Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data

Abstract

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern American ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations.

Full text

Its licence does not allow us to show the full text. Read it at PubMed Central:

References 68

1. 1.

   Genomes Project Consortium (2012 ) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56–65.

   Not in our library10.1038/nature11632

2. 2.

   O'Rourke DH, Raff JA (2010 ) The human genetic history of the Americas: the final frontier. Curr Biol 20: R202–R207.

   Not in our library10.1016/j.cub.2009.11.051

3. 3.

   Luis Lanata J, Martino L, Osella A, Garcia-Herbst A (2008 ) Demographic conditions necessary to colonize new spaces: the case for early human dispersal in the Americas. World Archaeology 40: 520–537.

   Not in our library

4. 4.

   Goebel T, Waters MR, O'Rourke DH (2008 ) The late Pleistocene dispersal of modern humans in the Americas. Science 319: 1497–1502.

   Not in our library10.1126/science.1153569

5. 5.

   Dillehay TD (2009 ) Probing deeper into first American studies. Proc Natl Acad Sci USA 106: 971–978.

   Not in our library10.1073/pnas.0808424106

6. 6.

   Dillehay TD, Ramrez C, Pino M, Collins MB, Rossen J, et al (2008 ) Monte Verde: seaweed, food, medicine, and the peopling of South America. Science 320: 784–786.

   Not in our library10.1126/science.1156533

7. 7.

   Bodner M, Perego UA, Huber G, Fendt L, Rock AW, et al (2012 ) Rapid coastal spread of First Americans: Novel insights from South America's Southern Cone mitochondrial genomes. Genome Res 22: 811–820.

   Not in our library10.1101/gr.131722.111

8. 8.

   Hurst CT (1943 ) A Folsom site in a mountain valley of Colorado. American Antiquity 8: 250–253.

   Not in our library

9. 9.

   Meltzer DJ (2009) First Peoples in a New World. Colonizing Ice Age America. Univ of California Press.

   Not in our library

10. 10.

    Rouse I (1992) The Tainos: Rise and decline of the people who greeted Columbus. Yale University Press.

    Not in our library

11. 11.

    Rodrguez-Ramos R (2010) Rethinking Puerto Rican Precolonial History. University Alabama Press.

    Not in our library

12. 12.

    Veloz Maggiolo M (1991) Panorama histórico del caribe precolombino. Quinto Centenario del Descubrimiento de América Banco Central de la República Dominicana.

    Not in our library

13. 13.

    Hopper R (2008 ) Taino Indians: Settlements of the Caribbean. Lambda Alpha Journal 38: 62–69.

    Not in our library

14. 14.

    Moscoso F (2008) Caciques, aldeas y población tana de Boriquén (Puerto Rico), 1492–1582. Academia Puertorriqueña de la Historia.

    Not in our library

15. 15.

    Alegra RE, Quiñones ER (1999) Historia y cultura de Puerto Rico: Desde la época pre-colombina hasta nuestros das. Fundación Francisco Carvajal.

    Not in our library

16. 16.
    History shaped the geographic distribution of genomic admixture on the island of Puerto Rico. · 2011

    Not checked
17. 17.

    Underhill PA, Jin L, Zemans R, Oefner PJ, Cavalli-Sforza LL (1996 ) A pre-Columbian Y chromosome-specific transition and its implications for human evolutionary history. Proc Natl Acad Sci USA 93: 196–200.

    Not in our library10.1073/pnas.93.1.196

18. 18.

    Lell JT, Brown MD, Schurr TG, Sukernik RI, Starikovskaya YB, et al (1997 ) Y chromosome polymorphisms in native American and Siberian populations: identification of native American Y chromosome haplotypes. Hum Genet 100: 536–543.

    Not in our library10.1007/s004390050548

19. 19.

    Bianchi NO, Catanesi CI, Bailliet G, Martinez-Marignac VL, Bravi CM, et al (1998 ) Characterization of ancestral and derived Y-chromosome haplotypes of New World native populations. Am J Hum Genet 63: 1862–1871.

    Not in our library10.1086/302141

20. 20.

    Karafet TM, Zegura SL, Posukh O, Osipova L, Bergen A, et al (1999 ) Ancestral Asian source(s) of new world Y-chromosome founder haplotypes. Am J Hum Genet 64: 817–831.

    Not in our library10.1086/302282

21. 21.

    Bortolini MC, Salzano FM, Thomas MG, Stuart S, Nasanen SPK, et al (2003 ) Y-chromosome evidence for differing ancient demographic histories in the Americas. Am J Hum Genet 73: 524–539.

    Not in our library10.1086/377588

22. 22.

    Mesa NR, Mondragón MC, Soto ID, Parra MV, Duque C, et al (2000 ) Autosomal, mtDNA, and Y-chromosome diversity in Amerinds: pre- and post-Columbian patterns of gene flow in South America. Am J Hum Genet 67: 1277–1286.

    Not in our library10.1016/s0002-9297(07)62955-3

23. 23.

    Bortolini MC, Salzano FM, Bau CHD, Layrisse Z, Petzl-Erler ML, et al (2002 ) Y-chromosome biallelic polymorphisms and Native American population structure. Ann Hum Genet 66: 255–259.

    Not in our library10.1017/s0003480002001148

24. 24.

    Bailliet G, Ramallo V, Muzzio M, García A, Santos MR, et al (2009 ) Brief communication: Restricted geographic distribution for Y-Q* paragroup in South America. Am J Phys Anthropol 140: 578–582.

    Not in our library10.1002/ajpa.21133

25. 25.

    Torroni A, Schurr TG, Cabell MF, Brown MD, Neel JV, et al (1993 ) Asian affinities and continental radiation of the four founding Native American mtDNAs. Am J Hum Genet 53: 563–590.

    Not in our library

26. 26.
    The Phylogeny of the Four Pan-American MtDNA Haplogroups: Implications for Evolutionary and Disease Studies · 2008

    No notice
27. 27.
    Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins · 2011

    Not checked
28. 28.

    Malhi RS, Cybulski JS, Tito RY, Johnson J, Harry H, et al (2010 ) Brief communication: mitochondrial haplotype C4c confirmed as a founding genome in the Americas. Am J Phys Anthropol 141: 494–497.

    Not in our library10.1002/ajpa.21238

29. 29.

    Perego UA, Achilli A, Angerhofer N, Accetturo M, Pala M, et al (2009 ) Distinctive Paleo-Indian migration routes from Beringia marked by two rare mtDNA haplogroups. Curr Biol 19: 1–8.

    Not in our library10.1016/j.cub.2008.11.058

30. 30.

    Perego UA, Angerhofer N, Pala M, Olivieri A, Lancioni H, et al (2010 ) The initial peopling of the Americas: a growing number of founding mitochondrial genomes from Beringia. Genome Res 20: 1174–1179.

    Not in our library10.1101/gr.109231.110

31. 31.
    Beringian Standstill and Spread of Native American Founders · 2007

    No notice
32. 32.

    Sandoval K, Buentello-Malo L, Peñaloza-Espinosa R, Avelino H, Salas A, et al (2009 ) Linguistic and maternal genetic diversity are not correlated in Native Mexicans. Hum Genet 126: 521–531.

    Not in our library10.1007/s00439-009-0693-y

33. 33.

    Bonatto SL, Salzano FM (1997 ) A single and early migration for the peopling of the Americas supported by mitochondrial DNA sequence data. Proc Natl Acad Sci USA 94: 1866–1871.

    Not in our library10.1073/pnas.94.5.1866

34. 34.

    Mulligan CJ, Kitchen A, Miyamoto MM (2008 ) Updated three-stage model for the peopling of the Americas. PLoS ONE 3: e3199.

    Not in our library10.1371/journal.pone.0003199

35. 35.

    Fagundes NJR, Kanitz R, Eckert R, Valls ACS, Bogo MR, et al (2008 ) Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas. Am J Hum Genet 82: 583–592.

    Not in our library10.1016/j.ajhg.2007.11.013

36. 36.
    Genetic Variation and Population Structure in Native Americans · 2007

    No notice
37. 37.

    Rojas W, Parra MV, Campo O, Caro MA, Lopera JG, et al (2010 ) Genetic make up and structure of Colombian populations by means of uniparental and biparental DNA markers. Am J Phys Anthropol 143: 13–20.

    Not in our library10.1002/ajpa.21270

38. 38.

    Yang NN, Mazieres S, Bravi C, Ray N, Wang S, et al (2010 ) Contrasting patterns of nuclear and mtDNA diversity in Native American populations. Ann Hum Genet 74: 525–538.

    Not in our library10.1111/j.1469-1809.2010.00608.x

39. 39.

    Scliar MO, Soares-Souza GB, Chevitarese J, Lemos L, Magalhães WCS, et al (2012 ) The population genetics of quechuas, the largest native south american group: Autosomal sequences, SNPs, and microsatellites evidence high level of diversity. Am J Phys Anthropol 147: 443–451.

    Not in our library10.1002/ajpa.22013

40. 40.

    Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, et al (2012 ) Reconstructing Native American population history. Nature 488: 370–374.

    Not in our library10.1038/nature11258

Cited by papers we hold 3

• Ancestry-specific recent effective population size in the Americas · 2018
  No notice
• Genomic Insights into the Ancestry and Demographic History of South America · 2015
  No notice
• The gut microbiota of Colombians differs from that of Americans, Europeans and Asians · 2014
  No notice

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.