Modelling the demographic history of human North African genomes points to a recent soft split divergence between populations.

BACKGROUND: North African human populations present a complex demographic scenario due to the presence of an autochthonous genetic component and population substructure, plus extensive gene flow from the Middle East, Europe, and sub-Saharan Africa. RESULTS: We conducted a comprehensive analysis of 364 genomes to construct detailed demographic models for the North African region, encompassing its two primary ethnic groups, the Arab and Amazigh populations. This was achieved through an Approximate Bayesian Computation with Deep Learning (ABC-DL) framework and a novel algorithm called Genetic Programming for Population Genetics (GP4PG). This innovative approach enabled us to effectively model intricate demographic scenarios, utilizing a subset of 16 whole genomes at > 30X coverage. The demographic model suggested by GP4PG exhibited a closer alignment with the observed data compared to the ABC-DL model. Both point to a back-to-Africa origin of North African individuals and a close relationship with Eurasian populations. Results support different origins for Amazigh and Arab populations, with Amazigh populations originating back in Epipaleolithic times, while GP4PG supports Arabization as the main source of Middle Eastern ancestry. The GP4PG model includes population substructure in surrounding populations (sub-Saharan Africa and Middle East) with continuous decaying gene flow after population split. Contrary to ABC-DL, the best GP4PG model does not require pulses of admixture from surrounding populations into North Africa pointing to soft splits as drivers of divergence in North Africa. CONCLUSIONS: We have built a demographic model on North Africa that points to a back-to-Africa expansion and a differential origin between Arab and Amazigh populations.

Population history of North Africa based on modern and ancient genomes.

Compared with the rest of the African continent, North Africa has provided limited genomic data. Nonetheless, the genetic data available show a complex demographic scenario characterized by extensive admixture and drift. Despite the continuous gene flow from the Middle East, Europe and sub-Saharan Africa, an autochthonous genetic component that dates back to pre-Holocene times is still present in North African groups. The comparison of ancient and modern genomes has evidenced a genetic continuity in the region since Epipaleolithic times. Later population movements, especially the gene flow from the Middle East associated with the Neolithic, have diluted the genetic autochthonous component, creating an east to west gradient. Recent historical movements, such as the Arabization, have also contributed to the genetic landscape observed currently in North Africa and have culturally transformed the region. Genome analyses have not shown evidence of a clear correlation between cultural and genetic diversity in North Africa, as there is no genetic pattern of differentiation between Tamazight (i.e. Berber) and Arab speakers as a whole. Besides the gene flow received from neighboring areas, the analysis of North African genomes has shown that the region has also acted as a source of gene flow since ancient times. As a result of the genetic uniqueness of North African groups and the lack of available data, there is an urgent need for the study of genetic variation in the region and its implications in health and disease.