Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes
Rozaimi Razali, Juan L. Rodríguez-Flores, Mohammadmersad Ghorbani, Haroon Naeem, Waleed Aamer, Elbay Aliyev, Ali Muhammad Jubran, Qatar Genome Project Management, Said I. Ismail, Wadha Al‐Muftah, Radja Badji, Hamdi Mbarek, Dima Darwish, Tasnim Fadl, Heba Yasin, Maryem Ennaifar, Rania G. Abdel‐latif, Fatima Alkuwari, Muhammad Arshad Alvi, Yasser Al‐Sarraj, Chadi Saad, Asmaa Althani, Biobank and Sample Preparation, Eleni Fethnou, Fatima Qafoud, Eiman Alkhayat, Nahla Afifi, Sequencing and Genotyping group, Sara Tomei, Wei Liu, Stephan Lorenz, Applied Bioinformatics Core, Najeeb Syed, Hakeem Almabrazi, Fazulur Rehaman Vempalli, Ramzi Temanni, Data Management and Computing Infrastructure group, Tariq Abu Saqri, Mohammedhusen Khatib, Mehshad Hamza, Tariq Abu Zaid, Ahmed El Khouly, Tushar Pathare, Shafeeq Poolat, Rashid Al‐Ali, Omar Albagha, Souhaila Al Khodor, Mashael Al‐Shafai, Ramin Badii, Lotfi Chouchane, Xavier Estivill, Khalid A. Fakhro, Younes Mokrab, Puthen V. Jithesh, Karsten Suhre, Zohreh Tatari-Calderone, Andrew G. Clark, Khalid A. Fakhro, Younes Mokrab
Abstract
Arab populations are largely understudied, notably their genetic structure and history. Here we present an in-depth analysis of 6,218 whole genomes from Qatar, revealing extensive diversity as well as genetic ancestries representing the main founding Arab genealogical lineages of Qahtanite (Peninsular Arabs) and Adnanite (General Arabs and West Eurasian Arabs). We find that Peninsular Arabs are the closest relatives of ancient hunter-gatherers and Neolithic farmers from the Levant, and that founder Arab populations experienced multiple splitting events 12-20 kya, consistent with the aridification of Arabia and farming in the Levant, giving rise to settler and nomadic communities. In terms of recent genetic flow, we show that these ancestries contributed significantly to European, South Asian as well as South American populations, likely as a result of Islamic expansion over the past 1400 years. Notably, we characterize a large cohort of men with the ChrY J1a2b haplogroup (n = 1,491), identifying 29 unique sub-haplogroups. Finally, we leverage genotype novelty to build a reference panel of 12,432 haplotypes, demonstrating improved genotype imputation for both rare and common alleles in Arabs and the wider Middle East.