Population Structure of Indigenous Inhabitants of Arabia

Overview

Journal PLoS Genet

Specialty Genetics

Date 2021 Jan 11

PMID 33428619

Citations 14

Authors

Katsuhiko Mineta

Kosuke Goto

Takashi Gojobori

Fowzan S Alkuraya

Affiliations

Soon will be listed here.

Abstract

Modern day Saudi Arabia occupies the majority of historical Arabia, which may have contributed to ancient waves of migration out of Africa. This ancient history has left a lasting imprint in the genetics of the region, including the diverse set of tribes that call Saudi Arabia their home. How these tribes relate to each other and to the world's major populations remains an unanswered question. In an attempt to improve our understanding of the population structure of Saudi Arabia, we conducted genomic profiling of 957 unrelated individuals who self-identify with 28 large tribes in Saudi Arabia. Consistent with the tradition of intra-tribal unions, the subjects showed strong clustering along tribal lines with the distance between clusters correlating with their geographical proximities in Arabia. However, these individuals form a unique cluster when compared to the world's major populations. The ancient origin of these tribal affiliations is supported by analyses that revealed little evidence of ancestral origin from within the 28 tribes. Our results disclose a granular map of population structure and have important implications for future genetic studies into Mendelian and common diseases in the region.

Citing Articles

Patterns of population structure and genetic variation within the Saudi Arabian population.

Malomane D, Williams M, Huber C, Mangul S, Abedalthagafi M, Chiang C bioRxiv. 2025; .

PMID: 39868174 PMC: 11761371. DOI: 10.1101/2025.01.10.632500.

A reference quality, fully annotated diploid genome from a Saudi individual.

Kulmanov M, Tawfiq R, Liu Y, Al Ali H, Abdelhakim M, Alarawi M Sci Data. 2024; 11(1):1278.

PMID: 39580486 PMC: 11585617. DOI: 10.1038/s41597-024-04121-2.

The impact of consanguinity on the design of iPSC banks.

Alkuraya I, De Vol E Stem Cell Reports. 2024; 19(8):1043-1047.

PMID: 38996491 PMC: 11368693. DOI: 10.1016/j.stemcr.2024.06.004.

Founder mutations and rare disease in the Arab world.

Marafi D Dis Model Mech. 2024; 17(6).

PMID: 38922202 PMC: 11225585. DOI: 10.1242/dmm.050715.

Imputation accuracy across global human populations.

Cahoon J, Rui X, Tang E, Simons C, Langie J, Chen M Am J Hum Genet. 2024; 111(5):979-989.

PMID: 38604166 PMC: 11080279. DOI: 10.1016/j.ajhg.2024.03.011.

References

Karafet T, Mendez F, Meilerman M, Underhill P, Zegura S, Hammer M . New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res. 2008; 18(5):830-8. PMC: 2336805. DOI: 10.1101/gr.7172008. View

Chang C, Chow C, Tellier L, Vattikuti S, Purcell S, Lee J . Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015; 4:7. PMC: 4342193. DOI: 10.1186/s13742-015-0047-8. View

Richards M, Rengo C, Cruciani F, Gratrix F, Wilson J, Scozzari R . Extensive female-mediated gene flow from sub-Saharan Africa into near eastern Arab populations. Am J Hum Genet. 2003; 72(4):1058-64. PMC: 1180338. DOI: 10.1086/374384. View

Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F . New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat Commun. 2012; 3:698. DOI: 10.1038/ncomms1701. View

Rasmussen M, Sikora M, Albrechtsen A, Korneliussen T, Moreno-Mayar J, Poznik G . The ancestry and affiliations of Kennewick Man. Nature. 2015; 523(7561):455-458. PMC: 4878456. DOI: 10.1038/nature14625. View

Bell C, Dinwiddie D, Miller N, Hateley S, Ganusova E, Mudge J . Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med. 2011; 3(65):65ra4. PMC: 3740116. DOI: 10.1126/scitranslmed.3001756. View

Abouelhoda M, Faquih T, El-Kalioby M, Alkuraya F . Revisiting the morbid genome of Mendelian disorders. Genome Biol. 2016; 17(1):235. PMC: 5123336. DOI: 10.1186/s13059-016-1102-1. View

Pickrell J, Pritchard J . Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 2012; 8(11):e1002967. PMC: 3499260. DOI: 10.1371/journal.pgen.1002967. View

Weissensteiner H, Pacher D, Kloss-Brandstatter A, Forer L, Specht G, Bandelt H . HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 2016; 44(W1):W58-63. PMC: 4987869. DOI: 10.1093/nar/gkw233. View

10.

Auton A, Brooks L, Durbin R, Garrison E, Kang H, Korbel J . A global reference for human genetic variation. Nature. 2015; 526(7571):68-74. PMC: 4750478. DOI: 10.1038/nature15393. View

11.

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M, Bender D . PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81(3):559-75. PMC: 1950838. DOI: 10.1086/519795. View

12.

Bradburd G, Ralph P, Coop G . Disentangling the effects of geographic and ecological isolation on genetic differentiation. Evolution. 2013; 67(11):3258-73. PMC: 3808528. DOI: 10.1111/evo.12193. View

13.

Przeworski M, Hudson R, Di Rienzo A . Adjusting the focus on human variation. Trends Genet. 2000; 16(7):296-302. DOI: 10.1016/s0168-9525(00)02030-8. View

14.

Scott E, Halees A, Itan Y, Spencer E, He Y, Azab M . Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery. Nat Genet. 2016; 48(9):1071-6. PMC: 5019950. DOI: 10.1038/ng.3592. View

15.

Alkuraya F . Discovery of mutations for Mendelian disorders. Hum Genet. 2016; 135(6):615-23. DOI: 10.1007/s00439-016-1664-8. View

16.

Zhou Y, Browning S, Browning B . A Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data. Am J Hum Genet. 2020; 106(4):426-437. PMC: 7118582. DOI: 10.1016/j.ajhg.2020.02.010. View

17.

Browning S, Browning B . Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent. Am J Hum Genet. 2015; 97(3):404-18. PMC: 4564943. DOI: 10.1016/j.ajhg.2015.07.012. View

18.

Alsmadi O, Thareja G, Alkayal F, Rajagopalan R, John S, Hebbar P . Genetic substructure of Kuwaiti population reveals migration history. PLoS One. 2013; 8(9):e74913. PMC: 3774671. DOI: 10.1371/journal.pone.0074913. View

19.

Browning S, Browning B . Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007; 81(5):1084-97. PMC: 2265661. DOI: 10.1086/521987. View

20.

Browning B, Zhou Y, Browning S . A One-Penny Imputed Genome from Next-Generation Reference Panels. Am J Hum Genet. 2018; 103(3):338-348. PMC: 6128308. DOI: 10.1016/j.ajhg.2018.07.015. View