Population structure of indigenous inhabitants of Arabia
Autoři:
Katsuhiko Mineta aff001; Kosuke Goto aff001; Takashi Gojobori aff001; Fowzan S. Alkuraya aff002
Působiště autorů:
Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
aff001; Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
aff002; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
aff003; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
aff004
Vyšlo v časopise:
Population structure of indigenous inhabitants of Arabia. PLoS Genet 17(1): e1009210. doi:10.1371/journal.pgen.1009210
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1009210
Souhrn
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.
Klíčová slova:
Asia – Europe – Haplogroups – Human genomics – Inbreeding – Population genetics – Saudi Arabia – principal component analysis
Zdroje
1. Przeworski M, Hudson RR, Di Rienzo A. Adjusting the focus on human variation. Trends in Genetics. 2000;16(7):296–302. doi: 10.1016/s0168-9525(00)02030-8 10858659
2. Reich DE, Schaffner SF, Daly MJ, McVean G, Mullikin JC, Higgins JM, et al. Human genome sequence variation and the influence of gene history, mutation and recombination. Nature genetics. 2002;32(1):135–42. doi: 10.1038/ng947 12161752
3. Frazer KA, Murray SS, Schork NJ, Topol EJ. Human genetic variation and its contribution to complex traits. Nature Reviews Genetics. 2009;10(4):241–51. doi: 10.1038/nrg2554 19293820
4. Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, Ganusova EE, Mudge J, et al. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Science translational medicine. 2011;3(65):65ra4–ra4. doi: 10.1126/scitranslmed.3001756 21228398
5. Manrai AK, Funke BH, Rehm HL, Olesen MS, Maron BA, Szolovits P, et al. Genetic misdiagnoses and the potential for health disparities. New England Journal of Medicine. 2016;375(7):655–65. doi: 10.1056/NEJMsa1507092 27532831
6. Wojcik GL, Graff M, Nishimura KK, Tao R, Haessler J, Gignoux CR, et al. Genetic analyses of diverse populations improves discovery for complex traits. Nature. 2019;570:514–8. doi: 10.1038/s41586-019-1310-4 31217584
7. Duncan L, Shen H, Gelaye B, Meijsen J, Ressler K, Feldman M, et al. Analysis of polygenic risk score usage and performance in diverse human populations. Nature communications. 2019;10(1):1–9. doi: 10.1038/s41467-018-07882-8 30602773
8. Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, et al. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nature communications. 2012;3:698. doi: 10.1038/ncomms1701 22426219
9. Rasmussen M, Sikora M, Albrechtsen A, Korneliussen TS, Moreno-Mayar JV, Poznik GD, et al. The ancestry and affiliations of Kennewick Man. Nature. 2015;523:455–8. doi: 10.1038/nature14625 26087396
10. Groucutt HS, Grün R, Zalmout IA, Drake NA, Armitage SJ, Candy I, et al. Homo sapiens in Arabia by 85,000 years ago. Nature ecology & evolution. 2018;2(5):800–9. doi: 10.1038/s41559-018-0518-2 29632352
11. Fernandes V, Alshamali F, Alves M, Costa MD, Pereira JB, Silva NM, et al. The Arabian cradle: mitochondrial relicts of the first steps along the southern route out of Africa. The American Journal of Human Genetics. 2012;90(2):347–55. doi: 10.1016/j.ajhg.2011.12.010 22284828
12. Alkuraya FS. Genetics and genomic medicine in Saudi Arabia. Molecular genetics & genomic medicine. 2014;2(5):369–78. doi: 10.1002/mgg3.97 25333061
13. Scott EM, Halees A, Itan Y, Spencer EG, He Y, Azab MA, et al. Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery. Nature Genetics. 2016;48:1071–6. doi: 10.1038/ng.3592 27428751
14. Alsalem AB, Halees AS, Anazi S, Alshamekh S, Alkuraya FS. Autozygome sequencing expands the horizon of human knockout research and provides novel insights into human phenotypic variation. PLoS Genet. 2013;9(12):e1004030. doi: 10.1371/journal.pgen.1004030 24367280
15. Consortium GP. A global reference for human genetic variation. Nature. 2015;526(7571):68–74. doi: 10.1038/nature15393 26432245
16. Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536(7616):285–91. doi: 10.1038/nature19057 27535533
17. Alsmadi O, Thareja G, Alkayal F, Rajagopalan R, John SE, Hebbar P, et al. Genetic substructure of Kuwaiti population reveals migration history. PloS one. 2013;8(9):e74913. doi: 10.1371/journal.pone.0074913 24066156
18. Hunter-Zinck H, Musharoff S, Salit J, Al-Ali KA, Chouchane L, Gohar A, et al. Population genetic structure of the people of Qatar. The American Journal of Human Genetics. 2010;87(1):17–25. doi: 10.1016/j.ajhg.2010.05.018 20579625
19. Rodriguez-Flores JL, Fakhro K, Agosto-Perez F, Ramstetter MD, Arbiza L, Vincent TL, et al. Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations. Genome research. 2016;26(2):151–62. doi: 10.1101/gr.191478.115 26728717
20. Richards M, Rengo C, Cruciani F, Gratrix F, Wilson JF, Scozzari R, et al. Extensive female-mediated gene flow from sub-Saharan Africa into near eastern Arab populations. The American Journal of Human Genetics. 2003;72(4):1058–64. doi: 10.1086/374384 12629598
21. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome research. 2008;18(5):830–8. doi: 10.1101/gr.7172008 18385274
22. Loogväli E-L, Roostalu U, Malyarchuk BA, Derenko MV, Kivisild T, Metspalu E, et al. Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia. Molecular Biology and Evolution. 2004;21(11):2012–21. doi: 10.1093/molbev/msh209 15254257
23. Ceballos FC, Joshi PK, Clark DW, Ramsay M, Wilson JF. Runs of homozygosity: windows into population history and trait architecture. Nature Reviews Genetics. 2018;19(4):220. doi: 10.1038/nrg.2017.109 29335644
24. Moorjani P, Patterson N, Hirschhorn JN, Keinan A, Hao L, Atzmon G, et al. The history of African gene flow into Southern Europeans, Levantines, and Jews. PLoS genetics. 2011;7(4):e1001373. doi: 10.1371/journal.pgen.1001373 21533020
25. Alkuraya F. Impact of new genomic tools on the practice of clinical genetics in consanguineous populations: the Saudi experience. Clinical genetics. 2013;84(3):203–8. doi: 10.1111/cge.12131 23451714
26. Alkuraya FS. Discovery of mutations for Mendelian disorders. Human genetics. 2016;135(6):615–23. doi: 10.1007/s00439-016-1664-8 27068822
27. Alazami AM, Hijazi H, Al-Dosari MS, Shaheen R, Hashem A, Aldahmesh MA, et al. Mutation in ADAT3, encoding adenosine deaminase acting on transfer RNA, causes intellectual disability and strabismus. Journal of medical genetics. 2013;50(7):425–30. doi: 10.1136/jmedgenet-2012-101378 23620220
28. Abouelhoda M, Faquih T, El-Kalioby M, Alkuraya FS. Revisiting the morbid genome of Mendelian disorders. Genome biology. 2016;17(1):235. doi: 10.1186/s13059-016-1102-1 27884173
29. Sidore C, Busonero F, Maschio A, Porcu E, Naitza S, Zoledziewska M, et al. Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers. Nature genetics. 2015;47(11):1272. doi: 10.1038/ng.3368 26366554
30. Al-Owain M, Al-Zaidan H, Al-Hassnan Z. Map of autosomal recessive genetic disorders in Saudi Arabia: concepts and future directions. American Journal of Medical Genetics Part A. 2012;158A(10):2629–40. doi: 10.1002/ajmg.a.35551 22903695
31. Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen W-M. Robust relationship inference in genome-wide association studies. Bioinformatics. 2010;26(22):2867–73. doi: 10.1093/bioinformatics/btq559 20926424
32. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics. 2007;81(3):559–75. doi: 10.1086/519795 17701901
33. Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015;4(1):7. doi: 10.1186/s13742-015-0047-8 25722852
34. Bergström A, McCarthy SA, Hui R, Almarri MA, Ayub Q, Danecek P, et al. Insights into human genetic variation and population history from 929 diverse genomes. Science. 2020;367(6484). doi: 10.1126/science.aay5012 32193295
35. Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, et al. The Simons genome diversity project: 300 genomes from 142 diverse populations. Nature. 2016;538(7624):201–6. doi: 10.1038/nature18964 27654912
36. Bradburd GS, Ralph PL, Coop GM. Disentangling the effects of geographic and ecological isolation on genetic differentiation. Evolution. 2013;67(11):3258–73. doi: 10.1111/evo.12193 24102455
37. Goudet J. Hierfstat, a package for R to compute and test hierarchical F-statistics. Molecular Ecology Notes. 2005;5(1):184–6.
38. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome research. 2009;19(9):1655–64. doi: 10.1101/gr.094052.109 19648217
39. Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS genetics. 2012;8(11):e1002967. doi: 10.1371/journal.pgen.1002967 23166502
40. Milanesi M, Capomaccio S, Vajana E, Bomba L, Garcia JF, Ajmone-Marsan P, et al. BITE: an R package for biodiversity analyses. BioRxiv. 2017:181610.
41. Felsenstein J. PHYLIP-Phylogeny Inference Package (Version 3.2) Cladistics 5: 164–166. 1989.
42. Loh P-R, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, et al. Inferring admixture histories of human populations using linkage disequilibrium. Genetics. 2013:genetics. 112.147330. doi: 10.1534/genetics.112.147330 23410830
43. Browning SR, Browning BL. Accurate non-parametric estimation of recent effective population size from segments of identity by descent. The American Journal of Human Genetics. 2015;97(3):404–18. doi: 10.1016/j.ajhg.2015.07.012 26299365
44. Browning BL, Zhou Y, Browning SR. A one-penny imputed genome from next-generation reference panels. The American Journal of Human Genetics. 2018;103(3):338–48. doi: 10.1016/j.ajhg.2018.07.015 30100085
45. Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. The American Journal of Human Genetics. 2007;81(5):1084–97. doi: 10.1086/521987 17924348
46. Zhou Y, Browning SR, Browning BL. A fast and simple method for detecting identity by descent segments in large-scale data. The American Journal of Human Genetics. 2020. doi: 10.1016/j.ajhg.2020.02.010 32169169
47. Jostins L, Xu Y, McCarthy S, Ayub Q, Durbin R, Barrett J, et al. YFitter: Maximum likelihood assignment of Y chromosome haplogroups from low-coverage sequence data. arXiv preprint arXiv:14077988. 2014.
48. Weissensteiner H, Pacher D, Kloss-Brandstätter A, Forer L, Specht G, Bandelt H-J, et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic acids research. 2016;44(W1):W58–W63. doi: 10.1093/nar/gkw233 27084951
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