The genomic history of the Middle East

The Middle East region is important to understand human evolution and migrations but is underrepresented in genomic studies. Here, we generated 137 high-coverage physically phased genome sequences from eight Middle Eastern populations using linked-read sequencing. We found no genetic traces of early expansions out-of-Africa in present-day populations but found Arabians have elevated Basal Eurasian ancestry that dilutes their Neanderthal ancestry. Population sizes within the region started diverging 15–20 kya, when Levantines expanded while Arabians maintained smaller populations that derived ancestry from local hunter-gatherers. Arabians suffered a population bottleneck around the aridification of Arabia 6 kya, while Levantines had a distinct bottleneck overlapping the 4.2 kya aridification event. We found an association between movement and admixture of populations in the region and the spread of Semitic languages. Finally, we identify variants that show evidence of selection, including polygenic selection. Our results provide detailed insights into the genomic and selective histories of the Middle East. [Display omitted] •Middle Easterners do not have ancestry from an early out-of-Africa expansion•Basal Eurasian and African ancestry in Arabians deplete their Neanderthal ancestry•Populations experienced bottlenecks overlapping aridification events•Identification of recent single and polygenic signals of selection in Arabia A high-coverage resource of physically phased genomes from eight Middle Eastern populations generated via linked-read sequencing provides insights into a genetically understudied region and enables more comprehensive study of population history and the detection of millions of variants common to the Middle East but outside short-read accessibility masks and not previously cataloged. It enhances our understanding of regional ancestry, the spread of languages, the effects of climate change on populations, and the evolutionary history of genetic variants.