Reconstructing the Population Genetic History of the Caribbean

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The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre -⁠ and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse—which today is reflected by shorter, older ancestry tracts—consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse—reflected by longer, younger tracts—is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived.

Vyšlo v časopise: Reconstructing the Population Genetic History of the Caribbean. PLoS Genet 9(11): e32767. doi:10.1371/journal.pgen.1003925
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003925

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Zdroje

1. BustamanteCD, BurchardEG, De la VegaFM (2011) Genomics for the world. Nature 475 : 163–165.

2. WangS, RayN, RojasW, ParraMV, BedoyaG, et al. (2008) Geographic patterns of genome admixture in Latin American Mestizos. PLoS Genet 4: e1000037.

3. BrycK, VelezC, KarafetT, Moreno-EstradaA, ReynoldsA, et al. (2010) Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proc Natl Acad Sci U S A 107 Suppl 2 : 8954–8961.

4. ViaM, GignouxCR, RothLA, FejermanL, GalanterJ, et al. (2011) History shaped the geographic distribution of genomic admixture on the island of Puerto Rico. PLoS ONE 6: e16513.

5. KiddJM, GravelS, ByrnesJ, Moreno-EstradaA, MusharoffS, et al. (2012) Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet 91 : 660–671.

6. AbecasisGR, AutonA, BrooksLD, DePristoMA, DurbinRM, et al. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491 : 56–65.

7. Martinez-CruzadoJ, Toro-LabradorG, Viera-VeraJ, Rivera-VegaM, StartekJ, et al. (2005) Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis. Am J Phys Anthropol 128 : 131–55.

8. ConsortiumIH, FrazerKA, BallingerDG, CoxDR, HindsDA, et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449 : 851–861.

9. NelsonMR, BrycK, KingKS, IndapA, BoykoAR, et al. (2008) The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research. Am J Hum Genet 83 : 347–358.

10. BrycK, AutonA, NelsonMR, OksenbergJR, HauserSL, et al. (2010) Genome-wide patterns of population structure and admixture in West Africans and African Americans. Proc Natl Acad Sci U S A 107 : 786–791.

11. ReichD, PattersonN, CampbellD, TandonA, MazieresS, et al. (2012) Reconstructing Native American population history. Nature 488 : 370–374.

12. AlexanderDH, NovembreJ, LangeK (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19 : 1655–1664.

13. SandovalK, Moreno-EstradaA, MendizabalI, UnderhillPA, Lopez-ValenzuelaM, et al. (2012) Y-chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the Americas. Am J Phys Anthropol 148 : 395–405.

14. WangS, LewisC, JakobssonM, RamachandranS, RayN, et al. (2007) Genetic Variation and Population Structure in Native Americans. PLoS Genet 3: e185.

15. NovembreJ, JohnsonT, BrycK, KutalikZ, BoykoAR, et al. (2008) Genes mirror geography within Europe. Nature 456 : 98–101.

16. AutonA, BrycK, BoykoA, LohmuellerK, NovembreJ, et al. (2009) Global distribution of genomic diversity underscores rich complex history of continental human populations. Genome Res 19 : 1–30.

17. RischN, ChoudhryS, ViaM, BasuA, SebroR, et al. (2009) Ancestry-related assortative mating in Latino populations. Genome Biology 10: R132.

18. PoolJE, NielsenR (2008) Inference of Historical Changes in Migration Rate From the Lengths of Migrant Tracts. Genetics 181 : 711–719.

19. BrisbinA, BrycK, ByrnesJ, ZakhariaF, OmbergL, et al. (2012) PCAdmix: Principal Components-Based Assignment of Ancestry Along Each Chromosome in Individuals with Admixed Ancestry from Two or More Populations. Hum Biol 84 : 343–364.

20. GravelS (2012) Population genetics models of local ancestry. Genetics 191 : 607–619.

21. Fernandez-Mendez E (1970) Historia cultural de Puerto Rico. San Juan, Puerto Rico: Ediciones El Cemí.

22. TremblayM, VezinaH (2000) New estimates of intergenerational time intervals for the calculation of age and origins of mutations. Am J Hum Genet 66 : 651–658.

23. JohnsonNA, CoramMA, ShriverMD, RomieuI, BarshGS, et al. (2011) Ancestral components of admixed genomes in a mexican cohort. PLoS Genet 7: e1002410.

24. BotigueLR, HennBM, GravelS, MaplesBK, GignouxCR, et al. (2013) Gene flow from North Africa contributes to differential human genetic diversity in southern Europe. Proc Natl Acad Sci U S A 110 : 11791–11796.

25. LaoO, LuTT, NothnagelM, JungeO, Freitag-WolfS, et al. (2008) Correlation between genetic and geographic structure in Europe. Curr Biol 18 : 1241–1248.

26. TorgersonDG, GignouxCR, GalanterJM, DrakeKA, RothLA, et al. (2012) Case-control admixture mapping in Latino populations enriches for known asthma-associated genes. J Allergy Clin Immunol 130 : 76–82.

27. Rodríguez RamosR (2010) What is the Caribbean? An archaeological perspective. Journal of Caribbean Archaeology 3 : 19–51.

28. Rouse I (1986) Migrations in prehistory : inferring population movement from cultural remains. New Haven: Yale University Press. XIV, 202 p.

29. Rouse I (1993) The Tainos: Rise and Decline of the People who greeted Columbus. New Haven: Yale University Press. 224 p.

30. DiamondJ, BellwoodP (2003) Farmers and their languages: the first expansions. Science 300 : 597–603.

31. Ruhlen M (1991) A guide to the world's languages. StanfordCalifornia: Stanford University Press. 463 p.

32. DemarchiDA, Garcia MinistroA (2008) Genetic Structure of Native Populations from the Gran Chaco Region, South America. Int J Hum Genet 8 : 131–141.

33. Lalueza-FoxC, CalderonFL, CalafellF, MoreraB, BertranpetitJ (2001) MtDNA from extinct Tainos and the peopling of the Caribbean. Ann Hum Genet 65 : 137–151.

34. Eltis D, Richardson D (2010) Atlas of the Transatlantic Slave Trade. New Haven: Yale University Press. 307 p.

35. MaoX, BighamAW, MeiR, GutierrezG, WeissKM, et al. (2007) A genomewide admixture mapping panel for Hispanic/Latino populations. Am J Hum Genet 80 : 1171–1178.

36. PriceAL, PattersonNJ, PlengeRM, WeinblattME, ShadickNA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38 : 904–909.

37. BrowningS, BrowningB (2007) Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies. Am J Hum Genet 81 : 1084–1097.

38. RaikoT, IlinA, KarhunenJ (2007) Principal component analysis for large scale problems with lots of missing values. Machine Learning: ECML 2007 : 691–698.

39. PurcellS, NealeB, Todd-BrownK, ThomasL, FerreiraMAR, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81 : 559–575.

40. LiJZ, AbsherDM, TangH, SouthwickAM, CastoAM, et al. (2008) Worldwide human relationships inferred from genome-wide patterns of variation. Science 319 : 1100–1104.