Study:Ancient DNA from the Green Sahara reveals ancestral North African lineage

[Gannicus]

Not sure if this study has been shared on here yet.

https://www.nature.com/articles/s41586-025-08793-7


Just came across a really interesting study not too long ago that was published in Nature (April 2025) that might reshape how we understand Ancient North African ancestry (ANA). It focuses on two ~7,000 year old female individuals from the Takarkori rock shelter in southwestern Libya, during the African Humid Period when the Sahara was green.

These individuals don’t show any significant Sub-Saharan African ancestry or signs of Levantine Neolithic farmer admixture. Instead, their DNA represents a deeply divergent North African lineage, what we’ve been calling ANA, that was likely widespread across the Sahara before the arrival of agriculture.

What makes it especially interesting is that the Takarkori individuals carry a trace amount of Neanderthal ancestry, which is the smoking gun for Out-of-Africa origin. Sub-Saharan Africans don’t have this, so the only way this DNA shows up is through a Eurasian population moving back into Africa, then staying relatively isolated.

The authors suggest that this ANA ancestry:

- Split from Sub-Saharan Africans around the same time that Eurasian ancestors did

- Probably represents an early Eurasian return into North Africa, well before the Neolithic

-Is genetically related to the Iberomaurusians from Taforalt from around 15,000 years ago, who show a similar mix of West Eurasian-like and deep African ancestry





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?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



I labeled the two samples that could be the right scaled coordinates "?" & "?2". Which ones are the correct scaled coordinates?



Distance to: Gannicus_MergedFile_officialDavidski_scaled
0.24842112 Libya_Takarkori_N:TKH001?
0.24845114 Libya_Takarkori_N:TKH001_tr.SG.TW?2
0.61238556 Libya_Takarkori_N:TKH001
0.61245699 Libya_Takarkori_N:TKH001_tr_all
0.61524935 Libya_Takarkori_N:TKH001_tr.SG.TW

[Gannicus]

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
Luxembourg_Loschbour.DG,0.130897,0.109677,0.203645 ,0.198,0.162492,0.059125,0.015041,0.038075,0.10021 7,0.016219,-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
GEO_Dzudzuana_UP_26kya:S2949,0.062603,0.099522,-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
ANE:RUS_AfontovaGora3_17kya:AfontovaGora3,0.093335 ,-0.01828,0.083344,0.231592,-0.091402,0.042949,-0.063688,-0.078228,-0.035383,-0.096221,0.047417,-0.0105,0.023637,-0.074454,0.020358,0.02254,-0.012908,0.003801,-0.003394,0.000625,-0.03706,0.015209,0.013927,0.009278,-0.005149
CMR_Shum_Laka:I10871_new_all,-0.607815,0.053823,0.013199,0.027132,0.000308,0.004 183,0.131371,-0.102688,0.009408,-0.008565,-0.00341,-0.025777,-0.020664,-0.006055,-0.001357,-0.00053,0.011995,0.022804,-0.005656,5e-04,-0.004617,0.000124,0.000616,-0.001205,-0.005748
ETH_Mota:I5950_new_WGS.SG,-0.515619,0.041637,-0.003394,-0.001292,-0.00277,-0.011713,0.054992,-0.052382,0.090604,-0.094581,-0.013478,0.003297,-0.031962,-0.001927,0.023615,-0.031291,0.031944,0.043454,-0.002388,-0.00963,-0.001248,0.00643,-0.005176,-0.003133,0.004071
BEL_GoyetQ116-1:Q116-1_28kya,0.043253,-0.005078,0.003017,0.093993,0.045547,0.001952,-0.00517,-0.000692,0.065857,0.024055,0.00341,0.000899,0.0093 66,-0.022983,0.019137,0.017634,0.011865,0.004561,-0.006034,0.034767,0.026079,0.002473,-0.023664,-0.061695,0.003712
BEL_GoyetQ2:GoyetQ2_35kya,0.071709,0.03859,0.06712 7,0.122095,0.085554,0.016176,-0.00188,0.006923,0.079764,0.015855,-0.013478,-0.017085,0.009217,-0.019267,0.044245,0.036197,0.002217,0.003547,-0.009302,0.045272,0.054778,0.003215,-0.034263,-0.101942,0.011376
Russia_Karelia_HG:I0061,0.125205,0.034528,0.137272 ,0.204137,-0.015695,0.057451,-0.026791,-0.03046,-0.01084,-0.090571,0.025982,-0.009591,0.022745,-0.048581,0.019679,0.016309,-0.022426,0.0019,-0.006913,0.017258,-0.004617,0.011747,0.007025,-0.020485,-0.008502
Israel_Natufian_d:I1072_enhanced_d,0.037562,0.1553 76,-0.023381,-0.137276,0.043085,-0.083388,-0.017861,-0.012923,0.124555,0.015672,0.030042,-0.020382,0.082209,0,0.003257,-0.012861,-0.008866,-0.010515,-0.017221,0.021385,0.015348,0.001855,0.008504,0.003 735,0
AHG:TUR_Pinarbasi_HG:ZBC_IPB001,0.114961,0.167562, 0.03017,-0.08075,0.072629,-0.039881,-0.00047,0.000231,0.046836,0.083282,0.004222,0.0077 93,-0.02215,-0.011836,-0.041123,-0.003845,0.043027,0.00114,0.008799,-0.004252,-0.011729,0.006801,-0.006286,-0.010122,-0.007784
Iran_GanjDareh_N:I1290,0.037562,0.072103,-0.154997,-0.007429,-0.122484,0.01255,0.015746,-0.005077,-0.081196,-0.050662,0.005521,-0.005995,0.008028,-0.017478,0.024837,0.068151,-0.006519,0.010642,0.01433,-0.035892,0.011355,-0.025102,-0.016638,-0.040006,0.029458
Italy_North_Villabruna_HG,0.121791,0.11577,0.18592 ,0.185726,0.156029,0.060798,0.017626,0.041537,0.09 3467,0.017859,-0.015752,-0.015886,0.020961,-0.005092,0.05361,0.064041,0.007562,0.004181,-0.00905,0.053401,0.099949,0.012489,-0.044123,-0.169904,0.018801


In this list are the proper scaled G25 coordinates (I think) for the Takarkori individuals

What I score compared to other populations like WHGs,EHGs,AHG,Natufian, Shum Laka (SSA) etc. :

Distance to: Gannicus_MergedFile_officialDavidski_scaled
0.13871696 GEO_Dzudzuana_UP_26kya:S2949
0.18631845 AHG:TUR_Pinarbasi_HG:ZBC_IPB001
0.21751062 BEL_GoyetQ116-1:Q116-1_28kya
0.22282728 BEL_GoyetQ2:GoyetQ2_35kya
0.24842112 Libya_Takarkori_N:TKH001?
0.24845114 Libya_Takarkori_N:TKH001_tr.SG.TW?2
0.26209452 Russia_Karelia_HG:I0061
0.28655282 Israel_Natufian_d:I1072_enhanced_d
0.32966287 Iran_GanjDareh_N:I1290
0.34214606 ANE:RUS_AfontovaGora3_17kya:AfontovaGora3
0.34358103 Italy_North_Villabruna_HG
0.37043055 Luxembourg_Loschbour.DG
0.68188151 ETH_Mota:I5950_new_WGS.SG
0.76776969 CMR_Shum_Laka:I10871_new_all

[Gannicus]

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 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.

�� How to Interpret G25 Distances
✅ General Guide for Interpreting G25 Scaled Distances:
Distance Interpretation
< 0.05 Essentially identical or very close relatives (modern intra-population or parent-child level)
0.05–0.10 Same ethnic group or nation — close modern population
0.10–0.20 Regionally related — likely same broad ancestry cluster
0.20–0.30 Distantly related — but still part of the same continental or subcontinental clade
0.30–0.40 Drifted or highly admixed relatives — possibly shared ancestry deep in time (~10,000+ years)
> 0.40 Little to no meaningful autosomal relatedness — major clade separation (e.g. SSA vs WHG vs ENA)



I'll give an example:

Distance to: Gannicus_MergedFile_officialDavidski_scaled
0.23204834 Yemenite_Amran
0.24255565 Yemenite_Dhamar
0.24384723 Yemenite_Al_Bayda
0.24665981 Yemenite_Ma'rib
0.24790571 Yemenite_Al_Jawf
0.25796502 Yemenite_Mahra


All Europeans and Near Easterners are classified as West Eurasians. Which is not just a geographic label. It refers also to the genetic interconnectedness of the peoples within the region. My distance to the Yemenis is less than 0.3. Indicating we are both within the same population classification. The reason for this is the common OoA source and neolithic near eastern farmers moving in to Europe. The Near Eastern farmers carried not just Anatolia Neolithic ancestry, but also some Natufian as well. Yemenis possess a high level of Natufian admixture. This is where our connection comes from and also gene flow from the near east into Europe in post neolithic periods, such as Phoenician trade/colonization and Mediterranean interactions during the Hellenistic and Roman periods.