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Genetic study Ancient DNA from the Green Sahara reveals ancestral North African lineage

qh777 said:
Question: Which one of these are the correct scaled coordinates?
View attachment 18151
Libya_Takarkori_N:TKH001,-0.455292,0.076165,-0.006411,-0.023579,0.00954,-0.015618,-0.059458,0.034845,0.076492,-0.022597,-0.005034,0.002098,0.01888,-0.025873,0.033116,-0.025855,0.009909,-0.029138,-0.037709,0.006503,-0.013726,-0.046493,0.027361,-0.002651,0.00491
Libya_Takarkori_N:TKH001_tr.SG.TW,-0.458707,0.076165,-0.002263,-0.028101,0.01231,-0.017291,-0.057578,0.034152,0.07506,-0.017859,-0.001786,0.006145,0.021556,-0.027525,0.03203,-0.02201,0.012126,-0.032179,-0.041229,0.003502,-0.014724,-0.043526,0.026991,-0.005181,0.002754
Libya_Takarkori_N:TKH001_tr_all,-0.455292,0.078196,-0.003771,-0.026486,0.010463,-0.018965,-0.058518,0.032537,0.077719,-0.019864,-0.001786,0.003897,0.020664,-0.025598,0.033387,-0.023734,0.010561,-0.032559,-0.036452,0.007504,-0.0141,-0.045504,0.029703,-0.006868,0.010179


Libya_Takarkori_N:TKH001,-0.04,0.0075,-0.0017,-0.0073,0.0031,-0.0056,-0.0253,0.0151,0.0374,-0.0124,-0.0031,0.0014,0.0127,-0.0188,0.0244,-0.0195,0.0076,-0.023,-0.03,0.0052,-0.011,-0.0376,0.0222,-0.0022,0.0041
Libya_Takarkori_N:TKH001_tr.SG.TW,-0.0403,0.0075,-0.0006,-0.0087,0.004,-0.0062,-0.0245,0.0148,0.0367,-0.0098,-0.0011,0.0041,0.0145,-0.02,0.0236,-0.0166,0.0093,-0.0254,-0.0328,0.0028,-0.0118,-0.0352,0.0219,-0.0043,0.0023
Click to expand...
I do not believe that Eurogenes (G25 included), Dodecad, MDLP, etc. calculators are capable of differentiating very old genetic elements from typical SSA elements. An example of this is that these calculators treat Neanderthals and Denisovans as 100% (100.00) SSA in the coordinates of their spreadsheets with reference populations, which is untrue. In this sense, these results should always be taken with a grain of salt, especially when compared to academic results. Using my original G25 coordinates with Takarkori coordinates (I do not know who obtained these coordinates), among other ancestral coordinates, I obtain these results. I suppose that the Takarkori samples in the "pink" color range are the best proxy.
CCcMwU8.png
 
I asked ChatGPT which ones are the correct scaled and it said:

1744657147536.png

1744657178806.png

So these two? Libya_Takarkori_N:TKH001?,-0.04,0.0075,-0.0017,-0.0073,0.0031,-0.0056,-0.0253,0.0151,0.0374,-0.0124,-0.0031,0.0014,0.0127,-0.0188,0.0244,-0.0195,0.0076,-0.023,-0.03,0.0052,-0.011,-0.0376,0.0222,-0.0022,0.0041
Libya_Takarkori_N:TKH001_tr.SG.TW?2,-0.0403,0.0075,-0.0006,-0.0087,0.004,-0.0062,-0.0245,0.0148,0.0367,-0.0098,-0.0011,0.0041,0.0145,-0.02,0.0236,-0.0166,0.0093,-0.0254,-0.0328,0.0028,-0.0118,-0.0352,0.0219,-0.0043,0.0023

1744657401810.png


1744657523419.png


Compared to WHGs, ANE, Dzudzuana, Shum Laka etc.:

1744658151537.png



Iberomaurusian with the two I used:

1744658737228.png


The other three produce a distance of 0.33 for Iberomaurusians
 
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qh777 said:
So these two? Libya_Takarkori_N:TKH001?,-0.04,0.0075,-0.0017,-0.0073,0.0031,-0.0056,-0.0253,0.0151,0.0374,-0.0124,-0.0031,0.0014,0.0127,-0.0188,0.0244,-0.0195,0.0076,-0.023,-0.03,0.0052,-0.011,-0.0376,0.0222,-0.0022,0.0041
Libya_Takarkori_N:TKH001_tr.SG.TW?2,-0.0403,0.0075,-0.0006,-0.0087,0.004,-0.0062,-0.0245,0.0148,0.0367,-0.0098,-0.0011,0.0041,0.0145,-0.02,0.0236,-0.0166,0.0093,-0.0254,-0.0328,0.0028,-0.0118,-0.0352,0.0219,-0.0043,0.0023
Click to expand...
Yes. That's it, I think.
5o2Ar8V.png
 
I'm going off what ChatGPT said. But hey it could be wrong.

1744667604792.png

1744667800642.png

1744667832002.png
 
qh777 said:
I'm going off what ChatGPT said. But hey it could be wrong.

View attachment 18163
View attachment 18164
View attachment 18165
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The degree of uncertainty is always very high. We can only draw trends. We see modern SSA always closer to Shum Laka and Mota. Shum Laka is the first proxy for West Africans, with the order being reversed with Mota being the first proxy for East Africans. Perfect. Large distances: Yes. No modern human would resemble them in autosomal term, much less the Eurasian populations of the Upper Paleolithic. The smaller distances of Hadza in relation to Shum Laka and Mota only reaffirm what is already known about this people: The Hadza are considered one of the oldest groups of humanity, along with the Khoisan of southern Africa. Perfectly adapted to the environment in which they have lived for millennia as hunters and gatherers, they did not need to accumulate many mutations throughout their evolutionary history to survive dramatic changes in the environment, flora, fauna and new diseases, as was the case with those who migrated inside the African Continent or to outside Africa.
 
I take the distances with very old samples lightly or I'm less particular about the distance number. For instance my distance to Dzudzuana is pretty close (0.13) considering it's from 26,000 years ago! It depends on context. The way I understand it, a distance of generally 0.3 or less means regional relatedness. Once you get over 0.4 and for the way most people understand, there is no genetic relatedness other than a very long time ago. It's something I'd like to ask population geneticists or Davidski himself.

Quick note here: I don't quite agree with ChatGPTs interpretation of <0.05 being indentical and 0.10 being in the same ethnic group.

1744679444806.png
 
qh777 said:
I take the distances with very old samples lightly or I'm less particular about the distance number. For instance my distance to Dzudzuana is pretty close (0.13) considering it's from 26,000 years ago! It depends on context. The way I understand it, a distance of generally 0.3 or less means regional relatedness. Once you get over 0.4 and for the way most people understand, there is no genetic relatedness other than a very long time ago. It's something I'd like to ask population geneticists or Davidski himself.

Quick note here: I don't quite agree with ChatGPTs interpretation of <0.05 being indentical and 0.10 being in the same ethnic group.

View attachment 18166
Click to expand...
Useful information from ChatGPT. THX. Yes. I agree with you. It depends on the context. For very old populations a distance of 0.13 is amazing, excellent. Just for illustration purposes, DNAgenics interprets G25 distances as follows:
Klr14xr.png

This interpretation is more applicable to distances of modern people with modern populations, IMO.
PS: dnagenics = Davidsky x 100, ie, 0.03 = 3.0
 
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Duarte said:
Useful information from ChatGPT. THX. Yes. I agree with you. It depends on the context. For very old populations a distance of 0.13 is amazing, excellent. Just for illustration purposes, DNAgenics interprets G25 distances as follows:
Klr14xr.png

This interpretation is more applicable to distances of modern people with modern populations, IMO.
Click to expand...
Yes I feel like this guide is suited towards modern populations. For example my distance to Iran_GanjDareh in G25 is 0.329, but I score ~8% of it in qpAdm with this sample selection indicating some genetic affinity:
1744683199474.png

Model with Dzudzuana:

1744685519909.png
 
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qh777 said:
Yes I feel like this guide is suited towards modern populations. For example my distance to Iran_GanjDareh in G25 is 0.329, but I score ~8% of it in qpAdm with this sample selection indicating some genetic affinity:
View attachment 18167
Model with Dzudzuana:

View attachment 18168
Click to expand...
In the G25, with the population sources highlighted in the table, I get the following result.
Peru_Lauricocha_8600BP_(n=3),0.050461333,-0.31819933,0.12168433,0.098838,-0.114688,-0.022776333,-0.29791533,-0.35275433,-0.014112333,-0.011906,-0.00157,-0.002698,0.00094133333,0.021744667,-0.003348,0.0023426667,0.0092573333,0.004561,0.00062866667,0.0076286667,0.0038263333,0.0065946667,0.000411,-0.0010443333,-0.0066656667
Brazil_Lapa_Do_Santo_9600BP_(n=5),0.0487162,-0.3046588,0.1209048,0.0994194,-0.1149138,-0.0164546,-0.279569,-0.331094,-0.012476,-0.0176766,0.0051638,-0.0008992,0.0016056,0.0183314,-0.003773,0.006046,0.00618,-0.0016724,0.0020112,0.002076,-0.0003242,0.0072708,0.0016022,-0.0036632,-0.0002394
Brazil_Lapa_Do_Santo_9900BP_(n=2),0.048944,-0.293488,0.1095535,0.099323,-0.1075585,-0.017291,-0.270027,-0.331025,-0.0104305,-0.0174945,0.0064145,-0.002323,0.0034935,0.0252535,-0.0118755,0.005436,0.0038465,-0.0019005,0.008799,0.0069405,-0.002059,0.001484,0.001602,0.0019885,0.005149
Italy_Veneto_Mesolithic_Villabruna_(n=1),0.121791,0.114755,0.18592,0.184111,0.156337,0.060798,0.020211,0.035998,0.092445,0.018041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
Luxembourg_Mesolithic_Loschbour_(n=1),0.130897,0.109677,0.203645,0.198,0.162492,0.059125,0.015041,0.038075,0.100217,0.016219,-0.015427,-0.017235,0.019921,-0.001239,0.061346,0.07067,0.002608,0.007348,-0.008925,0.065406,0.117543,0.010387,-0.049422,-0.173639,0.019519
Russia_Sidelkino_HG.SG,0.121791,0.041637,0.135386,0.195739,0.00277,0.054663,-0.021621,-0.020768,-0.004909,-0.073806,0.010555,-0.012889,0.029881,-0.044865,0.027144,0.02254,-0.004433,-0.004687,-0.010307,0.018634,-0.005989,0.013973,0.006286,-0.020846,-0.003473
Iran_N_Ganj_Dareh_(n=7),0.044065857,0.066154714,-0.15634357,0.0068752857,-0.124067,0.02263,0.015678714,-0.00039542857,-0.082101714,-0.054827,-0.0010208571,-0.0017127143,0.0049484286,-0.0081198571,0.033833143,0.055801143,-0.0064821429,0.0092844286,0.0096788571,-0.035034857,0.0075402857,-0.029800286,-0.011972571,-0.037320429,0.022187714
Anatolia_N_Ceramic_Barcin_(n=22),0.11884159,0.18104118,0.0035483182,-0.100835,0.051743727,-0.046397318,-0.0051914091,-0.0073214545,0.036860909,0.080971,0.0091897273,0.012064182,-0.023278818,0.00098209091,-0.041820318,-0.0091064091,0.021590318,0.00069668182,0.011752773,-0.0094704091,-0.013101909,0.0067503182,-0.0046665909,-0.0034506818,-0.0054648636
Russia_Samara_EBA_Yamnaya_(n=29),0.12265421,0.08898131,0.044110172,0.11446552,-0.027262276,0.045545793,0.0040274483,-0.0023793448,-0.054727793,-0.074653966,0.00097427586,-0.0005477931,-0.00097403448,-0.021706448,0.036808138,0.012134207,-0.0064877586,-0.0017474828,-0.002513931,0.01092769,-0.003807931,0.001262069,0.0098003448,0.019886379,-0.0044801724
Georgia_Mesolithic_Trialetian_Kotias_Klde_(CHG)_(n=1),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
Georgia_UP_Dzudzuana_(n=1),0.062603,0.099522,-0.009428,-0.002261,0.029852,-0.017012,0.001175,-0.001846,0.03211,0.02606,0.007632,-0.011989,0.001635,0.012799,0.000271,-0.003182,-0.01343,0.004687,-0.007416,0.003377,0.026453,0.007172,-0.01479,-0.029281,-0.00012
Morocco_UP_Iberomaurusian_Taforalt_(n=6),-0.19008467,0.082257667,-0.0242615,-0.084626,0.026620333,-0.056056833,-0.070463667,0.020037667,0.15632417,0.0034928333,0.0198655,-0.032521,0.07547,-0.051494,0.072248333,-0.038848833,0.003716,-0.0654345,-0.144134,0.0378515,-0.038473833,-0.124951,0.071894333,-0.013816833,0.016186
Israel_Epipaleolithic_Natufian_(n=2),0.0227645,0.141666,-0.0371465,-0.1406675,0.030775,-0.0787865,-0.023031,-0.01823,0.1154535,0.001731,0.0306105,-0.023904,0.0789385,0.000826,0.0147935,0.0102755,-0.017341,0.00057,-0.019609,0.0398315,0.0020585,0.00136,-0.00265,-0.002229,0.008502
Click to expand...
37Rb73f.png

Unfortunately, I still don't know how to use the qpAdm statistical tool as I would like or could. I know how to interpret the results posted by users of this forum, but I'm still a long way from using it to interpret my own raw data. I was able to watch Jovialis and Euraptor (users of this forum) exchange technical information about the use of this tool, which is essential in academic analyses of population genetics, but I confess that I was a bit lazy in going further. I'm not a big fan of the tools created by Davidsky, Dienekes and others, but since they provide a ready-made package, by the law of least effort (LOL), I take what they have and go ahead, even knowing that the results displayed by these so-called amateur tools must always be analyzed with a grain of salt and very well contextualized to avoid erroneous and misleading interpretations.
 
just want to add about e1b1a-m2
it is possible some downstream branches of it like e-m4231 and e-L485 were
present to some extent to the north of sahara at the roman period
only up until now there is no ancient dna to back this up 🤔
 
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