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High continuity of forager ancestry in the Neolithic period of the eastern Maghreb

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Abstract

Ancient DNA from the Mediterranean region has revealed long-range connections and population transformations associated with the spread of food-producing economies1,2,3,4,5,6. However, in contrast to Europe, genetic data from this key transition in northern Africa are limited, and have only been available from the far western Maghreb (Morocco)1,2,3. Here we present genome-wide data for nine individuals from the Later Stone Age through the Neolithic period from Algeria and Tunisia. The earliest individuals cluster with pre-Neolithic people of the western Maghreb (around 15,000–7,600 years before present (bp)), showing that this ‘Maghrebi’ ancestry profile had a substantial geographic and temporal extent. At least one individual from Djebba (Tunisia), dating to around 8,000 years bp, harboured ancestry from European hunter–gatherers, probably reflecting movement in the Early Holocene across the Strait of Sicily. Later Neolithic people from the eastern Maghreb retained largely local forager ancestry, together with smaller contributions from European farmers (by around 7,000 years bp) and Levantine groups (by around 6,800 years bp), and were thus far less impacted by external gene flow than were populations in other parts of the Neolithic Mediterranean.

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Fig. 1: Summary of the dataset.
Fig. 2: PCA results.
Fig. 3: Inferred ancestry proportions from qpAdm.
Fig. 4: ROH and IBD results.

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Data availability

The aligned sequences for the newly reported individuals are available through the European Nucleotide Archive under accession number PRJEB83667. Genotype data used in the analysis of the newly reported individuals are available through Dataverse (https://doi.org/10.7910/DVN/ILWB3K). The previously published data used in our analyses are available at the following: Allen Ancient DNA Resource (https://doi.org/10.7910/DVN/FFIDCW); western Maghreb ancient DNA data2, European Nucleotide Archive accession number PRJEB59008); 1000 Genomes haplotype reference panel (http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/); human reference genome hg19 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.13/); mitochondrial reference genome RSRS (https://doi.org/10.1016/j.ajhg.2012.03.002); YFull YTree phylogeny (https://www.yfull.com/tree/); and ISOGG Y-chromosome SNPs (https://ybrowse.org/). Open-science principles require making all data used to support the conclusions of a study maximally available, and we support these principles here by making fully publicly available not only the digital copies of the molecules (the uploaded sequences), but also the molecular copies (the ancient DNA libraries themselves, which constitute molecular data storage). Those researchers who wish to carry out deeper sequencing of libraries published in this study should make a request to corresponding author D.R. We commit to granting reasonable requests as long as the libraries remain preserved in our laboratories, with no requirement that we be included as collaborators or co-authors on any resulting publications.

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Acknowledgements

We are grateful to the current and former INP general directors, T. Baccouche and F. Mahfoudh, for their support; to S. Mulazzani for groundbreaking archaeological research in Tunisia that catalyzed this research; and to A. Marsilio for her key role in the excavation of DEK in 2022. We thank B. Barich and C. Broodbank for fruitful discussions that enriched this work. We acknowledge K. Callan, E. Curtis, A. M. Lawson, L. Qiu, J. N. Workman, F. Zalzala, R. Bernardos and A. Kearns for wet laboratory work and sample management, and M. Mah, A. Micco, G. Soos, Z. Zhang and I. Lazaridis for bioinformatics work. We thank A. Cervi for processing the DEK site plan image. The Northern Tunisia Archaeological Project received funding from the Italian Ministry of Foreign Affairs and International Cooperation, CNR and ISMEO. We are grateful for support from National Institutes of Health grant HG012287, from the Allen Discovery Center programme (a Paul G. Allen Frontiers Group advised programme of the Paul G. Allen Family Foundation), from John Templeton Foundation grant 61220, and from the Howard Hughes Medical Institute.

Author information

Author notes

  1. These authors jointly supervised this work: Giulio Lucarini, Swapan Mallick, Nadin Rohland, Alfredo Coppa, Ron Pinhasi, David Reich

Authors and Affiliations

  1. Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA

    Mark Lipson, Harald Ringbauer & David Reich

  2. Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

    Harald Ringbauer

  3. National Research Council of Italy, Institute of Heritage Science (CNR-ISPC), Rome, Italy

    Giulio Lucarini

  4. ISMEO – The International Association for Mediterranean and Oriental Studies, Rome, Italy

    Giulio Lucarini

  5. Institut National du Patrimoine (INP), Tunis, Tunisia

    Nabiha Aouadi, Ariane-Rym Dahmani, Nabila Mansouri & Fatma Touj

  6. UMR 7206 Éco-Anthropologie, équipe ABBA, CNRS-Muséum National d’Histoire Naturelle, Musée de l’Homme, Paris, France

    Louiza Aoudia

  7. Centre National de Recherche Préhistorique, Anthropologique et Historique (CNRPAH), Algiers, Algeria

    Louiza Aoudia

  8. Sousse Archaeological Museum, Sousse, Tunisia

    Lotfi Belhouchet

  9. Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria

    Olivia Cheronet, Alfredo Coppa & Ron Pinhasi

  10. Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, Vienna, Austria

    Olivia Cheronet & Ron Pinhasi

  11. Italian Institute of Oriental Studies, Sapienza University of Rome, Rome, Italy

    Francesco Genchi

  12. Department of Environmental Biology, Sapienza University of Rome, Rome, Italy

    Francesco La Pastina, Michaela Lucci & Alfredo Coppa

  13. Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, STEBICEF, University of Palermo, Palermo, Italy

    Francesco La Pastina

  14. Institut de Paléontologie Humaine (IPH), Fondation Albert–1Er Prince de Monaco, Paris, France

    Henry de Lumley

  15. Centre Européen de Recherches Préhistoriques de Tautavel (CERPT), Tautavel, France

    Henry de Lumley

  16. Department of Odontostomatological and Maxillo Facial Sciences, Sapienza University of Rome, Rome, Italy

    Alessia Nava

  17. Department of Genetics, Harvard Medical School, Boston, MA, USA

    Swapan Mallick, Nadin Rohland & David Reich

  18. Broad Institute of Harvard and MIT, Cambridge, MA, USA

    Swapan Mallick, Nadin Rohland & David Reich

  19. Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA

    Swapan Mallick & David Reich

  20. Department of Law and Digital Society, Unitelma Sapienza, Rome, Italy

    Alfredo Coppa

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  1. Mark Lipson
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Contributions

A.C., R.P. and D.R. designed the study. O.C., S.M., N.R., R.P. and D.R. generated the ancient DNA data. G.L., N.A., L.A., L.B., A.-R.D., F.G., F.L.P, M. Lucci, H.d.L., A.N., A.C. and R.P. were responsible for archaeological and bioanthropological analysis. G.L., N.A., L.A., A.-R.D., F.G., F.L.P., N.M. and F.T. excavated the sites. M. Lipson and H.R. conducted the formal analysis. M. Lipson, H.R., G.L. and A.C. wrote the original manuscript. M. Lipson, G.L., A.C., R.P. and D.R. reviewed and edited the paper. G.L., S.M., N.R., A.C., R.P. and D.R. supervised the study. G.L., A.C., R.P. and D.R. were responsible for funding acquisition.

Corresponding authors

Correspondence to Mark Lipson, Giulio Lucarini, Alfredo Coppa, Ron Pinhasi or David Reich.

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The authors declare no competing interests.

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Nature thanks Rosa Fregel and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data figures and tables

Extended Data Fig. 1 View of the Djebba Shelter.

Shown is an exterior view of the site of the excavations at Djebba (Tunisia).

Extended Data Fig. 2 Site plan from Doukanet el Khoutifa (DEK).

Shown is a diagram of the excavations from 2013, with the cemetery area indicated with a red rectangle.

Extended Data Fig. 3 Burial 2 from Hergla (SHM-1).

Shown is the skeleton of the individual sampled for ancient DNA in this study.

Extended Data Fig. 4 Comparative ROH results for the western Maghreb.

Left side, inferred runs of homozygosity (ROH) for ancient individuals from the western Maghreb; right side, expected distributions under different scenarios. Three individuals have signatures of likely parental relatedness: TAF010 and oub002 (first-cousin parents), and ktg005 (second-cousin parents).

Extended Data Table 1 Radiocarbon dates and uniparental markers for newly reported ancient individuals
Full size table
Extended Data Table 2 Radiocarbon dating of the different levels of the Afalou Bou Rhummel shelter
Full size table
Extended Data Table 3 Distribution and types of burials at the Afalou Bou Rhummel site
Full size table

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Lipson, M., Ringbauer, H., Lucarini, G. et al. High continuity of forager ancestry in the Neolithic period of the eastern Maghreb. Nature (2025). https://doi.org/10.1038/s41586-025-08699-4

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