Northwest African Neolithic initiated by migrants from Iberia and Levant

North Africa’s location between the Sahara, the Near East, and Mediterranean Europe has produced a complex human history with long-term hominin presence but a fragmented fossil record. Fifteen-thousand-year-old foragers from Taforalt (Morocco) show a distinct genetic makeup intermediate between Levantine foragers and sub-Saharan Africans. Present-day North Africans are largely related to Eurasians, likely due to back-to-Africa migrations. In Europe, Neolithic farmers dispersed from the northern Levant/Anatolia to Mediterranean regions, reaching Iberia by around 7,550 cal BP via coastal routes. In northwestern Africa, the Neolithic appears around 7,350 cal BP at Kaf Taht el-Ghar (KTG), with pottery, domestic cereals, and husbandry. Conflicting hypotheses propose either migration of European Neolithic farmers into North Africa or local adoption of innovations by hunter-gatherers. A prior genomic study at Ifri n'Amr o'Moussa (IAM) indicated continuity of local Maghrebi ancestry without European Neolithic admixture, supporting acculturation. However, substantial chronological and genomic gaps remained. This study sequences nine individuals spanning the Epipalaeolithic to Middle Neolithic in Morocco to clarify the timing and processes of Neolithization in the Maghreb and its relationship to European and Near Eastern dynamics.

Archaeological work documents rapid spread of Impressed/Cardial Ware along Mediterranean Europe to Iberia by ~7,550 cal BP. In northwestern Africa, earliest Neolithic elements appear slightly later at KTG (~7,350 cal BP). One genomic study had previously sampled IAM (Early Neolithic) and a Late Neolithic site, finding IAM lacked European Neolithic ancestry and suggested local continuity from Upper Palaeolithic/Epipalaeolithic groups and acculturation of Neolithic traits (e.g., Cardial-like ceramics, domestic cereals). Broader contexts include evidence for increasing Epipalaeolithic sedentism, early pottery in Africa, and climatic shifts favoring mobile herding; pastoralism appears to have spread into the Sahara between 7,000–6,000 cal BP, possibly from the Near East. European palaeogenomic studies of Neolithization are abundant, but North Africa lacked a dense temporal series prior to this work. Debates also concern whether early crossings into North Africa came from Iberia across the Gibraltar Strait or via the Sicily–Tunisian route; archaeological evidence varies by region and period.

The study generated whole-genome shotgun sequence data for nine ancient individuals from four Moroccan sites spanning Late Epipalaeolithic (Ifri Ouberrid, OUB; n=1), Early Neolithic (Kaf Taht el-Ghar, KTG, n=4; Ifri n'Amr o'Moussa, IAM, n=1 newly analyzed plus previously published individuals), and Middle Neolithic (Skhirat-Rouazi, SKH; n=3). Average genome coverage ranged from 45.8× to 0.017×, with five individuals exceeding 1× and three exceeding 9× coverage. DNA was extracted from bones/teeth, libraries prepared, and shotgun sequenced on Illumina platforms. Authenticity was assessed via fragment length distributions and terminal cytosine deamination typical of ancient DNA. Contamination was estimated for autosomes and mitochondria; most individuals showed low contamination, except skh003 with 10–16% nuclear contamination. Radiocarbon dates were calibrated using IntCal20. Newly generated data were co-analyzed with relevant ancient datasets and present-day populations from Africa, the Middle East, and Europe. Population-genetic analyses included PCA projections, model-based ancestry estimation assuming five components, formal tests (f4), qpAdm admixture modeling, and comparisons with European Neolithic and hunter-gatherer sources. Genetic diversity was characterized by runs of homozygosity (ROH) and heterozygosity; demographic history was inferred using pairwise sequentially Markovian coalescent (PSMC) on high-coverage genomes. Admixture timing was estimated using ancestry covariance and linkage disequilibrium decay methods, testing sources such as Iberia or Sicily Early Neolithic and Taforalt (TAF).

• Persistent Maghrebi lineage: From Upper Palaeolithic Taforalt (15,086–14,046 cal BP) through Epipalaeolithic OUB (7,660–7,506 cal BP) to Early Neolithic IAM (7,316–6,679 cal BP), there was marked genetic continuity with minimal gene flow across the Mediterranean for at least 7,000 years.
• Low diversity and bottleneck in Maghrebi ancestry: The Maghrebi lineage shows very low genetic diversity and extensive ROH. High-coverage OUB (45.8×) indicates a severe bottleneck, with effective population size declining to about N=1,400 between ~50,000 and 27,000 years ago.
• Early Neolithic variance between sites: IAM individuals exhibit autochthonous Maghrebi ancestry despite Neolithic material culture, supporting cultural adoption without genetic admixture. In contrast, KTG individuals are genetically similar to European Early Neolithic populations.
• European farmer ancestry at KTG with local admixture: KTG genomes carry European Early Neolithic ancestry with 15.4–27.4% Maghrebi admixture and a small Western Hunter-Gatherer (WHG) component. qpAdm modeling fits a mixture of 72 ± 4.4% Anatolian Neolithic, 10 ± 2.6% WHG, and 18 ± 3.3% Maghrebi ancestry (P=0.193). This indicates ancestors dispersed from Anatolia through Europe, admixed with hunter-gatherers, then crossed to North Africa, most parsimoniously via southern Iberia.
• Temporal shift within KTG: Earlier KTG individuals (7,429–7,267 cal BP) carry roughly double the Maghrebi ancestry (~25%) compared to later KTG (7,247–6,945 cal BP; ~13%), with a significant increase in European Neolithic ancestry (f4(KTG earlier, KTG later, Iberia EN, Mbuti) z = −5.01). Admixture timing is estimated within the last 6–13 generations, consistent with first contacts at 7,500–7,400 cal BP.
• Middle Neolithic Levantine influx: SKH individuals model as ~76.4 ± 4.0% Levant Neolithic ancestry plus 23.6 ± 4.0% local Maghrebi ancestry. Adding a European Neolithic source is rejected. This Levantine component is absent in contemporaneous European Neolithic populations, suggesting an independent Levant-to-North Africa expansion, coincident with the spread of pastoralism and new pottery traditions (e.g., Ashakar Ware).
• Persistence and blending of ancestries: The Levantine-associated component persists into the Late Neolithic (KEB) and in historical Guanches, with Late Neolithic groups modeling as mixes of ancestries already present by Early and Middle Neolithic.
• Demographic context: Northwestern African groups often show lower diversity and stronger ROH than European Neolithic populations, consistent with modest population sizes and periods of isolation. Archaeologically and genetically, interactions were asymmetric: gene flow was predominantly from local foragers into migrant farmers, while cultural transfer flowed from farmers to foragers.

The study resolves a longstanding debate on the origin of the Neolithic in northwestern Africa. Genetic data show that while some local groups (IAM) adopted Neolithic technologies without European admixture, the earliest farmers at KTG derive primarily from European Early Neolithic populations with additional Maghrebi and WHG ancestry. This establishes a demic component to Neolithization, with incoming Iberian-associated farmers introducing agriculture and material culture. The coexistence of genetically distinct local and migrant groups for several centuries, combined with unidirectional gene flow from locals to migrants and bidirectional cultural exchange, outlines a complex, heterogeneous Neolithic landscape. The later appearance of Levant-derived ancestry in Middle Neolithic SKH, independent of European routes, aligns with archaeological signals of pastoralism and new ceramic styles, indicating additional east-to-west movements across North Africa. Together, these findings demonstrate that Neolithization in the Maghreb was a multifaceted process involving multiple migrations and local adoption, differing from the more uniform demic diffusion patterns observed in many European regions.

High-resolution ancient genomic data from Morocco reveal long-standing Maghrebi genetic continuity from the Upper Palaeolithic to the Early Neolithic, followed by the arrival of European Early Neolithic farmers—most plausibly from Iberia—who introduced farming and Neolithic material culture. Local groups adopted aspects of this lifestyle, at times without genetic admixture, while migrants incorporated local ancestry. In the Middle Neolithic, an additional Levant-derived ancestry entered the region, likely associated with pastoralist expansions and new ceramic traditions, and persisted into the Late Neolithic and later historical periods. These multi-wave processes generated a heterogeneous cultural and economic mosaic with generally small and isolated populations, contributing to the distinctive genetic landscape of the Maghreb today.

• One Middle Neolithic individual (skh003) exhibits substantial nuclear contamination (10–16%), reducing confidence in individual-level inferences for that sample.
• The newly analyzed IAM individual (iam004/IAM.1) has insufficient coverage, limiting resolution for that genome.
• While Iberia Early Neolithic provides the best fit for the European ancestry in KTG, a contribution from Sicilian farmers cannot be excluded, indicating limited resolution to fully disentangle potential Mediterranean source mixtures.