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

PLoS Genetics

Volumn 9, Issue 12, 2013, Pages

  Gravel, Simon ^a   Zakharia, Fouad ^b   Moreno Estrada, Andres ^b   Byrnes, Jake K ^b,c   Muzzio, Marina ^b,d,m   Rodriguez Flores, Juan L ^e   Kenny, Eimear E ^b,f   Gignoux, Christopher R ^g   Maples, Brian K ^b   Guiblet, Wilfried ^h   Dutil, Julie ⁱ   Via, Marc ^g,j   Sandoval, Karla ^b   Bedoya, Gabriel ^k   Oleksyk, Taras K ^h   Ruiz Linares, Andres ^l   Burchard, Esteban G ^g   Martinez Cruzado, Juan Carlos ^h   Bustamante, Carlos D ^b  

^a MCGILL UNIVERSITY   (Canada)

^b STANFORD UNIVERSITY   (United States)

^c Ancestrycom DNA LLC   (United States)

^d Facultad de Ciencias Naturales e Instituto M Lillo   (Argentina)

^e WEILL CORNELL MEDICAL COLLEGE   (United States)

^f MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^g UNIVERSITY OF CALIFORNIA   (United States)

^h UNIVERSITY OF PUERTO RICO   (Puerto Rico)

ⁱ PONCE SCHOOL OF MEDICINE   (Puerto Rico)

^j UNIVERSITY OF BARCELONA   (Spain)

^k UNIVERSIDAD DE ANTIOQUIA   (Colombia)

^l UNIVERSITY COLLEGE LONDON   (United Kingdom)

^m UNIVERSIDAD NACIONAL DE LA PLATA   (Argentina)

more..

Author keywords

[No Author keywords available]

Indexed keywords

AMERICAN INDIAN; ARTICLE; CONTROLLED STUDY; EXOME; GENE FREQUENCY; GENOME ANALYSIS; HUMAN; POPULATION DISTRIBUTION; POPULATION GENETICS; POPULATION MIGRATION; SEQUENCE ANALYSIS;

AFRICAN CONTINENTAL ANCESTRY GROUP; CHROMOSOME MAPPING; CONTINENTAL POPULATION GROUPS; EUROPEAN CONTINENTAL ANCESTRY GROUP; EXOME; GENE FREQUENCY; GENETICS, POPULATION; GENOME, HUMAN; HISPANIC AMERICANS; HUMAN GENOME PROJECT; HUMAN MIGRATION; HUMANS; INDIANS, NORTH AMERICAN; MEXICAN AMERICANS; MEXICO; PUERTO RICO;

EID: 84892684329     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004023     Document Type: Article

References (68)

1. Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.
2. O'Rourke DH, Raff JA, (2010) The human genetic history of the Americas: the final frontier. Curr Biol 20: R202-R207.
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.
4. Goebel T, Waters MR, O'Rourke DH, (2008) The late Pleistocene dispersal of modern humans in the Americas. Science 319: 1497-1502.
5. Dillehay TD, (2009) Probing deeper into first American studies. Proc Natl Acad Sci USA 106: 971-978.
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.
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.
8. Hurst CT, (1943) A Folsom site in a mountain valley of Colorado. American Antiquity 8: 250-253.
9. Meltzer DJ (2009) First Peoples in a New World. Colonizing Ice Age America. Univ of California Press.
10. Rouse I (1992) The Tainos: Rise and decline of the people who greeted Columbus. Yale University Press.
11. Rodrguez-Ramos R (2010) Rethinking Puerto Rican Precolonial History. University Alabama Press.
12. Veloz Maggiolo M (1991) Panorama histórico del caribe precolombino. Quinto Centenario del Descubrimiento de América Banco Central de la República Dominicana.
13. Hopper R, (2008) Taino Indians: Settlements of the Caribbean. Lambda Alpha Journal 38: 62-69.
14. Moscoso F (2008) Caciques, aldeas y población tana de Boriquén (Puerto Rico), 1492-1582. Academia Puertorriqueña de la Historia.
15. Alegra RE, Quiñones ER (1999) Historia y cultura de Puerto Rico: Desde la época pre-colombina hasta nuestros das. Fundación Francisco Carvajal.
16. Via M, Gignoux CR, Roth LA, Fejerman L, Galanter J, et al. (2011) History Shaped the Geographic Distribution of Genomic Admixture on the Island of Puerto Rico. PLoS ONE 6: e16513.
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.
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.
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.
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.
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.
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.
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.
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.
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.
26. Achilli A, Perego UA, Bravi CM, Coble MD, Kong QP, et al. (2008) The Phylogeny of the Four Pan-American MtDNA Haplogroups: Implications for Evolutionary and Disease Studies. PLoS ONE 3: e1764.
27. Kumar S, Bellis C, Zlojutro M, Melton PE, Blangero J, et al. (2011) Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins. BMC Evol Biol 11: 293.
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.
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.
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.
31. Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, et al. (2007) Beringian standstill and spread of Native American founders. PLoS ONE 2: e829.
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.
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.
34. Mulligan CJ, Kitchen A, Miyamoto MM, (2008) Updated three-stage model for the peopling of the Americas. PLoS ONE 3: e3199.
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.
36. Wang S, Lewis CM, Jakobsson M, Ramachandran S, Ray N, et al. (2007) Genetic variation and population structure in native Americans. PLoS Genet 3: e185.
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.
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.
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.
40. Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, et al. (2012) Reconstructing Native American population history. Nature 488: 370-374.
41. Martínez-Cortés G, Salazar-Flores J, Fernández-Rodríguez LG, Rubi-Castellanos R, Rodrguez-Loya C, et al. (2012) Admixture and population structure in Mexican-Mestizos based on paternal lineages. J Hum Genet 57: 568-574.
42. Rubi-Castellanos R, Martínez-Cortés G, Muñoz-Valle JF, González-Martín A, Cerda-Flores RM, et al. (2009) Pre-Hispanic Mesoamerican demography approximates the present-day ancestry of Mestizos throughout the territory of Mexico. Am J Phys Anthropol 139: 284-294.
43. Bedoya G, Montoya P, García J, Soto I, Bourgeois S, et al. (2006) Admixture dynamics in Hispanics: a shift in the nuclear genetic ancestry of a South American population isolate. Proc Natl Acad Sci USA 103: 7234-7239.
44. Martínez-Cruzado JC, Toro-Labrador G, Viera-Vera J, Rivera-Vega MY, Startek J, et al. (2005) Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis. Am J Phys Anthropol 128: 131-155.
45. Bolnick DA, Bolnick DI, Smith DG, (2006) Asymmetric male and female genetic histories among Native Americans from Eastern North America. Mol Biol Evol 23: 2161-2174.
46. Carvajal-Carmona LG, Soto ID, Pineda N, Ortíz-Barrientos D, Duque C, et al. (2000) Strong Amerind/White Sex Bias and a Possible Sephardic Contribution among the Founders of a Population in Northwest Colombia. The American Journal of Human Genetics 67: 1287-1295.
47. Alexander DH, Novembre J, Lange K, (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19: 1655-1664.
48. Maples BK, Gravel S, Kenny EE, Bustamante CD, (2013) RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference. Am J Hum Genet 93: 278-288.
49. Galanter JM, Fernandez-Lopez JC, Gignoux CR, Barnholtz-Sloan J, Fernandez-Rozadilla C, et al. (2012) Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas. PLoS Genet 8: e1002554.
50. Moreno-Estrada A, Gravel S, Zakharia F, McCauley JL, Byrnes JK, et al. (2013) Reconstructing the Population Genetic History of the Caribbean. arXiv.
51. Moseley C, (2004) Encyclopedia of the World's Endangered Languages. Routledge.
52. Combes I, Lowrey K, (2006) Slaves without Masters? Arawakan Dynasties among the Chiriguano (Bolivian Chaco, Sixteenth to Twentieth Centuries). Ethnohistory 53: 689-714.
53. Gravel S, (2012) Population genetics models of local ancestry. Genetics 191: 607-619.
54. Kidd JM, Gravel S, Byrnes J, Moreno-Estrada A, Musharoff S, 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.
55. Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, et al. (2008) Whole population, genome-wide mapping of hidden relatedness. Genome Res 19: 318-326.
56. Palamara PF, Lencz T, Darvasi A, Pe'er I, (2012) Length distributions of identity by descent reveal fine-scale demographic history. Am J Hum Genet 91: 809-822.
57. Baran Y, Pasaniuc B, Sankararaman S, Torgerson DG, Gignoux C, et al. (2012) Fast and accurate inference of local ancestry in Latino populations. Bioinformatics 28: 1359-1367.
58. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD, (2009) Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet 5: e1000695.
59. Myers S, Fefferman C, Patterson N, (2008) Can one learn history from the allelic spectrum? Theor Popul Biol 73: 342-348.
60. Salzano FM, Bortolini MC (2005) The Evolution and Genetics of Latin American Populations. Cambridge University Press.
61. Moscoso F (2008) Caciques, aldeas y población taína de Boriquén (Puerto Rico), 1492-1582. Academia puertorriquena de la historia.
62. Dobyns HF, (1966) An appraisal of techniques with a new hemispheric estimate. Current Anthropology 7: 395-416.
63. Scally A, Durbin R, (2012) Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet 13: 745-753.
64. Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, et al. (2012) De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 485: 237-241.
65. Gorostiza A, Acunha-Alonzo V, Regalado-Liu L, Tirado S, Granados J, et al. (2012) Reconstructing the history of Mesoamerican populations through the study of the mitochondrial DNA control region. PLoS ONE 7: e44666.
66. Bryc K, Velez C, Karafet T, Moreno-Estrada A, Reynolds A, et al. (2010) Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proc Natl Acad Sci USA 107 Suppl 2: 8954-8961.
67. Wang S, Ray N, Rojas W, Parra MV, Bedoya G, et al. (2008) Geographic patterns of genome admixture in Latin American Mestizos. PLoS Genet 4: e1000037.
68. Tremblay M, Vézina H, (2000) New estimates of intergenerational time intervals for the calculation of age and origins of mutations. Am J Hum Genet 66: 651-658.