Genetic study reveals ancient human adaptation to agriculture and climate change in the Middle East

The most comprehensive study to date of genetic diversity in the Middle East has provided insight into the lives of ancient humans who lived through seismic events such as the development of agriculture and the formation of the Arabian Desert.

Researchers from the University of Birmingham and the Wellcome Sanger Institute, along with their international collaborators, have discovered signals in DNA that point to a population boom in the Levant coinciding with the transition to agriculture and a population collapse in Arabia then. the region dries up.

Published in Cell, this is the first comprehensive population-scale study of Middle Eastern DNA. He used linked-read sequencing, a technique that allowed the team to reconstruct the region’s population history in unprecedented detail. In addition to providing insight into ancient human history, these data will be an important resource for studying genetic health and adaptations, such as type 2 diabetes and lactose tolerance, in populations in the Middle East. East.

The fortunes of the ancient human populations of the Middle East were strongly influenced by its technological and climatic history. The region known as the Levant is considered the cradle of agriculture, while the region known as Arabia is today dominated by the largest sand desert in the world*.

Until around 6,000 years ago, however, Arabia was a much wetter and greener place until the climate began to change and create the desert we see today. Another aridification event about 4,000 years ago, one of the most important climatic events of the last 10,000 years, led to a phase of aridification of the region**.

Until now, the Middle East has been little studied in genomic research. Since human diversity and susceptibility to disease vary from population to population, the lack of detailed genetic data can exacerbate health inequities.

In this study, researchers at the Wellcome Sanger Institute collected 137 samples from individuals representing eight Middle Eastern populations*** and sequenced them using linked-read sequencing. The genomic data was then analyzed at the Wellcome Sanger Institute and the University of Birmingham to look for variations in genomes that could be used to map human evolution from 100,000 years ago to the present day.

The team identified 23.1 million variations in the DNA letters that make up the human genome, known as single nucleotide variations (SNVs). Of these, 4.8 million SNVs were new variants not previously discovered in other populations. While many of them were rare, around 370,000 were common and any of them could have medical relevance.

This analysis revealed that human populations in the Levant have experienced massive population growth over the past 15,000 years, which includes the period of transition to agriculture. But the populations of Arabia, who had switched to a lifestyle of herder-gatherers, experienced a demographic collapse during the aridification of the region. Around 4,000 years ago, the Levantine populations also suffered a collapse as the region dried out.
These population crashes resulted in evolutionary bottlenecks that limited genetic diversity and still have medical relevance for individuals in the Middle East today.

Dr Mohamed Almarri, first author of the study from the Wellcome Sanger Institute, said: “Our study helps uncover hidden genetic diversity in the Middle East, which has been largely understudied until now. In addition to identifying variants that provide fascinating insights into the life and adaptation of Middle Eastern ancestors, some of these variants are also important to health care in the region today. For example, we detected variants that were beneficial in the past, but now increase the risk of type 2 diabetes in certain Arab groups.

Clues to how people in the Middle East adapted to their changing circumstances can be found in their DNA. Those that helped humans adapt to their environment would have been subject to positive selection and increased in frequency.

Dr Marc Haber, corresponding author of the University of Birmingham study, said: “An interesting example of positive selection in our study was a variant associated with the ability to digest lactose in milk beyond the ‘childhood. Over the past 8,000 years, this variant has reached a frequency of 50% among the Arabs, coinciding with the transition from a hunter-gatherer lifestyle to a herder-gatherer lifestyle. This variant is much rarer in the Levant, and almost absent outside the region.

Looking even further back in time, researchers also found that Arab groups had the lowest Neanderthal ancestry of any known non-African population; instead, much of their ancestry comes from an ancient “ghost” population that probably did not interbreed with Neanderthals. This discovery lends weight to a recent theory**** about a mysterious “ghost” population that may either have left Africa and remained in the Middle East around 60,000 years ago, or remained in Africa until the disappearance of Neanderthals.

Dr Chris Tyler-Smith, lead author of the paper and alumnus of the Wellcome Sanger Institute, said: “Linked-read sequencing provides the resolution that allows reconstruction of the genetic histories of human populations at a level of detail that was previously not possible. Such work provides fascinating stories about our ancient past, will help us better understand the health and genetic diseases of Middle Eastern populations today, and bring us one step closer to recording all the richness of diversity. human.

Notes to editors:

  • To interview Dr Marc Haber, please contact Emma McKinney, Head of Media Relations (Health Sciences), University of Birmingham, tel. : +44 7815607157
  • To interview Dr Mohamed Almarri or Dr Chris Tyler-Smith, please contact Dr Matthew Midgley, Press Office, Wellcome Sanger Institute, tel. : 01223 494856
  • Mohammed et al (August 2021). “The Genomic History of the Middle East”. Cell.
  • The University of Birmingham is ranked among the top 100 institutions in the world. His work brings people from all over the world to Birmingham, including researchers, teachers and more than 6,500 international students from more than 150 countries.
  • The Wellcome Sanger Institute is a world-leading genomics research center. We undertake large-scale research that forms the foundation of knowledge in biology and medicine. We are open and collaborative; our data, results, tools and technologies are shared around the world to advance science. Our ambition is vast – we take on projects that are not possible anywhere else. We use the power of genome sequencing to understand and exploit the information contained in DNA. Funded by Wellcome, we have the freedom and support to push the boundaries of genomics. Our discoveries are used to improve health and understand life on Earth.
  • Wellcome supports science to solve the pressing health issues facing everyone. We support discovery research on life, health and well-being, and we address three global health challenges: mental health, global warming and infectious diseases.

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*The Levant refers to a region in the northern Middle East, which includes present-day Lebanon, Syria, Jordan, Israel and Palestine. South of this region is the Arabian Peninsula, an area dominated by the Arabian Desert, which includes Oman, Saudi Arabia, Yemen and the United Arab Emirates (UAE).

** Known as the 4.2 kilometer event, it was so severe that it has been suggested that it caused the collapse of several empires in the region, including the Old Kingdom in Egypt and the Akkadian Empire in Mesopotamia.

***The term “Arab” in this study refers to samples from the Arabian Peninsula (Emirati, Saudi, and Yemeni), Levantine for Syrians and Jordanians, and Iraqi-Arab and Iraqi-Kurdish for samples from Iraq.

****Lazaridis et al. (2016) Genomic Insights into the Origin of Agriculture in the Ancient Near East. Nature.

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