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

  1. #531
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    Quote Originally Posted by Angoliga View Post
    Of course! Thanks for sharing. If available, could you also please provide the nationality (Honduras, Belize.. ?) and/or sub-region?

    - I'll have it added shortly
    The thing is this Garifuna sample is simulated by me. Its not an actual individual (I create it based on how much African and Amerindian they score based on the DNA results of them that I saw). I don't think any Garifuna has done G25 yet. I actually have seen some Gedmatch results of Garifunas, but I'm too shy and feel a bit awkward to ask them to do G25 as I'm not related to them by DNA lol.

    Well it can be Garifuna_Honduras_simulated if you want as most Garifunas seem to come from these vicinities (Guatemala, Belize, Honduras, Nicaragua, etc). Not sure about the subregion in particular as I don't really know much about these countries.

    Quote Originally Posted by Angoliga
    Is there anyone knowledgeable on pre-Colombian source-samples for the Americas? Open to suggestions here -- I'm hoping there'd be less than 3 we can use to gauge a broad degree of ancient-American population substructure.

    At the moment, all we have is CHN_Tianyuan as a "deep-layer" catch-all for all ancient East-Asian/Amerindian-related ancestry against African samples.
    I can give some examples of some pre-Columbian samples that you can used such as PER_RioUnCallane_1800BP, CHL_Los_Rieles_10500_BP or ARG_LagunaChica_6800BP, USA_Anzick, etc.

    Quote Originally Posted by Angoliga
    In other news, we have what appears to be our first South-African user sample : ) The user has provided their cords, I'm just waiting on their confirmation of Nationality/ethnic-group..etc.
    Based on their results, I'm guessing their sub-region is within S.W. Africa.
    Can you link me to the page of the South African user sample? Want to see it.

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  3. #532
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    Quote Originally Posted by Angoliga View Post
    If I've understood correctly, here's a run using the swapped source-samples requested:

     


    *For comparison I had them run against all individual Sudanese including "7":


    Ranked by highest Dinka affinity:




    Ranked by best fit (distance%):



    Here's the requested run for E-HGs (KEN_LSA, and ETH_4500BP):

     


    As an AEA-proxy, I used both the Sudanese7 and the Dinka modern avg. for comparison:

    Target: ETH_4500BP
    Distance: 4.7672% / 0.04767159
    67.6 Dinka
    18.0 ZAF_2000BP
    6.8 Levant_Natufian
    3.8 CHN_Tianyuan
    2.0 Mbuti
    1.8 Yamnaya_UKR

    Target: KEN_LSA
    Distance: 4.2131% / 0.04213058
    59.2 Dinka
    19.6 ZAF_2000BP
    8.8 Mbuti
    7.6 RUS_Ust_Ishim
    3.8 Levant_Natufian
    0.8 GEO_CHG
    0.2 Levant_PPNC





    Target: ETH_4500BP
    Distance: 3.5518% / 0.03551820
    68.4 Sudanese
    17.8 ZAF_2000BP
    6.8 Levant_Natufian
    3.0 CHN_Tianyuan
    2.0 Mbuti
    2.0 Yamnaya_UKR

    Target: KEN_LSA
    Distance: 3.1078% / 0.03107795
    60.0 Sudanese
    19.4 ZAF_2000BP
    8.8 Mbuti
    6.8 RUS_Ust_Ishim
    2.6 Levant_PPNC
    1.4 Levant_PPNB
    0.4 Levant_Natufian
    0.4 MAR_Taforalt
    0.2 Yamnaya_UKR


    The "SUDANESE7" recommendation also seems to hold ground when run against the individual Dinka samples:

     

    - seeing quite the runup on "West-African" (Yoruba) with SUDANESE7 as an AEA-proxy:


    Until we come across a better source sample (modern or ancient), "SUDANESE7" actually looks to be the most conservative G25_scaled AEA-proxy - thanks @Mnemonics

    * I noticed some minor loss in ancient Eurasian-affinities vs. the Dinka avg. while running other admixed AEA samples but the overall higher capture of West-African (as high as 11.8% with some Dinka individuals) trumps returning to the Dinka avg.






    2D PCA: I thought it'd be neat for us to see where the Sudanese & Dinka individuals plot (*after this new revelation thanks to Mnemonics)


    Some of these outliers are quite interesting:


    • Sudanese11 drifting past Bulala might suggest a relation to Darfurian (W. Sudanese)-related groups
    • Sudanese3 clustering with Central-Sudanics might suggest being derived from a more southern S.Sudanese region (Equatorial) which are typically more of the C.S. stock
    • Sudanese8 is hovering nearly over the Hutu sample
    Minor note on the models for KEN_LSA and Mota, UstIshim is the preferred source for qpadm models for Mota's broadly Eurasian affinity and the qpF4ratios strongly indicates that Mota has very basal Eurasian ancestry.

    This isn't very apparent in G25 nmonte models because very old variation isn't captured very well by the PCA coordinates so it uses younger East Eurasian and West Eurasian sources to replace UstIshim.

    KEN_LSA's Neolithic Levantine ancestry seems legit. it seems to have minor pastoralist ancestry.

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  5. #533
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    Quote Originally Posted by Angoliga View Post
    Fascinating! Have these results compared well against ADMIXTURE results of some papers? I'm not knowledgeable enough on ANA to say... only the Lazardis et. al, 2018 paper stands out for me atm.

    It's just a little concerning, the amount of simulated cords needed in an attempt to produce meaningful results.
    It seems worrisome enough that a simulated ANA wouldn't tease-out inherent SSA (~>20%), and then on top, needing to add on other simulated source-samples of ancient cords thar we already have -- it seems kinda redundant




    Of course! Thanks for sharing. If available, could you also please provide the nationality (Honduras, Belize.. ) and/or sub-region?

    - I'll have it added shortly

    ---------

    Is there anyone knowledgeable on pre-Colombian source-samples for the Americas? Open to suggestions here --hoping there'd be less than 3 we can use to gauge a broad-degree of Ancient-Amerindian substructure:

    At the moment, all we have is CHN_Tianyuan as a "deep-layer" catch-all for all ancient East-Asian/Amerindian-related ancestry against African-related samples.
    It did ok as a proxy for paleolithic-related back migrations against native Africans within the interior but with this variety of modern ancestry, we could use something more definitive.

    ---------

    In other news, we have what appears to be our first South-African user sample : ) The user has provided their cords, I'm just waiting on their confirmation of Nationality/ethnic-group.
    Based on their results, I'm guessing their sub-region is within S.W. Africa.
    Btw here is another Garifuna_individual I simulated:

    Code:
    Garifuna_,-0.493838207,-0.011764753,0.041070957,0.033401623,-0.022306033,0.00613768,-0.081676272,-0.047966922,-0.032285815,0.013009524,-0.00014102,-0.002528981,0.004364035,0.006281133,-0.002352917,0.002705564,-0.000529801,0.000107772,-0.00022247,0.001361943,0.001178046,0.002908023,0.000590941,-0.001604668,-0.001042848
    This time I used Cameroon Mbo+DOM_Southeast_Ceramic (precolonial Amerindian samples from the Dominican Republic) as the parent populations to create it. This time I used Cameroon_Mbo because Garifunas also have significant Cameroonian-related ancestry: https://tracingafricanroots.wordpres...bbean-results/

    Target: Garifuna_2
    Distance: 0.7287% / 0.00728665
    51.2 Yoruba
    24.6 UGA_Munsa_500BP
    12.6 Karitiana
    7.0 Mixe
    4.0 Bakola
    0.6 Dinka

    Code:
    Dinka,-0.577083,0.050776,-0.000377,-0.00751,-0.005386,-0.001673,-0.017685,0.020422,0.081145,-0.09695,-0.02107,0.022742,-0.038317,-0.00117,0.010145,-0.021347,0.018612,-0.009438,0.024197,-0.024168,0.002402,0.003308,0.001479,0.000904,0.0097
    Surui,0.057822,-0.317454,0.117134,0.10672,-0.113806,-0.015395,-0.325819,-0.391691,-0.017548,-0.020775,0.002079,-0.004676,0.002319,0.035864,-0.013491,0.000583,0.0109,-0.001242,0.000251,0.001276,-0.003544,0.012662,-0.006779,-0.007447,-0.009149
    Spanish_Cataluna,0.114582,0.146236,0.045883,0.002369,0.047188,0,-0.002037,0.002384,0.022361,0.030494,-0.001895,0.008592,-0.016006,-0.010643,0.008867,0.001591,-0.000652,-0.001647,-0.001131,-0.000959,0.006197,-0.005729,-0.003903,-0.001928,0.000958
    Yoruba,-0.630062,0.062501,0.022113,0.016708,0.000503,0.012474,-0.044417,0.047767,-0.048881,0.032769,0.004621,0.00079,0.023056,0.000951,0.012523,-0.009607,0.007076,0.000449,0.006022,-0.00299,0.001554,0.002316,-0.001759,-0.000471,-0.000425
    Bakola,-0.641393,0.060424,0.026587,0.030847,0.001231,0.004183,0.157692,-0.122187,-0.015339,0.032256,0.006171,-0.089246,-0.02884,-0.00172,0.004682,-0.002917,0.001108,0.00266,0.000503,0.001563,-0.000873,-0.003957,-0.001479,0.001265,-0.001437
    MWI_Fingira_6100BP,-0.582774,0.060932,0.009805,0.024871,-0.002462,-0.006972,0.171558,-0.122764,0.048063,-0.025513,-0.009094,-0.034619,-0.022894,-0.003165,0.026465,-0.017502,0.029467,0.123901,-0.020363,-0.008379,-0.021961,0.006925,0.006286,-0.001325,-0.00479
    ZAF_2000BP,-0.641583,0.0558543,0.0258957,0.034884,0.001231,-0.0030677,0.2680687,-0.2072223,0.0104307,0.0153683,0.008715,-0.0659913,-0.0216053,0.0064223,0.023751,-0.0201537,0.034204,0.294593,-0.09574,0.0060447,-0.033857,-0.0039157,0.003163,-0.0029323,-0.000399
    UGA_Munsa_500BP,-0.623751,0.063978,0.012445,0.011951,-0.000308,0.017291,-0.014336,0.01523,-0.015135,-0.002369,0.001299,0.013638,-0.018731,0.007432,-0.033116,0.013126,-0.02386,-0.001394,-0.016844,0.014882,-0.001248,0.002844,0.001972,0.006627,-0.003113
    Mixe,0.057822,-0.320704,0.123017,0.094381,-0.107343,-0.015562,-0.278206,-0.334048,-0.012026,-0.014688,-0.007113,-0.006564,0.00446,0.020203,-0.008795,0.004004,0.006102,0.000456,-0.000453,-0.003602,0.001173,0.005861,0.003402,-0.001711,-0.001844
    Karitiana,0.058809,-0.320061,0.118353,0.108367,-0.113662,-0.013619,-0.323061,-0.382484,-0.015373,-0.017343,0.000947,-0.002698,-0.001635,0.027318,-0.004569,0.00442,0.011017,0.002597,0.000105,-0.000354,-0.005532,0.010902,-0.005546,-0.00253,-0.006786
    Last edited by Tsakhur; 10-27-2020 at 05:15 PM.

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  7. #534
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    Belize CARICOM United States of America African Union Belize
    @Tsakhur and @Angoliga I have 15 Belizeans under my profile between AncestryDNA and 23andMe with updated results. I guess you all seem only interested in Garinagu people and are simulating results, I have 2 who are only Garifuna and 1 who is 3/4 Garifuna.

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  9. #535
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    Quote Originally Posted by pgbk87 View Post
    @Tsakhur and @Angoliga I have 15 Belizeans under my profile between AncestryDNA and 23andMe with updated results. I guess you all seem only interested in Garinagu people and are simulating results, I have 2 who are only Garifuna and 1 who is 3/4 Garifuna.
    That's awesome. Can you convince/ask all 15 of them including the 2 Garinagu and 3/4 Garifuna to do G25? It would be awesome to see actual results

  10. #536
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    Quote Originally Posted by Tsakhur View Post
    That's awesome. Can you convince/ask all 15 of them including the 2 Garinagu and 3/4 Garifuna to do G25? It would be awesome to see actual results
    I'll see, but how different do simulated vs. actual results look? Especially for recently (-500 years) mixed populations. Can you give me an example?

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  12. #537
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    Quote Originally Posted by drobbah View Post
    Sudanese 11 has some minor Natufian/Levantine ancestry from the runs I tried before but I could be wrong, can that explain why it's clustering near the Bulala?
    Yep, seems the case. From runs on the previous post (first spoiler), Sudanese11 had 7% Natufian, and 1% GEO_CHG (could be IRAN_N/Semitic noise). Would be neat to see if Baggara and Darfurians (Zaghawa, Fur and Masalit) also cluster in the same vicinity on the PCA.

    From second glance of that run, Sudanese11's absolute lack of West-African did seem a bit odd, so I swapped the Dinka source-sample for our new de facto AEA-proxy (Sudanese7), and voila ....

    Target: Sudanese:SUDANESE11
    Distance: 1.5486% / 0.01548598
    88.6 Sudanese
    5.0 Levant_Natufian
    3.8 Yoruba
    2.6 Levant_PPNC


    *Apart from being widespread in deep-layer runs against Levant_Natufian in North-African pops, Levant_PPNC was also observed at non-neglible levels among several Great-Lakes pastoralist-related groups.


    Quote Originally Posted by Tsakhur View Post
    The thing is this Garifuna sample is simulated by me. Its not an actual individual (I create it based on how much African and Amerindian they score based on the DNA results of them that I saw). I don't think any Garifuna has done G25 yet. I actually have seen some Gedmatch results of Garifunas, but I'm too shy and feel a bit awkward to ask them to do G25 as I'm not related to them by DNA lol.

    Well it can be Garifuna_Honduras_simulated if you want as most Garifunas seem to come from these vicinities (Guatemala, Belize, Honduras, Nicaragua, etc). Not sure about the subregion in particular as I don't really know much about these countries.
    Ohh, I see -- in that case, we can add it without a prefix for nationality/ethnic group.


    Quote Originally Posted by Tsakhur View Post
    I can give some examples of some pre-Columbian samples that you can used such as PER_RioUnCallane_1800BP, CHL_Los_Rieles_10500_BP or ARG_LagunaChica_6800BP, USA_Anzick, etc.
    Can you provide what each sample represents in terms of their heightened ancestral component? (e.g. Sudanese7 = Ancestral East-African, Yoruba=West African, KEN_LSA=EHG)


    Quote Originally Posted by Tsakhur View Post
    Can you link me to the page of the South African user sample? Want to see it.
    The user PM'd me their cords, so I keep them private. That's the general rule for participants on the thread, those open to share typically post on the thread itself.


    Quote Originally Posted by Mnemonics View Post
    Minor note on the models for KEN_LSA and Mota, UstIshim is the preferred source for qpadm models for Mota's broadly Eurasian affinity and the qpF4ratios strongly indicates that Mota has very basal Eurasian ancestry.

    This isn't very apparent in G25 nmonte models because very old variation isn't captured very well by the PCA coordinates so it uses younger East Eurasian and West Eurasian sources to replace UstIshim.
    Poignant observation!

    Goes to show that G25 has it's limitations, *though I recall Davidski warning about the usage of source-samples across different periods -- so maybe anachronism is the culprit for producing inconsistencies with the qpadm models


    Quote Originally Posted by Mnemonics View Post
    KEN_LSA's Neolithic Levantine ancestry seems legit. it seems to have minor pastoralist ancestry.
    Wow, I hadn't really looked at the dates for KEN_LSA, if I've now read them correctly from the Prendergast et al. 2019 paper (Table 1), KEN_LSA is dated at 189515 ybp (Uncalibrated)/1880–1750 ybp (calibrated).

    That's plenty of time for intrusive pastoralist (embedded Natufian) ancestry to get in the mix there -- this whole time I thought KEN_LSA was literally dated from the Later Stone Age lol

    What are your thoughts on using some of the Malwian HGs as a proxy for HG ancestry vs. ZAF_2000bp, most of the MWI_HG samples are beyond pastoralist migrations, unlike some of these South-African ancients which have some degree of minor neolithic pastoralist ancestry.


    Quote Originally Posted by pgbk87 View Post
    @Tsakhur and @Angoliga I have 15 Belizeans under my profile between AncestryDNA and 23andMe with updated results. I guess you all seem only interested in Garinagu people and are simulating results, I have 2 who are only Garifuna and 1 who is 3/4 Garifuna.
    It would be nice to at least have 1 from each; a Belizean from the general population and a Garinagu. Could you ask those members to get their G25 results -- would be nice to have yours added as well if interested (no pressure : )

    I'm hesitant to permanently add simulated samples on the online PCA since they're not based on actual genomic data and deviate from the standard we have across currently added samples.

    -- that said, I can still add the simulated samples temporarily and take screenshots so we can at least have an idea where they'd hypothetically plot
    .... .. I have spoken."

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  14. #538
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    "ZAF_Zulu_Sotho_Swati_Sabz " user added:






    Updated All-African PCA :

     



    (North-African, Tropical-African, South-African)

    ◇= Ancients
    X= Active users
    = Samples/Modern Avgs



    3D PCA: https://plot.ly/~Angoliga/3/ (allow ~less than a minute to load)
    2D PCA: https://plot.ly/~Angoliga/4/



    Deep-layer run:

    Distance: 5.2596% / 0.05259567
    69.4 Yoruba
    17.2 ZAF_2000BP
    9.4 Sudanese
    4.0 KEN_LSA


    Source Samples:
     
    KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
    ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
    Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
    Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
    Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
    CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
    Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
    Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
    Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
    Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
    Sudanese:SUDANESE7,-0.571392,0.046714,-0.007165,-0.007429,-0.005232,-0.002789,-0.00799,0.018922,0.0904,-0.108977,-0.018512,0.020831,-0.047125,0.000688,0.013165,-0.023734,0.021644,-0.012035,0.026145,-0.023261,-0.000998,0.004822,-0.000986,-0.001687,0.003712
    ZAF_2000BP,-0.641583,0.0558543,0.0258957,0.034884,0.001231,-0.0030677,0.2680687,-0.2072223,0.0104307,0.0153683,0.008715,-0.0659913,-0.0216053,0.0064223,0.023751,-0.0201537,0.034204,0.294593,-0.09574,0.0060447,-0.033857,-0.0039157,0.003163,-0.0029323,-0.000399
    Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
    IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
    IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
    HUN_Koros_N_HG,0.137726,0.12491,0.180264,0.154395, 0.128332,0.042112,0.015041,0.03646,0.071992,0.0069 25,-0.005196,-0.013488,0.014717,-0.003303,0.028637,0.046141,0.018384,0.005954,-0.008296,0.045772,0.061142,0.010634,-0.040672,-0.124475,0.013053
    GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
    MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
    MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
    MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
    .... .. I have spoken."

  15. The Following 6 Users Say Thank You to Angoliga For This Useful Post:

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  16. #539
    Gold Class Member
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    Somaliland Ethiopia Adal Sultanate Yemen Canada
    PCA's like this makes me visualize and appreciate how diverse we are as a continent! Thank you for your work Ben!

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  18. #540
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    Canada Somaliland
    I haven't really bothered with the Malawi HG samples due to their relatively low coverage.

    Nevertheless there are benefits to sticking to distinct streams of ancestry when we are dealing with samples we don't know the major components of so I would stick to using ZAF_2000BP for verification until we can get a clearer view of what the makeup of the Malawi HGs is like.

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