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Middle Eastern Genomes Provide Look at Genetic Variation, Population Histories

NEW YORK – A team led by investigators at the Wellcome Sanger Institute has sequenced the genomes of more than 100 Middle Eastern individuals, identifying genetic variants that provide a look at present population patterns and past migrations and interactions in the region.

"We used this new resource to uncover prehistorical and undocumented events associated with lifestyle transitions, climate change, and population movements that occurred thousands of years ago and left a trace in the genomes of Middle Eastern populations," co-first author and co-corresponding author Mohamed Almarri, a researcher affiliated with the Sanger Institute and the Dubai Police forensic science and criminology department, said in an email.

"The Middle East is an important region to understand human history, migrations, and evolution: It is where modern humans first expanded out of Africa, where hunter-gatherers first settled and transitioned into farmers, where the first writing systems developed, and where the first major known civilizations emerged," he explained. "However, despite this importance, the region has been historically understudied in genomic studies."

As they reported in Cell on Wednesday, he and his colleagues used linked-read sequencing to do high-coverage whole-genome sequencing on 137 individuals from eight Middle Eastern populations, coming up with phased genomes that were subsequently compared to one another and to those from populations around the world. The analyses highlighted some 4.8 million variants that have not been detected in the past, while providing clues to the historical events that influenced Middle Eastern ancestral groups — from migrations to a desertification event in the area some 4,200 years ago or the introduction of farming.

"Our study fills a major gap in international genomic projects by cataloguing genetic variation in the Middle East," Chris Tyler-Smith, a researcher at the Wellcome Sanger Institute, said in a statement. "The millions of new variants we found in our study will improve future medical association studies in the region."

With the new sequence data, the team was able to retrace ancestral populations contributing to present-day populations in the Middle East, including a proposed "basal Eurasian" population ancestral to present-day Arabian populations that appeared to have experienced little or no mixing with Neanderthals. Together with non-Neanderthal admixed ancestry from Africa, ancestry from this "ghost" Eurasian population appears to have led to markedly low Neanderthal ancestry in Arabian populations compared to Eurasian populations in other parts of the world.

The Middle Eastern populations did not appear to carry genetic signatures associated with previously reported remains going back more than 80,000 years in the Middle East, the researchers reported. Instead, African ancestry in the region appeared more closely related to populations that moved out of Africa more recently.

The available genetic data "collectively suggest that present-day Middle Eastern populations do not harbor any significant traces from an early expansion out of Africa," the authors wrote, "and all descend from the same population that expanded out of the continent [around 50,000 to 60,000 years ago]."

The investigators also got a look at relative population sizes in the area over time, including agriculture-related population expansions in the Levant and distinct trajectories patterns in the Levant and Saudi Arabia that began an estimated 15,000 to 20,000 years ago. In contrast, there appeared to be a dip in Arabian population size and related population bottleneck starting some 6,000 years ago during a so-called aridification event when the region shifted from green and moist to sandy in response to climate shifts.

Along with interactions between populations, the team saw hints that migrations from the Levant regions into Arabia and East Africa may have helped to spread Semitic languages. It also looked at parts of the genome that have been subjected to positive selection in Middle Eastern populations, as well as variants linked to conditions such as type 2 diabetes that were found at distinct allele frequencies in the past.

"Our results indicate that polygenic selection might have played a role in increasing the frequency of variants that that were potentially beneficial in the past but today are associated with diseases such as [type 2 diabetes]," the authors wrote.