Northwest African Neolithic initiated by migrants from Iberia and Levant

Northwestern Africa's transition to food production around 7,400 years ago remains a topic of debate. Archaeological evidence suggests two competing narratives. One proposes that the Neolithic lifestyle was introduced by migrating European farmers. The other suggests that local hunter-gatherer populations adopted agricultural practices and technologies independently. Prior archaeogenetic studies have yielded inconclusive results. This study aimed to clarify this ambiguity by examining a time series of human remains from Morocco, encompassing the Epipalaeolithic to the Middle Neolithic periods. The researchers hypothesize that the transition was a complex process involving both migration and cultural exchange, and that the genetic landscape of the region would reflect this heterogeneity. The importance of this study lies in its potential to resolve long-standing questions about the origins and spread of agriculture in North Africa, offering a more nuanced and complete picture of this crucial period in human history. The geographic location of North Africa, positioned between the Sahara Desert, the fertile Near East, and Mediterranean Europe, is crucial to understanding its complex history. While the fossil record indicates long-term hominid presence, continuity over the last 100,000 years is uncertain due to fragmented data. Late Pleistocene forager remains show a genetic makeup intermediate between Levantine foragers and sub-Saharan African populations. Currently, North Africans show a strong Eurasian genetic component, likely resulting from back-to-Africa migrations. Archaeologically and archaeogenomically, Neolithic farmers (distinct from European foragers) dispersed from the Levant and Anatolia across the Mediterranean.

Previous research on the Neolithic transition in northwestern Africa yielded conflicting results. Some studies suggest a simultaneous appearance of Neolithic practices in both northwestern Africa and Iberia around 7,550 calibrated years before present (cal BP). Other studies propose that the earliest evidence in northern Morocco appears approximately two centuries later. The earliest genomic analysis of Early Neolithic farmers from northwestern Africa showed no European Neolithic ancestry, indicating potential local development. This stands in contrast to the European Neolithic transition, established as a result of demic diffusion from Anatolia. The hypothesis that the transition was due to local adaptation of technologies and practices is supported by the presence of impressed Cardial-like ceramics and domesticated cereals in northwestern African sites. However, the lack of genomic data from across the relevant time period has hindered a comprehensive understanding of the process. This absence of genomic data is addressed in the current study, which investigates a time series of human remains.

This study analyzed genomic sequence data from nine ancient individuals excavated from four archaeological sites in modern-day Morocco. The sites included Ifri Ouberrid (OUB, Epipalaeolithic), Ifri n'Amr o'Moussa (IAM, Early Neolithic), Kaf Taht el-Ghar (KTG, Early Neolithic), and Skhirat-Rouazi (SKH, Middle Neolithic). The data encompassed a time span of over 1,000 years. The researchers generated genomic sequence data with varying genome coverage, ranging from 45.75-fold to 0.017-fold. DNA was extracted from bones and teeth and shotgun sequenced on an Illumina platform. The libraries exhibited typical ancient DNA degradation patterns, with short fragment sizes and cytosine deamination at read ends. Contamination estimates were generally low except for one individual. To assess relationships with other populations, the researchers co-analyzed their data with relevant ancient and present-day groups from Africa, the Middle East, and Europe. Statistical analyses, including Principal Component Analysis (PCA), *f*₄ tests of admixture, qpAdm, and methods based on ancestry covariance patterns and linkage disequilibrium decay were employed to determine ancestry proportions, population relationships, and admixture timings. Runs of homozygosity (ROH) and heterozygosity were calculated to assess genetic diversity.

The study revealed 8,000 years of population continuity in northwestern Africa, from the Upper Palaeolithic (Taforalt) through the Epipalaeolithic (OUB) to the Early Neolithic (IAM). The Epipalaeolithic individual (oub002) showed strong genetic similarity to individuals from Taforalt and Early Neolithic individuals from IAM, demonstrating a marked population continuity with no substantial gene flow across the Mediterranean Sea for at least 7,000 years. This Maghrebi lineage exhibited low genetic diversity and long runs of homozygosity, suggesting long-lasting isolation and a population bottleneck. Analysis of the Early Neolithic site of KTG, located on the North African Mediterranean coast, revealed a different pattern. Individuals from KTG showed significant genetic similarity to European Early Neolithic populations, with admixture (15.4–27.4%) with local North African groups. A small proportion of WHG ancestry was also identified. The data suggests that KTG farmers originated from European Neolithic populations, likely dispersing from Anatolia and admixing with European hunter-gatherers before reaching North Africa, with Iberia identified as the most likely source population for the European ancestry. The admixture between European and Maghrebi ancestries in KTG occurred within the last six to thirteen generations, consistent with archeological evidence. Interestingly, earlier KTG individuals showed a higher proportion of Maghrebi ancestry than later individuals, indicating a decline in Maghrebi ancestry and increase in European ancestry over time. Genetic diversity was lower and ROH higher in KTG than most Early Neolithic European populations, reflecting the influence of the Maghrebi ancestry. A distinct Levantine ancestry was identified in the Middle Neolithic individuals from SKH. This ancestry appears to represent an independent migration from the Levant, coinciding with the arrival of pastoralism and a new ceramic tradition in the region. This Levantine component persisted into the Late Neolithic, highlighting complex demographic processes in northwestern Africa. Late Neolithic individuals from KEB showed a mix of previously existing ancestries, indicating a lack of substantial migrations between the Middle and Late Neolithic periods. Overall, genetic patterns revealed a unidirectional admixture process, with European farmers assimilating local forager ancestry. The coexistence of genetically unmixed local populations and incoming farming communities demonstrates a complex process involving both migration and cultural adaptation.

The findings demonstrate that the Neolithic transition in northwestern Africa was not a uniform process. The introduction of farming was driven by migration of Neolithic farmers from Europe (most likely Iberia), but these migrants interacted and interbred with existing populations in a complex pattern of gene flow and cultural exchange. While the migration from Iberia brought farming practices, the local populations retained a distinct genetic identity, adapting aspects of the Neolithic lifestyle without significant genetic admixture in some cases. Later, the arrival of Levantine ancestry further diversified the region's genetic landscape. The heterogeneous nature of the Neolithization process contrasts with other regions, revealing a more multifaceted interplay of migration, adaptation, and cultural diffusion. The observed reduced effective population size and lower genetic diversity in many Neolithic groups point to smaller population sizes throughout the period, potentially due to isolation. These results challenge simple models of Neolithic spread and highlight the importance of considering cultural and genetic exchanges during such transitions.

This study provides a detailed chronology and high-resolution genomic data for the Neolithization of northwestern Africa. The findings reveal a complex process involving migration from both Europe (Iberia) and the Levant, along with the adoption of agricultural practices by local populations. This study emphasizes the interplay between migration, adaptation, and cultural exchange in shaping the genetic and cultural landscape of the region. Future research could further explore the interactions between different groups, investigating the extent of cultural and technological transfer versus genetic admixture.

While this study provides a significant advance in our understanding of the Neolithic transition in northwestern Africa, limitations exist. The sample size, while substantial, remains limited, and future studies incorporating larger datasets would strengthen the conclusions. Further, the analysis focuses on a specific geographic region in Morocco; expanding the geographic scope of analysis to other parts of North Africa is necessary to ensure more generalizable results. Lastly, the reliance on genetic data necessitates careful consideration of cultural and environmental factors not directly reflected in the genetic data.