Genetic Structure of Cartagena de Indias Population Using Hypervariable Markers of Y Chromosome


Ethnicity has been associated with the incidence of diseases and consequently it is a cornerstone in medical genetic studies. It is mainly important in admixture populations, where the population stratification can produce spurious results that lead to erroneous conclusions. Consequently, population stratification has become one of the most important confounding factors in population-based genetic association studies, especially in Latino populations. Cartagena de Indias is a cosmopolitan city with dissimilar ancestry proportions due to recent miscegenation. This population mainly exhibits African and Amerindian matrilineal ancestries. Nevertheless, important asymmetries in the paternal genetic history related to the complex patterns of migration in the colonial period increase the male genetic diversity in this population. As a result of this recent admixture, population stratification has arisen, where each subpopulation is not equally represented. Consequently, the allele differences between cases and controls could be related with different frequencies among different population strata rather than the association of the genes with the disease. In order to define the patrilineal substructure of the Cartagena’s population, a total of 130 unrelated men were ancestrally studied using 15 Y-STR loci routinely employed in anthropological, forensic and population genetics. Our results show that Cartagena is an admixture population consisting of European (80%), Amerindian (10%) and African ancestries (10%), which are represented by haplogroups R1b and I2a (xI2a1), Q-M242/Q-M3, and E1b1a/E1b1b, respectively. Complex genetic patterns found in Cartagena’s population emphasize the importance to know the genetic variation in order to diminish the inconsistence for future genetic association studies. In addition, our findings illustrate the complex genetic background of Cartagena population and reinforce the need to encompass more geographic regions to generate more robust data for anthropological and forensic applications.

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G.-Camargo, D. , Camacho-Mejorado, R. , Gómez-Alegría, C. , Alario, A. , H.-Tobías, E. , García, G. , M.-Ríos, M. and Gómez, R. (2015) Genetic Structure of Cartagena de Indias Population Using Hypervariable Markers of Y Chromosome. Open Journal of Genetics, 5, 27-41. doi: 10.4236/ojgen.2015.51003.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Lemaitre, E., Herazo, D.B. and Patrón, F.S. (1983) Historia General De Cartagena. Banco de la Republica, Bogotá.
[2] Wheat, D. (2011) The First Great Waves: African Provenance Zones for the Transatlantic Slave Trade to Cartagena De Indias, 1570-1640. The Journal of African History, 52, 1-22.
[3] Rojas, W., Parra, M.V., Campo, O., Caro, M.A., Lopera, J.G., Arias, W., et al.(2010) Genetic Make up and Structure of Colombian Populations by Means of Uniparental and Biparental DNA Markers. American Journal of Physical Anthropology, 143, 13-20.
[4] Bryc, K., Velez, C., Karafet, T., Moreno-Estrada, A., Reynolds, A., Auton, A., et al. (2010) Colloquium Paper: Genome-Wide Patterns of Population Structure and Admixture among Hispanic/Latino Populations. Proceedings of the National Academy of Sciences of the United States of America , 107, 8954-8961.
[5] Vergara, C., Caraballo, L., Mercado, D., Jimenez, S., Rojas, W., Rafaels, N., et al. (2009) African Ancestry Is Associated with Risk of Asthma and High Total Serum IgE in a Population from the Caribbean Coast of Colombia. Human Genetics, 125, 565-579.
[6] Attia, J., Ioannidis, J.P., Thakkinstian, A., McEvoy, M., Scott, R.J., Minelli, C., et al. (2009) How to Use an Article About Genetic Association: B: Are the Results of the Study Valid? JAMA: The Journal of the American Medical Association, 301, 191-197.
[7] Bouaziz, M., Paccard, C., Guedj, M. and Ambroise, C. (2012) Ships: Spectral Hierarchical Clustering for the Inference of Population Structure in Genetic Studies. PLoS One, 7,e45685.
[8] Neuditschko, M., Khatkar, M.S. and Raadsma, H.W. (2012) Netview: A High-Definition Network-Visualization Approach to Detect Fine-Scale Population Structures from Genome-Wide Patterns of Variation. PLoS One, 7, e48375.
[9] Wang, S.J., Ray, N., Rojas, W., Parra, M.V., Bedoya, G., Gallo, C., et al. (2008) Geographic Patterns of Genome Admixture in Latin American Mestizos. PLoS Genetics, 4, e1000037.
[10] Little, J., Higgins, J.P., Ioannidis, J.P., Moher, D., Gagnon, F., von Elm, E., et al. (2009) Strengthening the Reporting of Genetic Association Studies (STREGA)—an Extension of the STROBE Statement. European Journal of Clinical Investigation, 39, 247-266.
[11] Butler, J.M., Schoske, R., Vallone, P.M., Kline, M.C., Redd, A.J. and Hammer, M.F. (2002) A Novel Multiplex for Simultaneous Amplification of 20 Y Chromosome STR Markers. Forensic Science International, 129, 10-24.
[12] Butler, J.M., Schoske, R., Vallone, P.M., Redman, J.W. and Kline, M.C. (2003) Allele Frequencies for 15 Autosomal STR Loci on U.S. Caucasian, African American, and Hispanic Populations. Journal of Forensic Sciences, 48, 908-911.
[13] Magana, J.J., Gomez, R., Maldonado-Rodriguez, M., Velazquez-Perez, L., Tapia-Guerrero, Y.S., Cortes, H., et al. (2013) Origin of the Spinocerebellar Ataxia Type 7 Gene Mutation in Mexican Population. The Cerebellum, 12, 902-905.
[14] Excoffie, L. and Lischer, H.E.L. (2010) Arlequin Suite Ver 3.5: A New Series of Programs to Perform Population Genetic Analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567.
[15] Yunis, J.J., Acevedo, L.E., Campo, D.S. and Yunis, E.J. (2005) Population Data of Y-STR Minimal Haplotypes in a Sample of Caucasian-Mestizo and African Descent Individuals of Colombia. Forensic Science International, 151, 307-313.
[16] de Filippo, C., Barbieri, C., Whitten, M., Mpoloka, S.W., Gunnarsdottir, E.D., Bostoen, K., et al. (2011) Y-Chromosomal Variation in Sub-Saharan Africa: Insights into the History of Niger-Congo Groups. Molecular Biology and Evolution, 28, 1255-1269.
[17] Rodriguez, V., Tomas, C., Sanchez, J.J., Castro, J.A., Ramon, M.M., Barbaro, A., et al. (2009) Genetic Sub-Structure in Western Mediterranean Populations Revealed by 12 Y-Chromosome STR Loci. International Journal of Legal Medicine, 123, 137-141.
[18] Athey, T.W. (2005) Haplogroup Prediction from Y-STR Values Using an Allele-Frequency Approach. Journal of Genetic Genealogy, 1, 1-7.
[19] Bandelt, H.J., Forster, P. and Rohl, A. (1999) Median-Joining Networks for Inferring Intraspecific Phylogenies. Molecular Biology and Evolution, 16, 37-48.
[20] O’Connor, T.D., Kiezun, A., Bamshad, M., Rich, S.S., Smith, J.D., Turner, E., et al. (2013) Fine-Scale Patterns of Population Stratification Confound Rare Variant Association Tests. PLoS ONE, 8, e65834.
[21] Tsai, H.J., Choudhry, S., Naqvi, M., Rodriguez-Cintron, W., Burchard, E.G. and Ziv, E. (2005) Comparison of Three Methods to Estimate Genetic Ancestry and Control for Stratification in Genetic Association Studies among Admixed Populations. Human Genetics, 118, 424-433.
[22] Choudhry, S., Coyle, N.E., Tang, H., Salari, K., Lind, D., Clark, S.L., et al. (2006) Population Stratification Confounds Genetic Association Studies among Latinos. Human Genetics, 118, 652-664.
[23] Hao, K., Chudin, E., Greenawalt, D. and Schadt, E.E. (2010) Magnitude of Stratification in Human Populations and Impacts on Genome Wide Association Studies. PLoS ONE, 5, e8695.
[24] Jiang, Y., Epstein, M.P. and Conneely, K.N. (2013) Assessing the Impact of Population Stratification on Association Studies of Rare Variation. Human Heredity, 76, 28-35.
[25] Abdellaoui, A., Hottenga, J.J., Xiao, X., Scheet, P., Ehli, E.A., Davies, G.E., et al. (2013) Association between Autozygosity and Major Depression: Stratification Due to Religious Assortment. Behavior Genetics, 43, 455-467.
[26] Nievergelt, C.M., Maihofer, A.X., Shekhtman, T., Libiger, O., Wang, X., Kidd, K.K., et al. (2013) Inference of Human Continental Origin and Admixture Proportions Using a Highly Discriminative Ancestry Informative 41-SNP Panel. Investigative Genetics, 4, 13-19.
[27] Lleras Perez, R. (1993) La Historia Prehispánica Tardía Del Noroeste De Suramérica 800 a 1500 D.C. Revista de Arqueología Americana, 91, 51-70.
[28] Aguilera Diaz, M. and Meisel Roca, A. (2009) Tres Siglos De Historia Demográfica De Cartagena De Indias. Banco de la República, Bogotá.
[29] Múnera, A. and Molina, L.F. (1998) El Fracaso De La Nación: Región, Clase Y Raza En El Caribe Colombiano (1717-1821). El Ancora Editores, Banco de la República.
[30] Adams, S.M., Bosch, E., Balaresque, P.L., Ballereau, S.J., Lee, A.C., Arroyo, E., et al. (2008) The Genetic Legacy of Religious Diversity and Intolerance: Paternal Lineages of Christians, Jews, and Muslims in the Iberian Peninsula. American Journal of Human Genetics, 83, 725-736.
[31] Young, K.L., Sun, G., Deka, R. and Crawford, M.H. (2011) Paternal Genetic History of the Basque Population of Spain. Human Biology, 83, 455-475.
[32] Capelli, V. (2006) Entre “Macondo” Y Barranquilla. Los Italianos En La Colombia Caribea. De Finales Del Siglo XIX Hasta La Segunda Guerra Mundial. Memoria & Sociedad, 10, 25-48.
[33] Lasso, M. (2006) Race War and Nation in Caribbean Gran Colombia, Cartagena, 1810-1832. The American Historical Review, 111, 336-361.
[34] Rodas, C., Gelvez, N. and Keyeux, G. (2003) Mitochondrial DNA Studies Show Asymmetrical Amerindian Admixture in Afro-Colombian and Mestizo Populations. Human Biology, 75, 13-30.
[35] Friedemann, N. (2000) Huellas De Africanía En La Diversidad Colombiana. In: Encuentros De Africanía, F.C.C. Negra, Bogotá.
[36] Schurr, T.G. and Sherry, S.T. (2004) Mitochondrial DNA and Y Chromosome Diversity and the Peopling of the Americas: Evolutionary and Demographic Evidence. American Journal of Human Biology, 16, 420-439.
[37] Benn-Torres, J., Bonilla, C., Robbins, C.M., Waterman, L., Moses, T.Y., Hernandez, W., et al. (2008) Admixture and Population Stratification in African Caribbean Populations. Annals of Human Genetics, 72, 90-98.
[38] Mesa, N.R., Mondragon, M.C., Soto, I.D., Parra, M.V., Duque, C., Ortiz-Barrientos, D., et al. (2000) Autosomal, mtDNA, and Y-Chromosome Diversity in Amerinds: Pre- and Post-Columbian Patterns of Gene Flow in South America. American Journal of Human Genetics, 67, 1277-1286.
[39] Bedoya, G., Montoya, P., Garcia, J., Soto, I., Bourgeois, S., Carvajal, L., et al. (2006) Admixture Dynamics in Hispanics: A Shift in the Nuclear Genetic Ancestry of a South American Population Isolate. Proceedings of the National Academy of Sciences of the United States of America, 103, 7234-7239.
[40] Gusmão, L., Butler, J.M., Carracedo, A., Gill, P., Kayser, M., Mayr, W.R., et al. (2006) DNA Commission of the International Society of Forensic Genetics (ISFG): An Update of the Recommendations on the Use of Y-STRs in Forensic Analysis. Forensic Science International, 157, 187-197.
[41] Redd, A.J., Agellon, A.B., Kearney, V.A., Contreras, V.A., Karafet, T., Park, H., et al. (2002) Forensic Value of 14 Novel STRs on the Human Y Chromosome. Forensic Science International, 130, 97-111.
[42] White, P.S., Tatum, O.L., Deaven, L.L. and Longmire, J.L. (1999) New, Male-Specific Microsatellite Markers from the Human Y Chromosome. Genomics, 57, 433-437.

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