Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies

American Journal of Physical Anthropology

Volumn 155, Issue 3, 2014, Pages 352-368

  Vilar, Miguel G ^a,b   Melendez, Carlalynne ^a   Sanders, Akiva B ^a   Walia, Akshay ^a   Gaieski, Jill B ^a   Owings, Amanda C ^a   Schurr, Theodore G ^a   Adhikarla, Syama ^c   Adler, Christina J ^d   Balanovska, Elena ^e   Balanovsky, Oleg ^e   Bertranpetit, Jaume ^f   Clarke, Andrew C ^g   Comas, David ^f   Cooper, Alan ^d   Der Sarkissian, Clio S I ^d   GaneshPrasad, ArunKumar ^c   Haak, Wolfgang ^d   Haber, Marc ^f,h   Hobbs, Angela ⁱ   Javed, Asif ^j   Jin, Li ^k   Kaplan, Matthew E ^l   Li, Shilin ^k   Martínez Cruz, Begoña ^f   Matisoo Smith, Elizabeth A ^g   Melé, Marta ^f   Merchant, Nirav C ^l   Mitchell, R John ^m   Parida, Laxmi ^j   Pitchappan, Ramasamy ^c   Platt, Daniel E ^j   Quintana Murci, Lluis ⁿ   Renfrew, Colin ^o   Lacerda, Daniela R ^p   Royyuru, Ajay K ^j   Santos, Fabrício R ^p   Soodyall, Himla ⁱ   Soria Hernanz, David F ^b   Swamikrishnan, Pandikumar ^j   Tyler Smith, Chris ^q   Santhakumari, Arun Varatharajan ^c   Vieira, Pedro Paulo ^r   Wells, R Spencer ^b   Zalloua, Pierre A ^h   Ziegle, Janet S ^s   more..

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b NATIONAL GEOGRAPHIC SOCIETY   (United States)

^c MADURAI KAMARAJ UNIVERSITY   (India)

^d UNIVERSITY OF ADELAIDE   (Australia)

^e RESEARCH CENTRE FOR MEDICAL GENETICS   (Russian Federation)

^f UNIVERSITAT POMPEU FABRA   (Spain)

^g UNIVERSITY OF OTAGO   (New Zealand)

^h LEBANESE AMERICAN UNIVERSITY   (Lebanon)

ⁱ NATIONAL HEALTH LABORATORY SERVICE   (South Africa)

^j IBM   (United States)

^k FUDAN UNIVERSITY   (China)

^l UNIVERSITY OF ARIZONA   (United States)

^m LA TROBE UNIVERSITY   (Australia)

ⁿ INSTITUT PASTEUR   (France)

^o UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^p FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

^q WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^r FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^s APPLIED BIOSYSTEMS   (United States)

more..

Author keywords

Caribbean; Haplogroup; Haplotype; Migration; mtDNA; Y chromosome

Indexed keywords

MITOCHONDRIAL DNA;

AMERICAN INDIAN; ARTICLE; BRAZILIAN; COLOMBIAN; COLONIAL SPECIES; CONTROLLED STUDY; CUBAN; FEMALE; GENE LOCUS; GENETIC VARIABILITY; GUYANESE; HAPLOTYPE; HISTORY OF MEDICINE; HUMAN; MAJOR CLINICAL STUDY; MALE; MITOCHONDRIAL HAPLOGROUP; PUERTO RICAN; PUERTO RICO; SALVADORAN; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; TRINIDADIAN; VENEZUELAN; Y CHROMOSOME; Y CHROMOSOME HAPLOGROUP; CARIBBEAN ISLANDS; CAUCASIAN; GENETICS; MIGRATION; PHYSICAL ANTHROPOLOGY;

ANTHROPOLOGY, PHYSICAL; CHROMOSOMES, HUMAN, Y; DNA, MITOCHONDRIAL; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENETIC VARIATION; HAPLOTYPES; HUMAN MIGRATION; HUMANS; INDIANS, SOUTH AMERICAN; MALE; PUERTO RICO; WEST INDIES;

EID: 84908153889     PISSN: 00029483     EISSN: 10968644     Source Type: Journal    
DOI: 10.1002/ajpa.22569     Document Type: Article

References (143)

1. Achilli A, Perego UA, Bravi CM, Coble MD, Kong QP, Woodward SR, Salas A, Torroni A, Bandelt HJ. 2008. The phylogeny of the four Pan-American mtDNA haplogroups: implications for evolutionary and disease studies. PLoS One 3:e1764.
2. Achilli A, Rengo C, Magri C, Battaglia V, Olivieri A, Scozzari R, Cruciani F, Zeviani M, Briem E, Carelli V, Moral P, Dugoujon J-M, Roostalu U, Loogväli E-L, Kivisild T, Bandelt H-J, Richards M, Villems R, Silvana Santachiara-Benerecetti A, Semino O, Torroni A. 2004. The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. Am J Hum Genet 75:910-918.
3. Alegria R. 1965. On Porto Rican archaeology. Am Antiq 3:246-249.
4. Allaire L. 1980. On the historicity of Carib migrations in the Lesser Antilles. Am Antiq 45:238-245.
5. Allaire L. 1997. Anse Trabaud: rapport 1997. In: Giraud JP, editor. Le néolithique de la Martinique dans son contexte antillais. (Projet collectif de recherche) SRA Fort de France, Martiniques) (The sites of Norman Estate, Anse des Pères, and Hope Estate with a contribution to the 'La Hueca problem'), Vol. 4. Leiden: Archaeological Studies Leiden University. p 19-22.
6. Alves-Silva J, Santos MS, Guimaraes PEM, Ferreira ACS, Bandelt HJ, Pena SDJ, Ferreira Prado V. 2000. The ancestry of Brazilian mtDNA lineages. Am J Hum Genet 67: 144-161.
7. Anderson S, Bankier AT, Barrell BG, DeBruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlick DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG. 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-465.
8. Andrews RM, Kubacka I, Chinnery PF, Lightowlers N, Turnbull DM, Howell N. 1999. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147.
9. Arredi B, Poloni ES, Paracchini S, Zerjal T, Fathallah DM, Makrelouf M, Pascali VL, Novelletto A, Tyler-Smith C. 2004. A predominantly Neolithic origin for Y-chromosomal DNA variation in North Africa. Am J Hum Genet 75:338-345.
10. Bandelt HJ, Alves-Silva J, Guimaraes PEM, Santos MS, Brehm A, Pereira L, Coppa A, Larruga JM, Rengo C, Scozzari R, Torroni A, Prata MJ, Amorim A, Prado VF, Pena SDJ. 2001. Phylogeography of the human mitochondrial haplogroup L3e: a snapshot of African prehistory and Atlantic slave trade. Ann Hum Genet 65:549-563.
11. Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37-48.
12. Bandelt H-J, Quintana-Murci L, Salas A, Macaulay V. 2002. The fingerprint of phantom mutations in mitochondrial DNA data. Am J Hum Genet 71:1150-1160.
13. Benn Torres J, Bonilla C, Robbins CM, Waterman L, Moses TY, Hernandez W, Santos ER, Bennet F, Aiken W, Tullock T, Coard K, Hennis A, Wu S, Nemesure B, Leske CM, Freeman V, Carpten J, Kittles RA. 2008. Admixture and population stratification in African Caribbean populations. Ann Hum Genet 72(Pt 1):90-98.
14. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2010. GenBank. Nucleic Acids Res 38(Suppl 1):D46-D51.
15. 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.
16. Bolnick DA, Smith DG. 2003. Unexpected patterns of mitochondrial DNA variation among Native Americans from the southeastern United States. Am J Phys Anthropol 122:336-354.
17. Boyd-Bowman P. 1956. The regional origins of the earliest spanish colonists of America. PMLA 71:1152-1172.
18. Bryan A. 1973. Paleoenvironments and cultural diversity in late Pleistocene South America. Quaternary Res 3:237-256.
19. Bryc K, Velez C, Karafet T, Moreno-Estrada A, Reynolds A, Auton A, Hammer M, Bustamante CD, Ostrer H. 2010. Genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proc Nat Acad Sci USA 107:8954-8961.
20. Campbell L. 1997. American Indian languages: the historical linguistics of native America. New York: Oxford University Press.
21. Cardenas MMSG, Ribeiro-dos-Santos Â, Santos S, Mansur AJ, Pereira AC, Fridman C. 2013. Assessment of the relationship between self-declared ethnicity, mitochondrial haplogroups and genomic ancestry in Brazilian individuals. PLoS One 8: e62005.
22. Chandler JF. 2006. Estimating per-locus mutation rates. J Genet Geneal 2:27-33.
23. Coelho M, Sequeira F, Luiselli D, Beleza S, Rocha J. 2009. On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola. BMC Evol Biol 9: Article 80.
24. Crespillo M, Luque JA, Paredes M, Fernandez R, Ramirez E, Valverde JL. 2000. Mitochondrial DNA sequences for 118 individuals from northeastern Spain. Int J Legal Med 114: 130-132.
25. Crosby AW. 2003. The Columbian exchange: biological and cultural consequences of 1492. Westport: Praeger Publishers.
26. Cruciani F, La Fratta R, Trombetta B, Santolamazza P, Sellitto D, Colomb EB, Dugojong JM, Crivellaro F, Benincasa T, Pascone R, Moral P, Watson E, Melegh B, Barbujani G, Fuselli S, Vona G, Zagradisnik B, Assum G, Brdicka R, Kozlov AI, Efremov GD, Coppa A, Novelletto A, Scozzari R. 2007. Tracing past human male movements in northern/eastern Africa and western Eurasia: new clues from Y-chromosomal haplogroups E-M78 and J-M12. Mol Biol Evol 24:1300-1311.
27. Cruciani F, Santolamazza P, Shen P, Macaulay V, Moral P, Olckers A, Modiani D, Holmes S, Destro-Bisol G, Coia V, Wallace DC, Oefner PJ, Torroni A, Cavalli-Sforza LL, Scozzari R, Underhill PA. 2002. A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes. Am J Hum Genet 70: 1197-1214.
28. Curtin P. 1969. The Atlantic slave trade. Madison: University Of Wisconsin Press.
29. Deason ML, Salas A, Newman SP, Macaulay VA, A Morrison EY, Pitsiladis YP. 2012. Interdisciplinary approach to the demography of Jamaica. BMC Evol Biol 12:24.
30. Dietz JL. 1992. Historia económica de Puerto Rico. Torres Rivera Y, trans from 1989. Puerto Rico: Ediciones Huracán.
31. Dulik MC, Owings AC, Gaieski JB, Vilar MG, Andre A, Lennie C, Mackenzie MA, Kritsch I, Snowshoe S, Wright R, Martin J, Gibson N, Andrews TD, Schurr TG, Genographic Consortium. 2012a. Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations. Proc Natl Acad Sci USA 109: 8471-8476.
32. Dulik MC, Zhadanov SI, Osipova LP, Askapuli A, Gau L, Gokcumen O, Rubenstein S, Schurr TG. 2012b. Mitochondrial DNA and Y chromosome variation provides evidence for a recent common ancestry between native Americans and Indigenous Altaians. Am J Hum Genet 90:229-246.
33. Elhaik E, Greenspan E, Staats S, Krahn T, Tyler-Smith C, Xue Y, Tofanelli S, Francalacci P, Cucca F, Pagani L, Jin L, Li H, Schurr TG, Greenspan B, Spencer Wells RS. 2013. The Geno-Chip: a new tool for genetic anthropology. Genome Biol Evol 5:1021-1031.
34. Excoffier L, Laval G, Schneider S. 2005. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47-50.
35. Fernández-Armesto F. 1982. The Canary Islands after the conquest: the making of a colonial society in the early sixteenth century. New York: Oxford University Press.
36. Fewkes JW. 2009. The aborigines of Puerto Rico and neighboring islands. Tuscaloosa: University of Alabama Press.
37. Figueredo AE. 1978. The Virgin Islands as a historical frontier between the Tainos and the Caribs. Rev Rev Interam 8:393-399.
38. Fitzpatrick SM, Keegan WF. 2007. Human impacts and adaptations in the Caribbean Islands: an historical ecology approach. Trans R Soc Edinburgh 98:29-45.
39. Fitzpatrick SM, Ross AH. 2010. Island shores, distant pasts. Gainesville: University Press of Florida.
40. Forte M. 2005. Ruins of absence, presence of Caribs: (Post) colonial representations of aboriginality in Trinidad and Tobago. Tallahassee: University of Florida Press.
41. Gaieski JB, Elhaik E, Owings AC, Vilar MG, Walia A, Wells RS, Schurr TG, Genographic Consortium. 2012. Genetic ancestry and admixture analysis in a Bermudian population reveals evidence of Native American origins consistent with oral histories and genealogies. Am J Hum Genet Suppl 91:859.
42. Gaieski JB, Owings AC, Vilar MG, Dulik MC, Gaieski D, Gittelman RM, Lindo J, Gau L, Schurr TG, The Genographic Consortium. 2011. Genetic ancestry and indigenous heritage in a Native American descendant community in Bermuda. Am J Phys Anthropol 146:392-405.
43. Galloway PK, editor. 2006. The Hernando de Soto expedition: history, historiography, and 'discovery' in the Southeast. Lincoln: University of Nebraska Press.
44. Gomez-Carballa A, Ignacio-Veiga A, Alvarez-Iglesias V, Pastoriza-Mourelle A, Ruiz Y, Pineda L, Carracedo A, Salas A. 2012. A melting pot of multicontinental mtDNA lineages in admixed Venezuelans. Am J Phys Anthropol 147:78-87.
45. Gonc¸alves R, Freitas A, Branco M, Rosa A, Fernandes AT, Zhivotovsky LA, Underhill PA, Kivisild T, Brehm A. 2005. Y-chromosome lineages from Portugal, Madeira and Ac¸ores: record elements of Sephardim and Berber Ancestry. Ann Hum Genet 69:443-454.
46. Gonc¸alves VF, Carvalho CMB, Bortolini MC, Bydlowski SP, Pena SD. 2007. The phylogeography of African Brazilians. Hum Hered 65:23-32.
47. Granberry J. 2013. Indigenous languages of the Caribbean. In: Keegan W, editor. The oxford handbook of Caribbean archeology. Oxford: Oxford University Press. p 61-69.
48. Granberry J, Vescelius G. 2004. Languages of the Pre-Columbian Antilles. Tuscaloosa: University of Alabama Press.
49. Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Sandoval K, Bedoya G, The 1000 Genomes Project, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, Bustamante CD. 2013. Reconstructing native American migrations from whole-genome and wholeexome data. PLoS Genet 9:e1004023.
50. Guitar L. 2000. Criollos: the birth of a dynamic new Indo-Afro-European people and culture on Hispaniola. KACIKE: J Caribbean Amerindian History Anthropol 1:1-17.
51. Haag W. 1964. A comparison of Arawak sites in the Lesser Antilles. Proceedings of the 1st ICSPCLA 1:9-37.
52. Haines MR, Steckel RH. 2000. A population history of North America. New York: Cambridge University Press.
53. Hassan HY, Underhill PA, Cavalli-Sforza LL, Ibrahim ME. 2008. Y-chromosome variation among Sudanese: restricted gene flow, concordance with language, geography, and history. Am J Phys Anthropol 137:316-323.
54. Helgason A, Pálsson G, Pedersen HS, Angulalik E, Gunnarsdóttir ED, Yngvadóttir B. Stefánsson K. 2006. mtDNA variation in Inuit populations of Greenland and Canada: migration history and population structure. Am J Phys Anthropol 130:123-134.
55. Hofman CL, Bright AJ, Hoogland ML, Keegan WF. 2008. Attractive ideas, desirable goods: examining the Late Ceramic Age relationships between Greater and Lesser Antillean societies. J Island Coastal Arch 3:17-34.
56. Hoogland ML, Hofman CL. 1999. Expansion of the Taino cacicazgos towards the Lesser Antilles. J Société d Américanistes 85:93-113.
57. Hünemeier T, Carvalho C, Marrero AR, Salzano FM, Pena J, Danilo S, Bortolini, MC. 2007. Niger-Congo speaking populations and the formation of the Brazilian gene pool: mtDNA and Y-chromosome data. Am J Phys Anthropol 133:854-867.
58. Huoponen K, Torroni A, Wickman PR, Sellitto D, Gurley DS, Scozzari R, Wallace DC. 1996. Mitochondrial DNA and Y chromosome-specific polymorphisms in the Seminole tribe of Florida. Eur J Hum Genet 5:25-34.
59. Just RS, Diegoli TM, Saunier JL, Irwin JA, Parsons TJ. 2008. Complete mitochondrial genome sequences for 265 African American and U.S. "Hispanic" individuals. Forensic Sci Int Genet 2:e45-e48.
60. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF. 2008. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18:830-838.
61. Kaufman T. 1994. The native languages of South America. In: Mosley C, Asher RE, editors. Atlas of the world's languages. London: Routledge. p 46-76.
62. Keegan WF. 1995. Modeling dispersal in the prehistoric West Indies. World Archaeol 26:400-419.
63. Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, Leidinger P, Backes C, Khairat R, Forster M, Stade B, Franke A, Mayer J, Spangler J, McLaughlin S, Shah M, Lee C, Harkins TT, Sartori A, Moreno-Estrada A, Henn B, Sikora M, Semino O, Chiaroni J, Roosti S, Myres NM, Cabrera VM, Underhill PA, Bustamante CD, Vigl EE, Samadelli M, Cipollini G, Haas J, Katus J, O'Connor BD, Carlson MRJ, Meder B, Blin N, Meese E, Pusch CM, Zink A.. 2012. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat Commun 3: Article 698.
64. Kemp BM. 2006. Mesoamerica and Southwest prehistory, and the entrance of humans into the Americas: mitochondrial DNA evidence. Ph.D. Dissertation, University of California, Davis CA.
65. Kidd JM, Gravel S, Byrnes J, Moreno-Estrada A, Musharoff S, Bryc K, Degenhardt JD, Brisbin A, Sheth V, Chen R, McLaughlin SF, Peckham HE, Omberg L, Bormann Chung CA, Stanley S, Pearlstein K, Levandowsky E, Acevedo-Acevedo S, Auton A, Keinan A, Acuña-Alonzo V, Barquera-Lozano R, Canizales-Quinteros S, Eng C, Burchard EG, Russell A, Reynolds A, Clark AG, Reese MG, Lincoln SE, Butte AJ, De La Vega FM, Bustamante CD. 2012. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet 91:660-671.
66. Kumar S, Bellis C, Zlojutro M, Melton PE, Blangero J, Curran JE. 2011. Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins. BMC Evol Biol 11: Article 293.
67. Lalueza-Fox C, Gilbert MTP, Martínez-Fuentes MJ, Calafell F, Bertranpetit J. 2003. Mitochondrial DNA from pre-Columbian Ciboneys from Cuba and the prehistoric colonization of the Caribbean. Am J Phys Anthropol 121:97-108.
68. Lalueza-Fox C, Luna Calderon F, Calafell F, Morera B, Bertranpetit. 2001. MtDNA from extinct Tainos and the peopling of the Caribbean. Ann Hum Genet 65:137-151.
69. Lander N, Rojas MG, Chiurillo MA, Ramirez JL. 2008. Haplotype diversity in human mitochondrial DNA hypervariable regions I-III in the city of Caracas (Venezuela). Forensic Sci Int Genet 2:e61-e64.
70. Lappalainen T, Koivumäki S, Salmela E, Huoponen K, Sistonen P, Savontaus ML, Lahermo P. 2006. Regional differences among the Finns: a Y-chromosomal perspective. Gene 376:207-215.
71. Las Casas B, Griffin N, editor and translator. 1992. A short account of the destruction of the Indies. London: Penguin Books.
72. Lovejoy PE. 2000. Transformations in Slavery: a history of slavery in Africa. Cambridge: Cambridge University Press.
73. Lundberg ER. 1989. Preceramic procurement patterns at Krum Bay, Virgin Islands. Ph.D. Dissertation. University of Illinois, Urbana-Champaign, IL.
74. Maca-Meyer N, González AM, Pestano J, Flores C, Larruga JM, Cabrera VM. 2003. Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography. BMC Genet 4: Article 15.
75. Magnus M. 1995. Spanish historians on Spanish migration to America during the colonial period. Lat Am Res Rev 30: 251-255.
76. Mandarino LM. 2010. Mitochondrial DNA analysis of the Brazilian Macushi population. Master's Thesis, Department of Anthropology, State University of New York at Binghamton.
77. Martin C, Wasserman M. 2005. Latin America and its people. New York: Allyn & Bacon.
78. Martinez H, Rodriguez-Larralde R, Izaguirre MH, Castro De Guerra D. 2007. Admixture estimates for Caracas, Venezuela, based on autosomal, Y-chromosome, and mtDNA markers. Hum Biol 79(2): Article 5.
79. Martínez-Cruzado JC. 2010. The history of Amerindian mitochondrial DNA lineages in Puerto Rico. In: Fitzpatrick SM, Ross A, editors. Island shores, distant pasts: archaeological and biological approaches to the pre-Columbian settlement of the Caribbean. Gainesville: University of Florida. p 54-80.
80. Martínez-Cruzado JC, Toro-Labrador G, Ho-Fung V, Estevez-Montero, M Lobaina-Manzanet A, Padovani-Claudio DA, Sanchez-Cruz H, Ortiz-Bermudez P, Sanchez-Crespo A. 2001. Mitochondrial DNA analysis reveals substantial Native American ancestry in Puerto Rico. Hum Biol 73:491-511.
81. Martínez-Cruzado JC, Toro-Labrador G, Viera-Vera J, Rivera-Vega MY, Startek J, Latorre-Esteves M, Román-Colón A, Rivera-Torres R, Navarro-Millán IY, Gómez-Sánchez E, Caro-González HY, Valencia-Rivera P. 2005. Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis. Am J Phys Anthropol 128:131-155.
82. Melton PE, Baldi NF, Barrantes R, Crawford MH. 2013. Microevolution, migration, and the population structure of five Amerindian populations from Nicaragua and Costa Rica. Am J Hum Biol 25:480-490.
83. Mendizabal I, Sandoval K, Berniell-Lee G, Calafell F, Salas A, Martínez-Fuentes A, Comas D. 2008. Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba. BMC Evol Bio 8: Article 213.
84. Moreno-Estrada A, Gravel S, Zakharia F, McCauley JL, Byrnes JK, Gignoux CR, Ortiz-Tello PA, Martínez RJ, Hedges DJ, Morris RW, Eng C, Sandoval K, Acevedo-Acevedo S, Norman PJ, Layrisse Z, Parham P, Martínez-Cruzado JC, Burchard EG, Cuccaro ML, Martin ER, Bustamante CD. 2013. Reconstructing the population genetic history of the Caribbean. PLoS Genet 9:e1003925.
85. Morisson SE. 1939. The second voyage of Christopher Columbus from Cadiz to Hispaniola and the discovery of the Lesser Antilles. Oxford: The Clarendon Press.
86. Musicant I. 1998. Empire by default: the Spanish-American war and the dawn of the American century. New York: H. Holt.
87. Myres NM, Rootsi S, Lin AA, Jorve M, King RJ, Kutuev I, Cabrera VM, Khusnutdinova EL, Pshenichnov A, Yunusbayev B, Balanovsky O, Balanovska E, Rudan P, Baldovic M, Herrera RJ, Chiaroni J, Di Cristoaro J, Villems R, Kivisild T, Underhill PA. 2010. A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. Eur J Hum Genet 19:95-101.
88. O'Rourke DH, Raff JA. 2010. The human genetic history of the Americas: the final frontier. Curr Biol 20:R202-R207.
89. Ortiz J. 1976. Excavations at the preceramic Cerillo site, Southwest Puerto Rico. In: Proceedings of the sixth international congress for the study of pre-Columbian cultures of the Lesser Antilles, Centre Universitaire, Guadelope. p 269-271.
90. Owings AC, Dulik MC, Zhadanov SI, Gaieski JB, Cope A, Dorey D, Schurr TG, The Genographic Consortium. 2012. Genetic variation in Mi'kmaq populations from Nova Scotia and its implications for the history of Algonquian populations in northeastern North America. Am J Phys Anthropol Suppl 147(S54):231.
91. Pantel AG. 1976. Excavations at the preceramic Cerillo site, southwest Puerto Rico. Sixth IACA, Pointe-à-Pitre, Guadeloupe. p 269-271.
92. Petersen JB, Hofman CL, Curet LA. 2005. Time and culture: chronology and taxonomy in the eastern Caribbean and the Guianas. In: Delpuech A, Hofman CL, editors. Late Ceramic Age Societies in the Eastern Caribbean. British Archaeological Reports, 1273. Oxford: Archaeopress. p 17-32.
93. Plaza S, Salas A, Calafell F, Corte-Real F, Bertranpetit J, Carracedo A, Comas D. 2004. Insights into the western Bantu dispersal: mtDNA lineage analysis in Angola. Hum Genet 115:439-447.
94. Rando JC, Pinto F, González AM, Hernández M, Larruga LM, Cabrera VM, Bandelt H-J. 1998. Mitochondrial DNA analysis of Northwest African populations reveals genetic exchanges with European, Near-Eastern, and sub-Saharan populations. Ann Hum Genet 62:531-550.
95. Raudzens G. 2003. Technology, disease and colonial conquests, sixteenth to eighteenth centuries. Leiden: Brill.
96. Rawley JA, Behrendt SD. 2005. The Transatlantic Slave Trade: a history. Lincoln: University of Nebraska Press.
97. Richards MB, Macaulay VA, Bandelt HJ, Sykes BC. 1998. Phylogeography of mitochondrial DNA in Western Europe. Ann Hum Genet 62:241-260.
98. Rieder MJ, Taylor SL, Tobe VO, Nickerson DA. 1998. Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome. Nucleic Acid Res 26:967-973.
99. Righter E. 1997. The ceramics, art, and material culture of the early ceramic period in the Caribbean Islands. In: Wilson S, editor. The indigenous people of the Caribbean. Gainesville: University of Florida Press. p 70-79.
100. Righter E, Wild KS, Lundberg ER. 2004. Late Ceramic Age developments in the Virgins Archipelago: the Puerto Rican connection. In: Late Ceramic Age Societies in the Eastern Caribbean, Delpuech A, Hofman CL, editors. BAR International Series #1273. Paris Monographs in American Archaeology #14. Oxford: Archaeopress. p 101-120.
101. Rodriguez-Ramos R. 2010. Rethinking Puerto Rican precolonial history. Tuscaloosa: University of Alabama Press.
102. Rogozinski J. 1999. A brief history of the Caribbean: from the Arawak to the present. New York: Penguin Publishing.
103. Rootsi S, Myres NM, Lin AA, Järve M, King RJ, Kutuev I, Cabrera VM, Khusnutdinova EK, Varendi K, Sahakyan H, Behar DM, Khusainova R, Balanovsky O, Balanovska E, Rudan P, Yepiskoposyan L, Bahmanimehr A, Farjadian S, Kushniarevich A, Herrera RJ, Grugni V, Battaglia V, Nici C, Crobu F, Karachanak S, Hooshiar Kashani B, Houshmand M, Sanati MH, Toncheva D, Lisa A, Semino O, Chiaroni J, Di Cristofaro J, Villems R, Kivisild T, Underhill PA. 2012. Distinguishing the co-ancestries of haplogroup G Y-chromosomes in the populations of Europe and the Caucasus. Eur J Hum Genet 20:1275-1282.
104. Rosa A, Brehm A, Kivisild T, Metspalu E, Villems R. 2004. MtDNA profile of West Africa Guineans: towards a better understanding of the Senegambia region. Ann Hum Genet 68: 340-352.
105. Rosa A, Ornelas C, Jobling MA, Brehm A, Villems R. 2007. Y-chromosomal diversity in the population of Guinea-Bissau: a multiethnic perspective. BMC Evol Biol 7: Article 124.
106. Rouse IR. 1952. Porto Rican prehistory: introduction; Excavations in the west and north. In: Scientific survey of Porto Rico and the Virgin Islands, Vol. 18, Part 3. New York: New York Academy of Sciences.
107. Rouse IR. 1964. Prehistory of the West Indies. Science 144:499-508.
108. Rouse IR. 1992. The Tainos: rise and decline of the people who greeted Columbus. New Haven: Yale University Press.
109. Salas A, Acosta A, Alvaerz-Iglesias V, Cerezo M, Phillips C, Lareau MV, Carracedo A. 2008. The mtDNA ancestry of admixed Colombian populations. Am J Hum Biol 20:584-591.
110. Salas A, Lovo-Gómez J, Álvarez-Iglesias V, Cerezo M, Lareu MV, Macaulay V, Richards MB, Carracedo A. 2009. Mitochondrial echoes of first settlement and genetic continuity in El Salvador. PLoS One 4:e6882.
111. Salas A, Richards M, Lareau MV, Sorbino B, Silva S, Matamoros M, Macaulay V, Carracedo A. 2005. Shipwrecks and founder effects: divergent demographic histories revealed in Caribbean mtDNA. Am J Phys Anthropol 128:855-860.
112. Sandoval K, Buentello-Malo L, Peñaloza-Espinosa R, Avelino H, Salas A, Calafell F, Comas D. 2009. Linguistic and maternal genetic diversity are not correlated in Native Americans. Hum Genet 126:521-531.
113. Sandoval K, Moreno-Estrada A, Mendizabal I, Underhill PA, Lopez-Valenzuela M, Peñaloza-Espinosa R, Comas D. 2012. Y-chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the Americas. Am J Phys Anthropol 148:395-405.
114. Schurr TG. 2004. The peopling of the New World: perspectives from molecular anthropology. Ann Rev Anthropol 33:551-583.
115. Schurr TG. 2010. Coastal waves and island hopping: a genetic view of Caribbean prehistory in the context of New World colonization. In: SM Fitzpatrick, A Ross, editors. Island shores, distant pasts: archaeological and biological approaches to the pre-Columbian settlement of the Caribbean. Gainesville: University of Florida Press. p 177-198.
116. Schurr TG, Dulik MC, Owings AC, Zhadanov SI, Gaieski JB, Vilar MG, Ramos J, Moss MB, Natkong, F. 2012a. Clan, language, and migration history has shaped genetic diversity in Haida and Tlingit populations from Southeast Alaska. Am J Phys Anthropol 148:422-435.
117. Schurr TG, Sherry ST. 2004. Mitochondrial DNA and Y-chromosome diversity and the peopling of the Americas. Am J Hum Biol 16:420-439.
118. Schurr TG, Vilar MG, Gomez MR, Zillges H, Sanders A, Gaieski JB Owings AC, Genographic Consortium. 2012b. Genetic diversity and migration history of indigenous populations from the Central Valley of Mexico. Am J Hum Genet Suppl 91:871.
119. Semino O, Magri C, Benuzzi G, Lin AA, Al-Zahery N, Battaglia V. Maccioni L, Triantaphyllidis C, Shen P, Oefner PJ, Zhivotovsky LA, King R, Torroni A, Cavalli-Sforza LL, Underhill PA, Santachiara-Benerecetti AS. 2004. Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the Neolithization of Europe and later migratory events in the Mediterranean area. Am J Hum Genet 74:1023-1034.
120. Siegel PE, editor. 2005. Ancient Borinquen: archaeology and ethnohistory of Native Puerto Rico. Tuscaloosa: University of Alabama Press.
121. Simms TM, Rodriguez CE, Rodriguez R, Herrera RJ. 2010. The genetic structure of populations from Haiti and Jamaica reflect divergent demographic histories. Am J Phys Anthropol 142:49-66.
122. Simoni L, Calafell F, Pettener D, Bertranpetit J, Barbujani G. 2000. Geographic patterns of mtDNA diversity in Europe. Am J Hum Genet 66:262-278.
123. Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards MB. 2009. Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 84:740-759.
124. SPSS Inc. 2008. SPSS statistics for windows, version 17.0. Chicago: SPSS Inc.
125. Stefflova K, Dulik MC, Pai AA, Walker AH, Zeigler-Johnson CM, Gueye SM, Schurr TG, Rebbeck TR. 2009. Evaluation of group genetic ancestry of populations from Philadelphia and Dakar in the context of sex-biased admixture in the Americas. PLoS One 4:e7842.
126. Tamm E, Kivisild T, Reidla M, Metspalu M, Glenn-Smith D, Mulligan CJ, Bravi CM, Rickards, O, Martínez-Lambarga C, Khusnutdinova EK, Fedorova SA, Golubenko MV, Stepanov VA, Gubina MA, Zhadanov SI, Osipova LP, Damba L, Voevoda MO, Dipierri JE, Villems R, Malhi RS. 2007. Beringian standstill and spread of Native American founders. PLoS One 2: e829.
127. The Cuban mtDNA Group. 2013. Family tree geographical projects, Houston, TX. Available at: http://www.familytreedna.-com/public/CubaDNAProject/default.aspx. Accessed on 10 September 2013.
128. The Puerto Rican Geographical DNA Group. 2013. Family tree geographical projects, Houston, TX. Available at: http://www.familytreedna.com/public/puertoricansurname/. Accessed 10 September 2013.
129. Toro-Labrador G, Wever OR, Martínez-Cruzado JC. 2003. Mitochondrial DNA analysis in Aruba: strong maternal ancestry of closely related Amerindians and implications for the peopling of northwestern Venezuela. Carib J Sci 39:11-22.
130. Torroni A, Rengo C, Guida V, Cruciani F, Sellitto D, Coppa A, Calderon FL, Simionati B, Valle G, Richards M, Macaulay V, Scozzari R. 2001. Do the four clades of the mtDNA haplogroup L2 evolve at different rates? Am J Hum Genet 69: 1348-1356.
131. Torroni A, Schurr TG, Cabell MF, Brown MD, Neel JV, Larsen M, Smith DG, Vullo C, Wallace DC. 1993. Asian affinities and continental radiation of the four founding Native American mitochondrial DNAs. Am J Hum Genet 53:563-590.
132. van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30:E386-E394.
133. Veeramah K, Connell B, Pour N, Powell A, Plaster C, Zeitlyn D, Mendell M, Weale M, Bradman N, Thomas M. 2010. Little genetic differentiation as assessed by uniparental markers in the presence of substantial language variation in peoples of the Cross River region of Nigeria. BMC Evol Biol 10: Article 92.
134. Via M, Gignoux CR, Roth LA, Fejerman L, Galanter J, Choudry S, Toro-Labrador G, Viera-Vega J, Oleksyk TK, Beckman K, Ziv E, Risch N, Burchard EG, Martínez-Cruzsado JC. 2011. History shaped the geographic distribution of genomic admixture of the island of Puerto Rico. PLoS One 6:e16513.
135. Vilar MG, Dulik MC, Owings AC, Gaieski JB, Lennie C, Zillges H, Gittelman R, Lindo J, Keating K, Schurr TG. 2014. The Genographic Consortium. Genetic variation in Inuvialuit populations from the Northwest Territories and its implications for the human colonization of the Arctic. Am. J Phys Anthropol, in review.
136. Vilar MG, Gomez R, Zillges H, Brooks D, Sanders A, Gaieski JB, Owings A, Meraz MA, Schurr TG, Genographic Consortium. 2013. Genetic diversity in indigenous populations from Central Mexico and its implications for the peopling of the Americas. Am J Phys Anthropol Suppl 146:278.
137. Vilar MG, Lum JK, Melendez C, Owings A, Gaieski JB, Schurr TG, Genographic Consortium. 2011. Analysis of mtDNA haplogroup A2 frequency, distribution and diversity among populations from North and Central America and the Caribbean. Am J Phys Anthropol Suppl 144(S52):300.
138. Willey G. 1956. Settlement patterns in the Caribbean area. In: Willey G, editor. Prehistoric settlement patterns in the new world (Viking Fund Publications in Anthropology, No. 23). New York: Wenner-Gren Foundation for Anthropological Research. p 165-172.
139. Wilson SM. 2007. The archeology of the Caribbean. Cambridge: Cambridge University Press.
140. Wilson SM. 1997. The legacy of the indigenous people of the Caribbean. In: Wilson SM, editor. The indigenous people of the Caribbean. Gainesville: University of Florida Press. p 206-213.
141. Wilson JL, Saint-Louis V, Auguste JO, Jackson BA. 2012. Forensic analysis of mtDNA haplotypes from two rural communities in Haiti reflects their population history. J Forensic Sci 57:1457-1466.
142. Y Chromosome Consortium. 2002. A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res 12:339-348.
143. Zhadanov SI, Dulik MC, Markley M, Jennings G, Gaieski JB, Elias G, Schurr TG, The Genographic Consortium. 2010. Genetic heritage and native identity of the Seaconke Wampanoag tribe of Massachusetts. Am J Phys Anthropol 142:579-589.