Authors: IJHSB editorial board

Date: 6.2.2026

Abstract

Ancient DNA rarely survives in hot, arid settings, leaving the Holocene demographic history of the Sahara incompletely resolved. Genome-wide data from two ~7 ka BP Pastoral Neolithic women from Takarkori (southwestern Libya) provide the first ancient genome-wide (nuclear) dataset from the Central Sahara and identify a major, previously unsampled North African ancestry component. Admixture-graph modeling estimates that Takarkori derives ~93% of its ancestry from a deeply divergent North African lineage, with ~7% from a deeply ancient Levantine-related source. Takarkori shows strong affinity to Late Pleistocene Iberomaurusian-associated individuals from Taforalt Cave, supporting revised models in which Taforalt can be represented as ~60.8% Natufian-like and ~39.2% Takarkori-like ancestry. Despite increased ecological connectivity during the African Humid Period, Takarkori shows limited evidence for substantial mid-Holocene trans-Saharan admixture. Neanderthal ancestry is low but detectable in Takarkori (~0.15% for segments >0.05 cM), approximately an order of magnitude lower than in most out-of-Africa populations, and lower than Levantine farmer groups in the study’s comparisons. Collectively, these data are most consistent with cultural diffusion as a principal mechanism for the expansion of Saharan pastoralism into an established local population and underscore deep structure and regional continuity in North African prehistory.

Keywords: African Humid Period; Central Sahara; Takarkori; ancient DNA; North Africa; Taforalt; pastoralism; cultural diffusion; Neanderthal ancestry; Holocene demography.

Introduction

The Sahara’s current hyper-aridity conceals repeated late Quaternary oscillations between humid and arid phases that reshaped ecological corridors, mobility, and population structure across northern Africa. During the African Humid Period (AHP), strengthened monsoon dynamics and climate–vegetation–dust feedbacks expanded rainfall far northward, generating the “Green Sahara” and enabling widespread occupation across regions that later became desert [1,2]. Archaeological sequences from the Central Sahara, particularly stratified rockshelters in the Tadrart Acacus Mountains, document long-term settlement, broad-spectrum economies, and major cultural transitions across the early-to-mid Holocene, culminating in the consolidation of pastoral lifeways [3,4].

Despite this cultural record, the Sahara has remained underrepresented in ancient genomics because DNA preservation is generally poor in hot, arid environments. Demographic reconstructions for North Africa have therefore relied disproportionately on coastal contexts in the Maghreb and on later-period genomes. Even with limited sampling, ancient DNA shows that North Africa cannot be reduced to a single “Eurasian back-migration” narrative. Late Pleistocene individuals from Taforalt (~15 ka BP) display a complex ancestry profile that does not map neatly onto modern African or West Eurasian proxies [5]. Holocene datasets from the Maghreb indicate heterogeneous Neolithic trajectories, including local continuity in some regions and episodic gene flow from Iberia/Europe and the Levant in others [6–8].

Genetic evidence from Takarkori predates genome-wide work: mitochondrial genomes from two ~7 ka BP Takarkori individuals were previously reported, providing early genetic data for the Sahara and highlighting basal mitochondrial lineages in a Middle Pastoral context [9]. More recently, genome-wide nuclear data from two Pastoral Neolithic women buried at Takarkori provide the first ancient genome-wide (nuclear) window into the Central Sahara [10]. These data allow renewed evaluation of two persistent propositions: (i) whether the humid Sahara functioned as a demographic corridor producing substantial north–south gene flow between sub-Saharan and northern African populations during the mid-Holocene, and (ii) whether pastoralism spread into the Central Sahara primarily via demic diffusion or through cultural diffusion into established local populations.

Figure 1 provides a compact visual synthesis of the geographic setting, temporal framework, and principal inferences of this study, summarizing the Takarkori ancestry composition, the updated Taforalt mixture model, and the segment-based Neanderthal comparisons [2,5,9,10].

Figure 1. Context and key results of Central Saharan ancient genome-wide data: Takarkori ancestry composition, updated Taforalt modeling, and Neanderthal segment-based estimates.
^{A) Map of North Africa showing the locations of Takarkori (Central Sahara) and Taforalt (Maghreb), with the African Humid Period (AHP) indicated schematically as increased habitable extent [2]. B) Timeline placing Taforalt (~15 ka BP) [5] and Takarkori (~7 ka BP) [10] in relation to late Pleistocene–Holocene humid conditions (AHP); the years 2019 and 2025 denote publication years for prior mtDNA work [9] and subsequent genome-wide nuclear data [10], respectively (not years BP). C) Summary of admixture-model proportions reported for Takarkori (~93% deeply divergent North African lineage; ~7% deeply ancient Levantine-related source) and for an updated model of Taforalt (~60.8% Natufian-like; ~39.2% Takarkori-like) [10]. D) Segment-based Neanderthal ancestry estimates (>0.05 cM) showing low but detectable values in Takarkori relative to Taforalt/Neolithic Morocco and most out-of-Africa populations (comparative groups as in Salem et al. 2025) [10]. Ranges denote the spread across comparative groups (not confidence intervals). All elements are schematic and intended for conceptual orientation.}

Archaeological and paleoenvironmental context

Takarkori is among the best studied Central Saharan rockshelter sequences, preserving stratified deposits spanning substantial portions of the early-to-mid Holocene [3,4]. Paleoenvironmental analyses document local hydrological and ecological change through the AHP and its termination, providing a framework for interpreting the timing and tempo of economic and social transformations at the site and in adjacent Acacus contexts [3]. The rockshelter record also provides an unusually continuous archive in a region where many sites are open-air scatters lacking stratified sequences [4].

Biomolecular evidence reinforces the complexity of Saharan subsistence through this period. Organic residue analyses of ceramics document systematic processing of wild plant resources, including C3/C4 grasses and aquatic taxa, in Libyan Saharan contexts [11]. Separate lipid residue work provides direct evidence of dairying in green Saharan Africa by the fifth millennium BCE, indicating that milk and other secondary products were integrated into pastoral lifeways [12]. Together, these datasets support interpretations of pastoral adoption embedded within flexible local economies rather than a uniform “Neolithic package” arriving with wholesale population replacement.

Materials and analytical approach

Genome-wide nuclear data were generated from two adult female individuals dated to approximately ~7 ka BP and analyzed using standard ancient DNA authentication and SNP-based population genetic methods suited to low-coverage genomes [10]. Comparative inference drew on published ancient North African datasets (Taforalt and multiple Neolithic Maghreb contexts) [5–8], broader African ancient DNA studies (including population structure and pastoral transitions) [13–15], and Near Eastern archaeogenomic syntheses of early farming populations [16]. Neanderthal ancestry interpretation followed established principles derived from Neanderthal genome sequencing and analyses of the genomic landscape of archaic segments in present-day humans [17–20].

Results

Ancestry composition and deep divergence in Central Saharan pastoralists

Admixture-graph modeling estimates that Takarkori derives ~93% of its ancestry from a previously unsampled, deeply divergent North African lineage, with ~7% from a deeply ancient Levantine-related source [10]. The dominance of the Takarkori-related lineage indicates that Central Saharan pastoralists at ~7 ka BP cannot be parsimoniously explained as recent mixtures of better-characterized sub-Saharan and West Eurasian ancestries. While precise divergence-time estimates depend on model assumptions and the available reference panel, the requirement for a large, distinct North African component is a consistent qualitative outcome of the analysis [10].

The minor Levantine-related contribution is small relative to the dominant component and is inconsistent with large-scale demographic influx of Levantine farming or pastoralist populations into the Central Sahara by this time [10]. The “deeply ancient” characterization further indicates that the best-fitting signal reflects affinity to Levantine-related lineages used in the modeling framework, rather than identity with any single later Levantine population [10].

Relationship to Taforalt and refinement of Maghrebi Paleolithic ancestry models

Takarkori shows strong affinity to Late Pleistocene Iberomaurusian-associated individuals from Taforalt [5,10]. In earlier work, Taforalt ancestry was modeled using a combination of Near Eastern-related and sub-Saharan-related proxies, reflecting the absence of a directly sampled deep North African reference [5]. With Takarkori available as an ancient reference, the Takarkori study reports an alternative model in which Taforalt can be represented as ~60.8% (±1.8) Natufian-like Levantine ancestry and ~39.2% (±1.8) Takarkori-like deep North African ancestry [10]. This refinement implies that at least part of what proxy-based models approximated as “sub-Saharan-like” in Taforalt can be more parsimoniously explained as deep North African ancestry.

Holocene Maghreb datasets provide additional context for the variability of Neolithic demographic processes. Northwest African contexts include individuals with strong Iberian/European Neolithic contributions and later Levantine-related inputs [6,7], whereas eastern Maghreb contexts exhibit relatively high continuity with local forager ancestry and smaller external contributions [8]. Takarkori supplies a geographically central ancient anchor for deep North African ancestry and improves identifiability of mixture models in a region where reference bias has historically been a major limitation [10].

Constraints on mid-Holocene trans-Saharan admixture

Despite increased ecological connectivity during the AHP, the Takarkori genomes provide limited support for substantial mid-Holocene trans-Saharan admixture from sub-Saharan lineages at a scale that would dominate genome-wide ancestry profiles [10]. This should be treated as a constraint rather than a universal claim: two individuals from one locality and time slice do not exclude localized or low-level gene flow elsewhere or at other periods. Nevertheless, the absence of a major sub-Saharan ancestry component in Takarkori places an empirical bound on models positing that the Central Sahara served as a principal conduit producing extensive north–south demographic mixing by ~7 ka BP [10]. More generally, African ancient DNA studies indicate that deep regional structure can persist across long timescales and that admixture histories are strongly contingent on local geography and timing [14,15].

Neanderthal ancestry: low but detectable, and quantitatively bounded

Takarkori is not “Neanderthal-free.” Using segment-based estimates for segments >0.05 cM, Takarkori carries ~0.15% Neanderthal ancestry [10]. The same study reports higher values for Taforalt and Neolithic Moroccan individuals (~0.6–0.9%), and substantially higher levels in out-of-Africa populations (~1.4–2.36%) under comparable criteria [10]. In this framework, Takarkori is approximately an order of magnitude lower than most out-of-Africa populations, and is also lower than Levantine farmer groups in the study’s comparisons [10].

The admixture-graph results provide a coherent interpretation: the dominant Takarkori-like component likely contributed little Neanderthal ancestry, whereas the minor Levantine-related input is compatible with introducing a small, detectable archaic signal [10]. This interpretation accords with established findings that archaic segment abundance and genomic distribution reflect both admixture proportion and time depth [18,19].

Implications for the spread of pastoralism

Biomolecular evidence establishes dairying in green Saharan Africa by the fifth millennium BCE [12], but does not, by itself, distinguish cultural from demographic mechanisms. The ancestry composition reported for Takarkori (~93% deep North African; ~7% Levantine-related) is difficult to reconcile with models in which pastoralism arrived primarily through large-scale migration of Levantine farmers or pastoralists into the Central Sahara by ~7 ka BP [10]. Instead, the Takarkori data are most consistent with pastoral lifeways expanding largely through cultural diffusion into a resident population dominated by deep local ancestry [10].

Comparative African evidence underscores that pastoral transitions are not uniform. In eastern Africa, ancient DNA indicates multi-step processes involving admixture among incoming and local groups during pastoral expansions [13], whereas Neolithic Maghreb histories range from substantial external input in some contexts to relatively high continuity in others [6–8]. Takarkori contributes a Central Saharan case in which major economic change appears to have proceeded with limited genome-wide demographic replacement.

Discussion

The Takarkori genome-wide data revise demographic baselines for Holocene North Africa by demonstrating that a deeply divergent North African lineage persisted into the Pastoral Neolithic and dominated ancestry in the Central Sahara at ~7 ka BP [10]. This elevates the Sahara’s interior from a major sampling gap to a key locus of population history and indicates that long-lived regional substrates existed beyond the better-sampled coastal Maghreb. The affinity between Takarkori and Taforalt provides temporal depth and geographic linkage, and the revised Taforalt model (~60.8% Natufian-like; ~39.2% Takarkori-like) illustrates how adding a missing ancient reference can change the interpretation of ancestry components previously approximated using proxy sources [10].

The Takarkori data also qualify a common inference that the Green Sahara necessarily produced extensive demographic mixing between sub-Saharan and northern African populations. Increased habitability likely facilitated movement and exchange; however, Takarkori is inconsistent with large-scale sub-Saharan ancestry contributions into the Central Sahara by ~7 ka BP [10]. This is compatible with broader African archaeogenomic findings that deep regional structure can persist across the Holocene and that admixture histories are regionally contingent [14,15]. Cultural interaction and demographic exchange are therefore not interchangeable processes, and Takarkori provides a direct constraint on the scale of demographic mixing required for at least one Central Saharan pastoral context.

Neanderthal ancestry provides an additional quantitative constraint and corrects overly absolute framings. These values derive from segment-based inference using a >0.05 cM threshold and should be interpreted within that measurement framework [10]. Takarkori carries low but detectable Neanderthal ancestry (~0.15% for segments >0.05 cM), substantially below the values reported for Taforalt/Neolithic Moroccan individuals (~0.6–0.9%) and for most out-of-Africa populations (~1.4–2.36%) by comparable criteria [10]. The most parsimonious interpretation is that the dominant Takarkori-like lineage contributed little Neanderthal ancestry, while minor Levantine-related gene flow accounts for the small detectable signal [10]. This interpretation is consistent with foundational results showing that archaic segment abundance and distribution encode both admixture proportion and time depth [18,19].

These demographic constraints bear directly on the mechanism of pastoral expansion. Evidence for dairying demonstrates established pastoral economies [12], while Takarkori ancestry composition argues against substantial population replacement by Levantine-related groups in the Central Sahara by ~7 ka BP [10]. A model of cultural diffusion—transfer of domesticates, herding knowledge, and practices through networks of contact and limited mobility—better matches the genomic pattern observed at Takarkori. Comparative results from eastern Africa, where pastoral expansion is accompanied by detectable admixture, reinforce that pastoralism can spread via diverse combinations of cultural transmission and population movement, rather than a single universal pathway [13].

Limitations remain inherent to the evidence. Two individuals cannot capture the full spatial and temporal range of the Sahara across millennia of climatic change, and admixture graphs represent structured hypotheses rather than uniquely identifiable histories. Nonetheless, the Takarkori genome-wide data establish the existence and mid-Holocene persistence of a deep North African lineage and provide a critical reference point that will improve model identifiability as additional Saharan and adjacent datasets become available [10].

Conclusion

Ancient genome-wide (nuclear) data from two ~7 ka BP Pastoral Neolithic women from Takarkori provide the first such dataset from the Central Sahara and identify a predominant, deeply divergent North African lineage. Admixture modeling estimates ~93% ancestry from this lineage and ~7% from a deeply ancient Levantine-related source [10]. Takarkori’s affinity to Taforalt supports revised models of Maghrebi Paleolithic ancestry, including an alternative fit in which Taforalt can be represented as ~60.8% Natufian-like and ~39.2% Takarkori-like ancestry [10]. Despite increased ecological connectivity during the AHP, Takarkori shows limited evidence for substantial mid-Holocene trans-Saharan admixture [10]. Neanderthal ancestry in Takarkori is low but detectable (~0.15% for segments >0.05 cM), approximately an order of magnitude lower than in most out-of-Africa populations and lower than Levantine farmer groups in the study’s comparisons [10]. Collectively, these findings support cultural diffusion as a principal mechanism for the spread of pastoralism into an established Saharan population and underscore the importance of deep structure in North African prehistory.

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References

1. Kuper R, Kröpelin S. Climate-controlled Holocene occupation in the Sahara: motor of Africa’s evolution. Science. 2006;313(5788):803–807. doi:10.1126/science.1130989
2. Tierney JE, Pausata FSR, deMenocal PB. Rainfall regimes of the Green Sahara. Sci Adv. 2017;3:e1601503. doi:10.1126/sciadv.1601503
3. Cremaschi M, Zerboni A, Mercuri AM, et al. Takarkori rock shelter (SW Libya): an archive of Holocene climate and environmental changes in the central Sahara. Quat Sci Rev. 2014;101:36–60. doi:10.1016/j.quascirev.2014.07.004
4. Biagetti S, di Lernia S. Holocene deposits of Saharan rock shelters: the case of Takarkori and other sites from the Tadrart Acacus Mountains (Southwest Libya). Afr Archaeol Rev. 2013;30(3):305–338. doi:10.1007/s10437-013-9138-z
5. van de Loosdrecht MS, Bouzouggar A, Humphrey L, et al. Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Science. 2018;360(6388):548–552. doi:10.1126/science.aar8380
6. Simões LG, Günther T, Martínez Sánchez RM, et al. Northwest African Neolithic initiated by migrants from Iberia and Levant. Nature. 2023;618:550–556. doi:10.1038/s41586-023-06166-6
7. Fregel R, Méndez FL, Bokbot Y, et al. Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe. Proc Natl Acad Sci U S A. 2018;115(26):6774–6779. doi:10.1073/pnas.1800851115
8. Lipson M, Ringbauer H, Lucarini G, et al. High continuity of forager ancestry in the Neolithic period of the eastern Maghreb. Nature. 2025;641(8064):925–931. doi:10.1038/s41586-025-08699-4
9. Vai S, Sarno S, Lari M, et al. Ancestral mitochondrial N lineage from the Neolithic ‘green’ Sahara. Sci Rep. 2019;9:3530. doi:10.1038/s41598-019-39802-1
10. Salem N, van de Loosdrecht MS, Sümer AP, et al. Ancient DNA from the Green Sahara reveals ancestral North African lineage. Nature. 2025;641(8061):144–150. doi:10.1038/s41586-025-08793-7
11. Dunne J, Mercuri AM, Evershed RP, Bruni S, di Lernia S. Earliest direct evidence of plant processing in prehistoric Saharan pottery. Nat Plants. 2016;3:16194. doi:10.1038/nplants.2016.194
12. Dunne J, Evershed RP, Salque M, et al. First dairying in green Saharan Africa in the fifth millennium BCE. Nature. 2012;486(7403):390–394. doi:10.1038/nature11186
13. Prendergast ME, Lipson M, Sawchuk EA, et al. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. Science. 2019;365(6448):eaaw6275. doi:10.1126/science.aaw6275
14. Skoglund P, Thompson JC, Prendergast ME, et al. Reconstructing prehistoric African population structure. Cell. 2017;171(1):59–71.e21. doi:10.1016/j.cell.2017.08.049
15. Lipson M, Sawchuk EA, Thompson JC, et al. Ancient DNA and deep population structure in sub-Saharan African foragers. Nature. 2022;603(7900):290–296. doi:10.1038/s41586-022-04430-9
16. Lazaridis I, Nadel D, Rollefson G, et al. Genomic insights into the origin of farming in the ancient Near East. Nature. 2016;536:419–424. doi:10.1038/nature19310
17. Green RE, Krause J, Briggs AW, et al. A draft sequence of the Neandertal genome. Science. 2010;328(5979):710–722. doi:10.1126/science.1188021
18. Prüfer K, Racimo F, Patterson N, et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014;505(7481):43–49. doi:10.1038/nature12886
19. Sankararaman S, Vernot B, Patterson N, et al. The genomic landscape of Neanderthal ancestry in present-day humans. Nature. 2014;507:354–357. doi:10.1038/nature12961
20. Vernot B, Akey JM. Resurrecting surviving Neandertal lineages from modern human genomes. Science. 2014;343(6174):1017–1021. doi:10.1126/science.1245938