The upcoming study titled “Genome-wide ancient DNA data from two 7,000-year-old individuals from Takarkori Rockshelter in Libya, and Archaic admixture capture data from seven 15,000-year-old individuals from Taforalt Cave, Morocco.” teased the affinities of Saharan samples discovered at Takarkori rock shelter of modern day southern Libya. Mentioned before in a previous post of ours, ancient individuals from that site should help us understand and grasp the origins of modern day Africans. Though my post was titled “Modern West Africans are not a mystery” it was still to be seen how exactly new findings would fit in with the known African genetic landscape. After all, the work done on Revoiye previously was predictive and not entirely indicative of what will unfold. I’m glad to report, or at least suggest that said predictions were indeed quite indicative as the new sample from Takarkori seems to fit right in to the previous models suggested in a way so expected… it was quite unexpected.
click to see figure 1: admixture showing how the Takarkori RS individual fits in previous model
The samples were uploaded to the European Nucleotide Archive in February of 2025 along with novel reads and sequences from previously reported samples from Taforalt de pigeons.1 In this preliminary analysis we’ll simply look at the data as is with no fancy processing or phasing for downstream work. Psuedo-haploid calls were made using the methods seen in many modern aDNA studies and as per usual for this style of analysis and they were merged with our previous datasets.2
QpGraph3,4 results seem to suggest what was predicted prior; that ancient Saharans had a resemblance to modern day Nilo-Saharan-Chadic speakers but with a sort of Affinity towards Pleistocene and early Neolithic North Africans.5 It seems even more clear that more recent Africans in the region received ancestry from a source which brought more relic features evidenced by the seemingly lack of evidence for such features in sample TKH001. This is a phenomena noticed and reported on before morphologically when looking at the transition from Neolithic Saharans to Iron-Age Saharans like the Garamantes6,7; supposed linked to modern Tuareg and Toubou populations8–13. What we had could be a possible continuum of ancestry interrupted by ancestry still a bit unknown which likely came from south of the Sahara.
Metric data were taken on 2 adult individuals from Takarkori, namely RS-H1 (female, 30-35 years) and RS- H9 (female, 30-35 years). The comparative samples come from: the Garamantian site of Fewet, N=147; the funerary area near Tahala; the Wadi el-Ajal, N=24 (Garamantian sample); the sub-Saharan site of Gobero represented by two different phases of human occupation, namely the early Holocene (Kiffian) and the Mid-Holocene sample from Gobero B. In addition, the adult male individual from Herto, Middle-Awash valley in Ethiopia, was pooled as out-group on the basis of its archaic cranial morphology and its very ancient chronology: it is dated to between 160,000 and 154,000 years ago.
Populations from the Fezzan such as Fewet, Wadi-el-Ajal and Tahala, much younger chronologically than the Takarkori sample, are separated from it (according to the length of the branches that are proportional to the Euclidean distances between the metrical variables) and are, by contrast, more in relationship with one of the earliest representatives of our species such as the cranium from Herto. Paradoxically, therefore, although more recent than the two women from Takarkori, samples from this time period appear more “archaic” and closer to the root of the tree. We speculate that this occurrence is probably in relationship with the expression of recessive phenotypic features, which in turn suggests a certain degree of geographic and genetic isolation. It is likely, vice versa, that the great variability displayed by Middle Pastoral populations (represented in our preliminary analysis by Takarkori and Gobero B) have spread over a large territory thanks to favorable climatic conditions. This could have increased levels of gene flow, producing a high phenotypic variability of the skeletal material associated with these human populations of the “Green Sahara”.
Di Vincenzo, Fabio 2015
While it is possible that these individuals at Takarkori remained isolates, its seems even more likely that genetically similar people of the Sahara went on to contribute substantial amount of ancestry to East African Pastoralists like the Nilotic populations of Sudan and South Sudan and decent amount of ancestry to West Africans and in turn Bantu speakers.
The results show an ambiguous relationship between TKH001 and Pleistocene Maghreb populations. While both can generate acceptable models using ancestry from each other, we can’t report that either 2-way model exists as they purport a certain degree of anachronism. Nonetheless they both would score high for outlying ancestry; being 50% Nilotic and the other 41% Levantine farmer (Natufian) for Takarkori and Ifri Ouberrid respectively.
Figure 2: Proposed Phylotree Modeling West African, Prehistoric North African and Nilotic Ancestries updated with evidence from holocene Sahrans . Theoretical populations associated with Ancestral North African (ANA) are colored blue. Said populations with clear affinities to contemporary Africans are colored cyan. Admixture is denoted by broken lines dotted or dashed. More theoretical admixture weights have grayed edges.
More clarity on ANA.
It seems to be the case that ANA is comprised of a varying degree of potentially differentiated ancestry vaguely related to both Sub-Saharan Africans and MENA (Middle East and North African) populations.14,15 As far as this sample is concerned, a cohort of Ancestry can be clearly defined. We labeled this ancestry ‘Early Saharan African’ here. This is not to include ancestry types possibly included in the Iberomaurasian with different paths and relatedness to both SSA and West Eurasian populations. I’m referring to outlying archaic ancestry, potential ghost or basal African ancestry, and Natufian or WHG-related ancestry not entirely found or discoverable in Early Saharan Africans. What should also be noted is the small population sizes coupled with relative isolation over long periods of time for the Iberomaurasian. Their high genetic differentiation seen across many studies could be due to a couple of factors mentioned previously, and until more resolution is provided, it remains uncertain which signatures are indicative of ancestry from which known population. To be clear, “Ancestral North African” was simply an umbrella term used to describe ancestry not (putative) West Eurasian in Pleistocene and Early Neolithic North African populations.
Table 1. qpAdm estimates for TKH001, Taforalt, Natufian & an individual from Kakapeli rock shelter in western Kenya. Only best 2 way ancestry models of select populations were shown. All 3 way models involving the 5 candidate populations could safely be rejected due to low significance. Bold numbers in the p-val column indicates a statistically significant model. See Below for information on reference populations.
Our very own ANA estimates took that into account by trying to control for known Basal and Central African ancestry which could be captured in Taforalts “ANA” ancestry. The results then suggested high affinity with Sudanese Pastoralists when allowing for east African ancestry not necessarily represented in North Africans to be represented. We see a similar pattern now that the Takarkori individual can represent their ancestry. It seems quite clear that the ANA population that we were testing for and predicting to exist is well represented by the Takarkori individual. Judging by the ancestral estimates provided by the admixtures graphs, roughly 71% of TKH001’s ancestry could be categorized as ANA. Therefore it seems appropriate given the age, location and lithics of the sample, to refer to such ancestry type as Saharan African.
Another thing to note is the major affinity TKH001 has to KPL003 a 900 year old individual found in Kenya Kakapeli Rockshelter. The individual was likely descended from Similar Saharan populations given the statistical likelihood (p 0.93) that Takarkori contributed around81.5% of their DNA to them (other 18.5% related to Earlier individuals from the same site). Said individual was also predicted to have some of the highest proportion of ANA in our previous report. This is a pattern that will likely continue with populations like the Oromo, Toubou, and Pastoral Neolithic East Africans.
Figure 3: Admixture graph with only 9 admixture events including Africans and West Eurasians. (click to hide)
9 admixture events fitting
Supplementary data and information
Here and below are a list of admixture graphs showing how TKRSH1 and Oub02 (Morocco Epipaleolithic) clusters with various Africans and West Eurasians. Graphs with the best scores have been plucked out and presented here. Download links for png versions of each graph is available below Each graph.
Figure 5.
Figure 6.
Figure 10.
Figure 11.
Methods and right populations for qpADM
To formulate the graphs I used the “qpgraph” and “findgraph” functions of the admixtools2 package as done here. Positioning in the charts were mostly generated using “findgraph” functions and final graphs were calculated using “qpgraph.” Initial graph positioning per population was posited by a previous run (figure 7). Multiple graphs were printed for each iteration to which they were compared and selected for analysis by virtue of “qpgraph_resample_multi” and “compare_graphs” functions. Charts with the lowest inverse likelihood scores were selected at each step. qpAdm was ran from the original admixtool package. Left populations where permutations of the test samples in table 1. Right populations were: China_Tianyuan (outgroup), Ust_Ishim.DG, Russia_Afanasievo.DG, Romania_IronGates_Mesolithic, Luxembourg_Loschbour.DG, Laos_Hoabinhian, Japan_Jomon.SG, Ethiopia_4500BP.DG, Cameroon_SMA.DG, BallitoBay and TUR_Pınarbaşı_EpiP (When not included in Left pop permutation).
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