Abstract
The maritime Phoenician civilization from the Levant transformed the entire Mediterranean during the first millennium bce1,2,3. However, the extent of human movement between the Levantine Phoenician homeland and Phoenician–Punic settlements in the central and western Mediterranean has been unclear in the absence of comprehensive ancient DNA studies. Here, we generated genome-wide data for 210 individuals, including 196 from 14 sites traditionally identified as Phoenician and Punic in the Levant, North Africa, Iberia, Sicily, Sardinia and Ibiza, and an early Iron Age individual from Algeria. Levantine Phoenicians made little genetic contribution to Punic settlements in the central and western Mediterranean between the sixth and second centuries bce, despite abundant archaeological evidence of cultural, historical, linguistic and religious links4. Instead, these inheritors of Levantine Phoenician culture derived most of their ancestry from a genetic profile similar to that of Sicily and the Aegean. Much of the remaining ancestry originated from North Africa, reflecting the growing influence of Carthage5. However, this was a minority contributor of ancestry in all of the sampled sites, including in Carthage itself. Different Punic sites across the central and western Mediterranean show similar patterns of high genetic diversity. We also detect genetic relationships across the Mediterranean, reflecting shared demographic processes that shaped the Punic world.
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Data availability
Open science principles require making all data used to support the conclusions of a study fully available, and we support these principles here by making publicly available not only the digital copies of molecules (the uploaded sequences) but also the molecular copies (the aDNA libraries themselves, which constitute molecular data storage). Researchers who wish to carry out deeper sequencing of libraries published in this study should make a request to the 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. The raw DNA sequences for individuals newly sequenced in this study are deposited in the European Nucleotide Archive under accession number PRJEB86313. Their processed genotype data in pseudohaploid eigenstrat format can be obtained from the Harvard Dataverse repository (https://doi.org/10.7910/DVN/UPDESR). We include other newly reported data such as radiocarbon dates and archaeological context information in the Article and its Supplementary Information. We plotted the maps in Figs. 1 and 4 using the Python package basemap. The land-sea mask, coastline, lake, river and political boundary data are extracted from the GSHHG datasets (v.2.3.6) using GMT (5.x series). They are included under the terms of the open-source LGPLv3+ license.
Code availability
We deposited the code for analysing the data and producing the figures in this Article at GitHub (https://github.com/hringbauer/punic_aDNA).
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Acknowledgements
C.L.-F. was supported by PID2021-124590NB-100 grant (MCIU/AEI/FEDER, UE). H.R. was supported by the Max Planck–Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM). I.G., A.S.-M. and D. Regev were supported by ISF grant number 1045/20. L.S., A.C.F., C.D.V. and D.L. were supported by AGED PRIN 2017 project, MUR Italy. D. Reich was supported by National Institutes of Health grant HG012287; by John Templeton Foundation grant 61220; by the Howard Hughes Medical Institute (HHMI), a gift from J.-F. Clin; by the Allen Discovery Center, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation; and by a grant from the Getty Foundation “The Classical World in Context: the Near East”. We thank V. Moses and M. McCormick for their comments. The project received funding from the Italian Ministry of Foreign Affairs and International Cooperation, and ISMEO. The D-REAMS Radiocarbon analysis was supported by the Exilarch Foundation for the Dangoor Research Accelerator Mass Spectrometer. We thank the Musée de l’Homme for providing us access to the human remains from Khenchela cave.
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We annotate author contributions using the CRediT Taxonomy labels; where multiple authors serve in the same role, we specify the degree of contribution as lead, equal or support. Conceptualization (design of study): D. Reich, I.G. and D. Regev. Data curation (archaeology and bioanthropology): lead, R.P., C.L.-F., D. Regev, A.C., L.S., D.C., P.v.D. and D.P. Data curation (DNA): lead, H.R., I.G., D. Reich and S.M. Formal analysis: lead, H.R. and I.G.; support, A.S.-M., I.O., T.P., A. Mittnik, I.L., A.S. and S.M. Funding acquisition: D. Reich and I.G. Resources: G.F., M.B., A. Mezquida, B.C., H.J., P. Smith, S.V., A. Modi, K.C., E. Curtis, A.K., A.M.L., M.M., A. Micco, J.O., L.Q., K.S., J.N.W., N.M.-G., A.M.S.R., M.L.L.F., J.M.J.-A., I.J.T.M., E.V., J.S.P., S.L.C., T.M.-B., E.L., A.R.R., F.O., P.T., V.G., A.B., L.C., E.B., M.F., M.L., F.L.P., A.N., F.G., C.D.V., G.L., F.M., P. Sconzo, G.C., E. Cilli, A.C.F., F.F., D.L., B.J.C., N.R. and L.N. Supervision: lead, D. Reich and I.G. Visualization: lead, H.R., I.G. and A.S.-M. Writing (original draft preparation): H.R., I.G. and D. Reich. Writing (review and editing): all of the authors.
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Extended data figures and tables
Extended Data Fig. 1 PCA of Punic individuals grouped according to site and chronology.
We project individuals sequenced at over 20,000 SNPs onto the same two PCs as in Fig. 1 (calculated from modern individuals, grey dots). Here, we plot all individuals from Punic archaeological sites, excluding the Phoenician site of Akhziv and including the 20 individuals dated to the Roman period (Supplementary Table 5). We split the sample into panels representing our four major geographic regions: Iberia, Sardinia, North Africa, and Sicily. The shape of the symbols indicates the site (lower left legend), and the colour indicates the date range of each individual (as described in the upper right legend).
Extended Data Fig. 2 Ancestry models inferred for 122 Phoenician-Punic individuals using unsupervised ADMIXTURE with K = 2, 3, 4 and 5 latent ancestry components.
The 122 Phoenician-Punic individuals sequenced for more than 100,000 SNPs were jointly analysed with 24 individuals from related ancient populations across the Mediterranean (Supplementary Table 12). (a) The model with the highest likelihood was obtained for each value of K among 50 replicate runs. Individuals are grouped based on region. Values of the ΔK score of58 are specified for K = 3,4, with a higher score obtained for K = 3, suggesting optimal fit. (b) A more detailed depiction of the best model obtained with K = 3 latent ancestry components corresponding to North African ancestry (red), eastern ancestry (green), and central/western Mediterranean ancestry (blue). Individuals are partitioned within each region according to site and time range (see legend). The unsupervised ADMIXTURE model does not adequately differentiate between Levantine ancestry and ancestry found in other Mediterranean locations (e.g., Anatolia and Sicily), unlike the qpAdm models of Extended Data Fig. 3.
Extended Data Fig. 3 Ancestry models inferred for the 140 Phoenician-Punic individuals in our data set by qpAdm.
We partitioned individuals by region: (a) North Africa, (b) Sicily, (c) Sardinia, (d) Iberia, and (e) the Levant. Within each region, we grouped individuals by site, and for sites in Sicily, Sardinia, and Iberia, also by broad date ranges (see legend for colour code). We ordered the models of each individual according to their P-values (grey bar above each model). We report P-values assuming that the LRT statistic is chi-squared distributed with degrees of freedom determined by the number of populations and of contributing source populations. We did not correct these P-values for multiple testing, but this approach is conservative since we report models with comparatively high P-values (those that are not rejected by the test). Individuals with low coverage (fewer than 100,000 SNPs) are indicated by an asterisk (*) next to the sample ID. Eastern ancestry models are indicated by a contribution of the proxy sources Levant MLBA. In contrast, western ancestry models are indicated by contributions from either Greece BA (Myc), Sicily EBA, Sardinia LBA, Iberia LBA, or Steppe MLBA. There are five individuals for whom no valid eastern or western model was inferred. For four of them, we inferred valid models under the broad ancestry scheme (marked by an asterisk above the vertical bar), and for one (I22122 from Tharros, Sardinia), we could not infer any valid model.
Extended Data Fig. 4 Proportions of North African ancestry inferred using the 2D PCA and qpAdm for 123 Punic individuals.
We exclude from this analysis the Akhziv sample, the three individuals from Sicily and Sardinia that cluster near Levantine individuals in the 2D PCA, and one individual for which we could not fit a qpAdm model. The qpAdm estimates are based on the smallest proportions estimated for the individual in a valid qpAdm model (see Methods). The PCA-based estimates of North African ancestry were computed by projecting the location of each sample in the PCA onto a cline from the cluster defined by Bronze Age individuals from Sicily to the cluster defined by North African individuals (see Supplementary Information S3 for more details). The two approaches yield similar estimates, with qpAdm being more sensitive to low ancestry proportions. Individuals from Kerkouane (depicted as squares) appear to have a broad range of North African ancestry (0 - 94%). Individuals from Sicily typically have lower proportions of North African ancestry (<20%), and we observe no significant shift in time. On the other hand, in Sardinia, none of the 12 individuals for which we inferred more than 10% North African ancestry (according to at least one of the two approaches) dated before 400 BCE, suggesting that North African ancestry was likely introduced around that time (Supplementary Information S3). We see a similar pattern in Iberia, but since we only have one individual from Iberia dating before 400 BCE, we cannot confidently infer the absence of North African ancestry during this time.
Extended Data Fig. 5 Y Haplogroup Diversity in male individuals from Phoenician and Punic contexts.
We inferred the first four characters of the ISOGG 2019 Y haplogroup classification for all Phoenician and Punic males with more than 100,000 autosomal SNPs covered (as those in almost all cases have sufficient coverage on the Y chromosome; see Methods). (a) Pie chart of Y haplogroup frequencies. (b) We visualize the Y haplogroup diversity partitioned per Phoenician or Punic site and denote each individual’s haplotype by one circle. We set the height of the bar to the overall frequency (as depicted in panel a). The numbers in brackets indicate the total Y haplotype sample size.
Extended Data Fig. 6 Autosomal and Y Diversity without the contribution of filtered North African ancestry, per site in Phoenician-Punic contexts and the published aDNA record.
(a) Y haplogroup diversity measured using the Inverse Simpson index. This value is computed as in Fig. 3a, excluding the three Punic individuals (from Kerkouane, Villaricos and Selinunte) with distinct North African Y haplogroups E1a and L (see Extended Data Fig. 5). (b) autosomal diversity measured using the first two PCs from Fig. 1 and the mean pairwise distance of those coordinates. This value is computed as in Fig. 3b, excluding individuals with more than 10% North African ancestry based on qpAdm in Phoenician-Punic sites (see Extended Data Fig. 4). Here, we combined individuals from the nearby Sicilian sites of Birgi, Motya, and Lilybaeum into one group (labelled Lilybaeum here). In both panels, the diversity measures for the context populations are as in Fig. 3 (without any additional filtering), and the dashed horizontal bar in both panels indicates the maximum diversity observed in sites dating before 500 BCE. See Supplementary Information S5 for a more detailed description of this analysis.
Extended Data Fig. 7 Two reconstructed pedigrees of Punic individuals.
We reconstructed two pedigrees based on inferring biological relatives with pairwise kinship (using IBD segment sharing) and uniparental haplogroups: (a) A pedigree linking five individuals from Kerkouane, North Africa; (b) A pedigree linking three individuals from Tharros, Sardinia. In the Kerkouane pedigree in (a), individuals I24215 and I24194 are inferred to be 3rd-4th degree relatives of the two siblings I24494 and I24193, but the exact pedigree relationship cannot be resolved. Each panel depicts the projection of the related individuals onto the two major PCs used in Fig. 1. Each pedigree specifies the sample IDs for all individuals, the mitochondrial (maternal) haplogroup and the Y (paternal) haplogroup for males. Both pedigrees contain individuals dating to 800–400 calBCE and link several individuals via the maternal lineage: We infer four identical maternal haplogroups in Kerkouane and a maternal grandfather in Tharros–two observations that are inconsistent with strict patrilocality.
Extended Data Fig. 8 Runs of homozygosity inferred in Phoenician and Punic individuals and ancient individuals of relevant Bronze and Iron Age contexts.
We computed runs of homozygosity (ROH) in all individuals with more than 400,000 SNPs covered and recorded the total length (in cM) of ROHs binned by length into four categories (see legend). We label individuals with at least 50 and 100 cM of their genome in long ROH (>20 cM) with triangle and square marks as in30 - to indicate offspring of close biological parental relatives. (a) ROH in Phoenician and Punic individuals, grouped by site. (b) ROH in individuals from relevant Bronze and Iron Age contexts (as depicted in Fig. 1). (c) Expected ROH for offspring of various cousin matings (according to the degree of relation between parents) and for individuals sampled in populations with small effective size (calculated as described in30).
Extended Data Fig. 9
Ancestry models inferred using qpAdm for individuals from Sicily from (a) the indigenous Iron Age sites of Polizzello and Monte Falcone, (b) from Phoenician sites before Roman expansion (as shown in Extended Data Fig. 3b), and (c) from Punic sites after Roman expansion. Colour horizontal bars indicate radiocarbon dates. The models of each individual are sorted according to their P-values (grey bar above each model). We report P-values assuming that the LRT statistic is chi-squared distributed with degrees of freedom determined by the number of populations and of contributing source populations. We did not correct these P-values for multiple testing, but this approach is conservative since we report models with comparatively high P-values (those that are not rejected by the test). Eastern ancestry models are indicated by a contribution of the proxy source Levant MLBA. In contrast, western ancestry models are indicated by contributions from either Greece BA (Myc), Sicily EBA, Sardinia LBA, Iberia LBA, or Steppe MLBA. There are seven individuals for which no valid eastern or western model was inferred. We inferred valid models under the broad ancestry scheme (marked by an asterisk above the vertical bar) for five of them. Two individuals were inferred to be related through IBD-sharing and are indicated in the figure. The analysis suggests that indigenous populations in Sicily have similar ancestry patterns as observed in the Phoenician sites but without North African ancestry. In later periods, we see the introduction of diverse ancestry sources (Levantine and western Mediterranean), likely associated with the Roman expansion into Sicily. See Supplementary Information S3 for more details.
Extended Data Fig. 10 Additional PCA projections.
(a) Bronze and Iron Age reference and Levantine populations. We show the same PCA as in Fig. 1 but focus on the ancient reference populations. (b) Zoom in PCA projections of Levantine populations. We show the same PCA depicted in (a), but zooming into the region where Levantine individuals project. We also include additional Bronze and Iron Age Levant individuals not included in Fig. 1. Those previously published individuals originate from Sidon in present-day Lebanon17 and various sites in present-day Israel (Megiddo, Yehud, Hazor, Baq’ah25, Tel Shadud64, Ashkelon64,65). Abbreviations: MLBA: Middle-Late Bronze Age, MBA: Middle Bronze Age, IA: Iron Age. All 13 individuals from Akhziv cluster next to other Levantine individuals, together with a single outlier individual from Tharros (I22119) inferred to have Levantine ancestry (Extended Data Fig. 3). Abbreviations: M/N: Mesolithic/Neolithic, MLBA: Middle-Late Bronze Age, MBA: Middle Bronze Age, LBA: Late Bronze Age, IA: Iron Age.
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Supplementary Information 1–6, Supplementary Tables 13–21 and Supplementary Figs. 1–6.
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Supplementary Tables 1–12.
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Ringbauer, H., Salman-Minkov, A., Regev, D. et al. Punic people were genetically diverse with almost no Levantine ancestors. Nature 643, 139–147 (2025). https://doi.org/10.1038/s41586-025-08913-3
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DOI: https://doi.org/10.1038/s41586-025-08913-3
