANA and half Eurasian, more southerly Iberomaurusian groups (e.g. in parts of North Africa significantly south of the Mediterranean coast region) would likely have had considerably more ANA (and perhaps sometimes other African) ancestry.


    Valid point -- distinction should be made when referring to non-SSA (ANA\Basal Eurasian) contribution in SSA pops
    Given the lack of aDNA, it's still quite fascinating that nMonte's fits manages to mirror Lazardis' model for a non-SSA pop into Yoruba (12.5%±1.1%)



    Here's a barebone run for "MAR_EN" (IAM), I was curious to see which modern SSAs nMonte would select:

    - I removed modern North-Africans/Saharans and admixed East-Africans modern and ancient

    Code:
    [1] "distance%=7.8563" MAR_EN MAR_Iberomaurusian,69.2 Levant_Natufian,20.3 Mandenka,5.1 Gambian,1.3 Dinka,1.3 Levant_PPNC,1 RUS_West_Siberia_N_low_res,0.6 Iberia_Southeast_c.5-8CE,0.4 Koinanbe,0.3 Australian,0.2 Papuan,0.1 USA_NM_Chaco,0.1 AFG_Darra_i_kur_low_res,0.1
    Geographically, the Mandenka are a reasonable choice given their West-Central African presence in and around Mali.
    At minor levels, nMonte's next SSA choice for neighboring Gambians is also appropriate along with the minor Dinka given their supposed presence further east in the southern-central green sahara.

    Maybe one day we'll be able to compare these SSA proportions for Kiffians "southerly Iberomaurusian groups"
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  9. #5
    Do you have a Fulani sample? I’d imagine their numbers would be very interesting given the Fischer component which peaked in them in the recent Tishkoff paper? The Mende are also quite mysterious, they have a larger than expected CHG component, larger than a lot of more easterly groups despite the fact that there is no know history of pygmies that far west in their current teritory
    Last edited by Brwn_trd; 06-27-2019 at 11:34 PM.

  10. #6
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    Quote Originally Posted by Brwn_trd View Post
    Do you have a Fulani sample?
    Unfortunately, there's no G25 cords for the Fulani yet.
    It would be nice if Davidski got a hold of some -- it looks like the samples from the recent Fulani paper (Vicente, 2019) are only available for academics"

    @Generalissimo, would that SNP count be adequate for G25?

    Genome-wide SNP typing
    A subset of 55 Fulani and 7 Czech/Slovak individuals were selected for genome-wide genotyping on the Illumina Omni2.5-Octo BeadChip (which contains the T–13910 SNP). The data was aligned to the Human Genome built version 37.

    Data management and quality filtering was carried out using PLINK v.1.90 software (Chang et al. 2015). A total of 2,608,742 SNPs were obtained from the 62 individuals. All individuals passed 0.15 data missingness threshold. We subsequently filtered to keep only autosomal SNPs with a SNP missingness filter of 0.1. To account for possible genotyping errors, we applied a Hardy-Weinberg equilibrium filter (HWE) that excluded 90 SNPs (for p ≤ 1e-4). AT and CG SNPs were excluded to prevent strand flipping errors when merging with comparative datasets. Relatedness was measured by identical by state (IBS) analysis and two Fulani individuals were excluded due to potential genetic relatedness. A total of 2,359,821 SNPs and 60 individuals were kept for the study.

    The newly generated data will be made available for academic research use through the ArrayExpress database accession number XXXX.

    Quote Originally Posted by Brwn_trd View Post
    I’d imagine their numbers would be very interesting given the Fischer component which peaked in them in the recent Tishkoff paper?
    What "Fischer" component are you referring to -- do you mean the Fuschia colour at K14 from the 09, Tishkoff paper ? I think that's just ADMIXTURE indicating close relatedness within the Fulani.
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    Quote Originally Posted by Jm8 View Post
    "YRI -- maybe this will get corrected after we get more aDNA... after all we now know Yourba are ~12% Eurasian"

    According to Lazaridis the Yoruba (or at least those sampled) are about 12% Iberomaurusian-like/Taforalt-like, and he models Taforalt (the Iberomaurusians from Northern Morocco) as about half (45-50%) ANA and about half (50-55%) Eurasian. The ANA (Ancient North African) population is an African one (albeit one native to North Africa and distinct from other populations) rather than an OOA/Eurasian population, and is more basal than BE/Basal Eurasian. So the Yoruba, according to Lazaridis would seem to be about 6-7% Eurasian (rather than 12%).
    ... not too far off : )

    This recent paper (Bergström, 19) couldn't have come out at a better time :

    The West African Yoruba also display a Neanderthal admixture signal, similar in shape but much less 380 pronounced than the signal in non-Africans (Fig. 6D). Other African populations do not clearly display the same behaviour. These results provide evidence for low amounts of Neanderthal ancestry in West Africa, consistent with previous results based on other approaches (15, 19), and we estimate this at 0.18%±0.06% in Yoruba using an f4-ratio (assuming Mbuti has none). The most likely source for this is West Eurasian admixture (37), 385 and assuming a simple linear relationship to Neanderthal ancestry, our estimate implies 8.6%±3% Eurasian ancestry in Yoruba.
    *That's corroboration between 3 independent methods
    Last edited by NiloSaharan; 06-28-2019 at 04:55 AM. Reason: *That's corroboration between 3 independent methods
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    Quote Originally Posted by Brwn_trd View Post
    The Mende are also quite mysterious, they have a larger than expected CHG component, larger than a lot of more easterly groups despite the fact that there is no know history of pygmies that far west in their current teritory
    Proportionately, the ancient non-SSA (ANA/Basal-Eurasian) in West-Africans might suggests they're directly derived from Ancient East-Africans so could it be this archaic SSA affinity which is the main factor pulling West-Africans closer to the San relative to Nilotes on PCAs? Perhaps this is the case since both the Dinka and Yoruba appear to have similar non-SSA contributions (MAR_EN\MAR_Iberomaurusian) -- it's the difference between their archaic SSA which is most profound.


    ... we find that the west African Yoruba have a closer relationship to non-Africans than to the central African Mbuti at high allele frequencies but the opposite relationship at low frequencies (Fig. 2 B ), suggesting recent gene flow between Mbuti and Yoruba since the divergence of non-Africans.


    Code:
    1] "distance%=31.1751"
    
             Esan_Nigeria
    
    MWI_Fingira_6100BP,67.1
    MAR_Iberomaurusian,15.5
    MWI_Fingira_2500BP,12.4
    MAR_EN,4.1
    RUS_Ust_Ishim,0.4
    Anatolia_N_Kumtepe_low_res,0.4
    
    [1] "distance%=29.943"
    
             Igbo
    
    MWI_Fingira_6100BP,69.5
    MAR_Iberomaurusian,16
    MWI_Fingira_2500BP,10.9
    MAR_EN,3.3
    Anatolia_N_Kumtepe_low_res,0.3
    
    [1] "distance%=31.2193"
    
             Yoruba
    
    MWI_Fingira_6100BP,70.6
    MAR_Iberomaurusian,15.8
    MWI_Fingira_2500BP,8.5
    MAR_EN,4.7
    BLZ_SakiTzul_7400BP,0.2
    CHL_LosRieles_5100BP,0.1
    Anatolia_N_Kumtepe_low_res,0.1
    
    
    
    [1] "distance%=28.1667"
    
             Gambian
    
    MWI_Fingira_6100BP,68.7
    MAR_Iberomaurusian,19
    MWI_Fingira_2500BP,7.3
    MAR_EN,4.6
    Anatolia_N_Kumtepe_low_res,0.3
    
    [1] "distance%=28.2958"
    
             Mandenka
    
    MWI_Fingira_6100BP,69.6
    MAR_Iberomaurusian,19.6
    MWI_Fingira_2500BP,6.4
    MAR_EN,4
    Anatolia_N_Kumtepe_low_res,0.2
    BLZ_SakiTzul_7400BP,0.1
    PER_Laramate_900BP,0.1
    
    [1] "distance%=25.7217"
    
             Dinka
    
    MWI_Fingira_6100BP,72.5
    MAR_Iberomaurusian,20.7
    MAR_EN,4.5
    MWI_Fingira_2500BP,2
    Eskimo_Sireniki,0.1
    BRA_Laranjal_6700BP,0.1
    PER_Lauricocha_3500BP,0.1
    Last edited by NiloSaharan; 06-28-2019 at 04:37 AM.
    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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  16. #9
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    H5a1

    I would say that trying models with Mbuti may help here. I've seen similar stuff with my own runs.

    There will always be new stuff coming that changes models. One thing to also consider is R1b and G2 among the Yoruba and Mende respectively. So, it's more than just Iberomaurusian ancestry.

  17. #10
    Quote Originally Posted by NiloSaharan View Post
    What "Fischer" component are you referring to -- do you mean the Fuschia colour at K14 from the 09, Tishkoff paper ? I think that's just ADMIXTURE indicating close relatedness within the Fulani.
    Pardon me, I was on my phone, autocorrect changed it. I did mean fuschia

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