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Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture
The Levant is a region in the Near East with an impressive record of continuous human existence and major cultural developments since the Paleolithic period. Genetic and archeological studies present solid evidence placing the Middle East and the Arabian Peninsula as the first stepping-stone outside Africa. There is, however, little understanding of demographic changes in the Middle East, particularly the Levant, after the first Out-of-Africa expansion and how the Levantine peoples relate genetically to each other and to their neighbors. In this study we analyze more than 500,000 genome-wide SNPs in 1,341 new samples from the Levant and compare them to samples from 48 populations worldwide. Our results show recent genetic stratifications in the Levant are driven by the religious affiliations of the populations within the region. Cultural changes within the last two millennia appear to have facilitated/maintained admixture between culturally similar populations from the Levant, Arabian Peninsula, and Africa. The same cultural changes seem to have resulted in genetic isolation of other groups by limiting admixture with culturally different neighboring populations. Consequently, Levant populations today fall into two main groups: one sharing more genetic characteristics with modern-day Europeans and Central Asians, and the other with closer genetic affinities to other Middle Easterners and Africans. Finally, we identify a putative Levantine ancestral component that diverged from other Middle Easterners ∼23,700–15,500 years ago during the last glacial period, and diverged from Europeans ∼15,900–9,100 years ago between the last glacial warming and the start of the Neolithic.
Vyšlo v časopise: Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture. PLoS Genet 9(2): e32767. doi:10.1371/journal.pgen.1003316
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003316Souhrn
The Levant is a region in the Near East with an impressive record of continuous human existence and major cultural developments since the Paleolithic period. Genetic and archeological studies present solid evidence placing the Middle East and the Arabian Peninsula as the first stepping-stone outside Africa. There is, however, little understanding of demographic changes in the Middle East, particularly the Levant, after the first Out-of-Africa expansion and how the Levantine peoples relate genetically to each other and to their neighbors. In this study we analyze more than 500,000 genome-wide SNPs in 1,341 new samples from the Levant and compare them to samples from 48 populations worldwide. Our results show recent genetic stratifications in the Levant are driven by the religious affiliations of the populations within the region. Cultural changes within the last two millennia appear to have facilitated/maintained admixture between culturally similar populations from the Levant, Arabian Peninsula, and Africa. The same cultural changes seem to have resulted in genetic isolation of other groups by limiting admixture with culturally different neighboring populations. Consequently, Levant populations today fall into two main groups: one sharing more genetic characteristics with modern-day Europeans and Central Asians, and the other with closer genetic affinities to other Middle Easterners and Africans. Finally, we identify a putative Levantine ancestral component that diverged from other Middle Easterners ∼23,700–15,500 years ago during the last glacial period, and diverged from Europeans ∼15,900–9,100 years ago between the last glacial warming and the start of the Neolithic.
Zdroje
1. El-SibaiM, PlattDE, HaberM, XueY, YouhannaSC, et al. (2009) Geographical structure of the Y-chromosomal genetic landscape of the Levant: a coastal-inland contrast. Ann Hum Genet 73 : 568–581.
2. HammerMF, BeharDM, KarafetTM, MendezFL, HallmarkB, et al. (2009) Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood. Hum Genet 126 : 707–717.
3. HaberM, PlattDE, BadroDA, XueY, El-SibaiM, et al. (2011) Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon. Eur J Hum Genet 19 : 334–340.
4. BeharDM, MetspaluE, KivisildT, AchilliA, HadidY, et al. (2006) The matrilineal ancestry of Ashkenazi Jewry: portrait of a recent founder event. Am J Hum Genet 78 : 487–497.
5. ZallouaPA, XueY, KhalifeJ, MakhoulN, DebianeL, et al. (2008) Y-chromosomal diversity in Lebanon is structured by recent historical events. Am J Hum Genet 82 : 873–882.
6. AtzmonG, HaoL, Pe'erI, VelezC, PearlmanA, et al. (2010) Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry. Am J Hum Genet 86 : 850–859.
7. BeharDM, YunusbayevB, MetspaluM, MetspaluE, RossetS, et al. (2010) The genome-wide structure of the Jewish people. Nature 466 : 238–242.
8. MoorjaniP, PattersonN, HirschhornJN, KeinanA, HaoL, et al. (2011) The history of African gene flow into Southern Europeans, Levantines, and Jews. PLoS Genet 7: e1001373
9. LiJZ, AbsherDM, TangH, SouthwickAM, CastoAM, et al. (2008) Worldwide human relationships inferred from genome-wide patterns of variation. Science 319: doi:10.1371/journal.pgen.10013731100–1104.
10. AlexanderDH, NovembreJ, LangeK (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19 : 1655–1664.
11. BraySM, MulleJG, DoddAF, PulverAE, WoodingS, et al. (2010) Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population. Proc Natl Acad Sci U S A 107 : 16222–16227.
12. ConradDF, JakobssonM, CoopG, WenX, WallJD, et al. (2006) A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet 38 : 1251–1260.
13. HellenthalG, AutonA, FalushD (2008) Inferring human colonization history using a copying model. PLoS Genet 4: e1000078 doi:10.1371/journal.pgen.1000078
14. JakobssonM, ScholzSW, ScheetP, GibbsJR, VanLiereJM, et al. (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451 : 998–1003.
15. GattepailleLM, JakobssonM (2012) Combining markers into haplotypes can improve population structure inference. Genetics 190 : 159–174.
16. LawsonDJ, HellenthalG, MyersS, FalushD (2012) Inference of population structure using dense haplotype data. PLoS Genet 8: e1002453 doi:10.1371/journal.pgen.1002453
17. PattersonN, PriceAL, ReichD (2006) Population structure and eigenanalysis. PLoS Genet 2: e190 doi:10.1371/journal.pgen.0020190
18. AlexanderDH, LangeK (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics 12 : 246.
19. BouazizM, PaccardC, GuedjM, AmbroiseC (2012) SHIPS: Spectral Hierarchical Clustering for the Inference of Population Structure in Genetic Studies. PLoS ONE 7: e45685 doi:10.1371/journal.pone.0045685
20. LawsonDJ, FalushD (2012) Population identification using genetic data. Annu Rev Genomics Hum Genet 13 : 337–361.
21. MaherLA, RichterT, StockJT (2012) The Pre-Natufian Epipaleolithic: Long-term Behavioral Trends in the Levant. Evol Anthropol 21 : 69–81.
22. Bar-YosefO (1998) The Natufian culture in the Levant, threshold to the origins of agriculture. Evolutionary Anthropology 6 : 159–177.
23. BalaresqueP, BowdenGR, AdamsSM, LeungHY, KingTE, et al. (2010) A predominantly neolithic origin for European paternal lineages. PLoS Biol 8: e1000285 doi:10.1371/journal.pbio.1000285
24. HaakW, BalanovskyO, SanchezJJ, KoshelS, ZaporozhchenkoV, et al. (2010) Ancient DNA from European early neolithic farmers reveals their near eastern affinities. PLoS Biol 8: e1000536 doi:10.1371/journal.pbio.1000536
25. DupanloupI, BertorelleG, ChikhiL, BarbujaniG (2004) Estimating the impact of prehistoric admixture on the genome of Europeans. Mol Biol Evol 21 : 1361–1372.
26. PalaM, OlivieriA, AchilliA, AccetturoM, MetspaluE, et al. (2012) Mitochondrial DNA signals of late glacial recolonization of Europe from near eastern refugia. Am J Hum Genet 90 : 915–924.
27. HoltBM, FormicolaV (2008) Hunters of the Ice Age: The biology of Upper Paleolithic people. Am J Phys Anthropol Suppl 47 70–99.
28. MaherLA, RichterT, MacdonaldD, JonesMD, MartinL, et al. (2012) Twenty thousand-year-old huts at a hunter-gatherer settlement in eastern Jordan. PLoS ONE 7: e31447 doi:10.1371/journal.pone.0031447
29. PurcellS, NealeB, Todd-BrownK, ThomasL, FerreiraMA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81 : 559–575.
30. R Development Core Team (2011) R: A language and environment for statistical computing. R Foundation for Statistical Computing.
31. DelaneauO, MarchiniJ, ZaguryJF (2012) A linear complexity phasing method for thousands of genomes. Nat Methods 9 : 179–181.
32. FrazerKA, BallingerDG, CoxDR, HindsDA, StuveLL, et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449 : 851–861.
33. HolsingerKE, WeirBS (2009) Genetics in geographically structured populations: defining, estimating and interpreting F(ST). Nat Rev Genet 10 : 639–650.
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Genetika Reprodukčná medicína
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