Genomic Ancestry of North Africans Supports Back-to-Africa Migrations
North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.
Vyšlo v časopise:
Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. PLoS Genet 8(1): e32767. doi:10.1371/journal.pgen.1002397
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002397
Souhrn
North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.
Zdroje
1. AgencyCI 2008 The World Factbook
2. Jasinska-MygaBKachergusJVilario-GellCWiderCSoto-OrtolazaA 2010 Comprehensive sequencing of the LRRK2 gene in patients with familial Parkinson's disease from North Africa. Mov Disord 25 2052 2058
3. LesageSCondroyerCLannuzelALohmannETroianoA 2009 Molecular analyses of the LRRK2 gene in European and North African autosomal dominant Parkinson's disease. Br Med J 46 458464
4. LesageSPatinECondroyerCLeuteneggerALohmannE 2010 Parkinson's disease-related LRRK2 G2019S mutation results from independent mutational events in humans. Hum Mol Genet 19 1998 2004
5. ZhernakovaAElbersCFerwerdaBRomanosJTrynkaG 2010 Evolutionary and functional analysis of celiac risk loci reveals SH2B3 as a protective factor against bacterial infection. Am J Hum Genet 86 970 977
6. BarbujaniGPilastroADe DomenicoSRenfrewC 1994 Genetic variation in North Africa and Eurasia: Neolithic demic diffusion vs. Paleolithic colonisation. Am J Phys Anthropol 95 137 154
7. BoschECalafellFPerez-LezaunAComasDMateuE 1997 Population history of north Africa: evidence from classical genetic markers. Hum Biol 69 295 311
8. OlivieriAAchilliAPalaMBattagliaVFornarinoS 2006 The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa. Science 314 1767 1770
9. Maca-MeyerNGonzalezAMPestanoJFloresCLarrugaJM 2003 Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography. BMC Genet 4 15
10. Fadhlaoui ZidKRodrÌguez BotiguÈLNaouiNBenammar ElgaaiedACalafellF 2011 Mitochondrial DNA structure in North Africa reveals a genetic discontinuity in the Nile Valley. Am J Phys Anthropol 145 107 117
11. ArrediBPoloniEParacchiniSZerjalTFathallahD 2004 A predominantly neolithic origin for Y-chromosomal DNA variation in North Africa. Am J Hum Genet 75 338 345
12. BoschECalafellFComasDOefnerPJUnderhillPA 2001 High-resolution analysis of human Y-chromosome variation shows a sharp discontinuity and limited gene flow between northwestern Africa and the Iberian Peninsula. Am J Hum Genet 68 1019 1029
13. CloseAEWendorfF 1987 Prehistory of arid North Africa: essays in honor of Fred Wendorf: Southern Methodist Univ Press
14. ComasDCalafellFBenchemsiNHelalALefrancG 2000 Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits. Hum Genet 107 312 319
15. CrucianiFTrombettaBSellittoDMassaiaADestro-BisolG 2010 Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages. Eur J Hum Genet 18 800 807
16. HarichNCostaMFernandesVKandilMPereiraJ 2010 The trans-Saharan slave trade- clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages. BMC Evol Biol 10 138
17. LiJZAbsherDMTangHSouthwickAMCastoAM 2008 Worldwide human relationships inferred from genome-wide patterns of variation. Science 319 1100 1104
18. PriceATandonAPattersonNBarnesKRafaelsN 2009 Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet 5 e1000519 doi:10.1371/journal.pgen.1000519
19. ZakhariaFBasuAAbsherDAssimesTGoA 2009 Characterizing the admixed African ancestry of African Americans. Genome Biol 10 R141
20. BrycKAutonANelsonMROksenbergJRHauserSL 2010 Genome-wide patterns of population structure and admixture in West Africans and African Americans. Proc Natl Acad Sci USA 107 786 791
21. BrycKVelezCKarafetTMoreno-EstradaAReynoldsA 2010 Genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proc Natl Acad Sci USA 107 8954 8961
22. HancockDRomieuIShiMSienra-MongeJWuH 2009 Genome-wide association study implicates chromosome 9q21. 31 as a susceptibility locus for asthma in Mexican children. PLoS Genet 5 e1000623 doi:10.1371/journal.pgen.1000623
23. KlimentidisYMillerGShriverM 2009 Genetic admixture, self reported ethnicity, self estimated admixture, and skin pigmentation among Hispanics and Native Americans. Am J Phys Anthropol 138 375 383
24. ViaMGignouxCRRothLAFejermanLGalanterJ 2011 History Shaped the Geographic Distribution of Genomic Admixture on the Island of Puerto Rico. PLoS ONE 6 e16513 doi:10.1371/journal.pone.0016513
25. AlexanderDHNovembreJLangeK 2009 Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19 1655
26. IdaghdourYCzikaWShiannaKVLeeSHVisscherPM 2009 Geographical genomics of human leukocyte gene expression variation in southern Morocco. Nat Genet 42 62 67
27. GusevALoweJStoffelMDalyMAltshulerD 2009 Whole population, genome-wide mapping of hidden relatedness. Genome Res 19 318 326
28. BrisbinA 2010 Linkage Analaysis for Categorical Traits and Ancestry Assignment in Admixed Individuals Ithaca Cornell University
29. SankararamanSSridharSKimmelGHalperinE 2008 Estimating local ancestry in admixed populations. Am J Hum Genet 82 290 303
30. PoolJNielsenR 2009 Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics 181 711 719
31. AlbrechtsenANielsenFNielsenR 2010 Research article: Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol 27 2534 2547
32. HennBMGignouxCRJobinMGrankaJMMacphersonJ 2011 Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proc Natl Acad Sci USA 108 5154 5162
33. HellenthalGAutonAFalushD 2008 Inferring human colonization history using a copying model. PLoS Genet 4 doi:10.1371/journal.pgen.1000078
34. ZallouaPPlattDEl SibaiMKhalifeJMakhoulN 2008 Identifying genetic traces of historical expansions: Phoenician footprints in the Mediterranean. Am J Hum Genet 83 633 642
35. GarceaEAA 2010 South-Eastern Mediterranean Peoples Between 130,000 and 10,000 Years Ago: Oxbow Books
36. TangHCoramMWangPZhuXRischN 2006 Reconstructing genetic ancestry blocks in admixed individuals. Am J Hum Genet 79 1 12
37. ConradDJakobssonMCoopGWenXWallJ 2006 A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet 38 1251 1260
38. AlzualdeAIzagirreNAlonsoSAlonsoADe La R˙aC 2005 Temporal mitochondrial DNA variation in the Basque Country: Influence of Post Neolithic events. Ann Hum Genet 69 665 679
39. RodrÌguez-EzpeletaNAlvarez-BustoJImazLRegueiroMAzcrateMN 2010 High-density SNP genotyping detects homogeneity of Spanish and French Basques, and confirms their genomic distinctiveness from other European populations. Hum Genet 128 113 117
40. MoorjaniPPattersonNHirschhornJNKeinanAHaoL 2011 The History of African Gene Flow into Southern Europeans, Levantines, and Jews. PLoS Genet 7 e1001373 doi:10.1371/journal.pgen.1001373
41. TremblayMVÈzinaH 2000 New estimates of intergenerational time intervals for the calculation of age and origins of mutations. Am J Hum Genet 66 651 658
42. SeldinMFPasaniucBPriceAL 2011 New approaches to disease mapping in admixed populations. Nat Rev Genet 12 523 528
43. AltshulerDGibbsRPeltonenLDermitzakisESchaffnerS 2010 Integrating common and rare genetic variation in diverse human populations. Nature 467 52 58
44. Hunter-ZinckHMusharoffSSalitJAl-AliKChouchaneL 2010 Population Genetic Structure of the People of Qatar. Am J Hum Genet 7 17 25
45. PurcellSNealeBTodd-BrownKThomasLFerreiraMAR 2007 PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81 559 575
46. HolsingerKEWeirBS 2009 Genetics in geographically structured populations: defining, estimating and interpreting FST. Nature Reviews Genetics 10 639 650
47. BrowningSRBrowningBL 2007 Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81 1084 1097
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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