Genetic Diversity and Differentiation in Urban and Indigenous Populations of Mexico: Patterns of Mitochondrial DNA and Y-Chromosome Lineages

References

• Achilli, A., U. A. Perego, C. M. Bravi, M. D. Coble, Q. P. Kong, S. R. Woodward, A. Salas, A. Torroni, and H. J. Bandelt. 2008. The phylogeny of the four Pan-American mtDNA haplogroups: Implications for evolutionary and disease studies. PloS One 3 (3):e1764. doi:10.1371/journal.pone.0001764.
   PubMed Web of Science ®Google Scholar
• Adams, S. M., E. Bosch, P. L. Balaresque, S. J. Ballereau, A. C. Lee, E. Arroyo, A. M. López-Parra, 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 83:725–36. doi:10.1016/j.ajhg.2008.11.007.
   PubMed Web of Science ®Google Scholar
• Aguirre Beltrán, G. 1946. La población negra de México. Estudio etnohistórico. Mexico, MX: Fuente cultural.
   Google Scholar
• Aguirre Beltrán, G. 1967. Regiones de refugio. El desarrollo de la comunidad y el proceso dominical en mestizoamérica, 1991. Mexico, MX: Fondo de Cultura Económica.
   Google Scholar
• Alba-Hernández, F. 1976. La población de México. Mexico, MX: Centro de Estudios Económicos y Demográficos, El Colegio de México.
   Google Scholar
• Behar, D. M., S. Rosset, J. Blue-Smith, O. Balanovsky, S. Tzur, D. Comas, R. J. Mitchell, L. Quintana-Murci, C. Tyler-Smith, and R. S. Wells. 2007. The Genographic Project Public Participation Mitochondrial DNA Database. PLoS Genetics 3 (6):e104. doi:10.1371/journal.pgen.0030104.
   Google Scholar
• Blanton, R. E., L. Finsten, S. A. Kowalewski, and G. Feinman. 1996. Migration and population change in the Prehispanic Valley of Oaxaca, Mexico. In Arqueología mesoamericana. Homenaje a William T. Sanders, ed. A. G. Mastache, J. R. Parsons, R. S. Santley, and M. C. Serra-Puche, 11–36. Mexico, MX: Instituto Nacional de Antropología e Historia.
   Google Scholar
• CDI-UNDP (Comisión Nacional para el Desarrollo de los Pueblos Indígenas-United Nations Development Programme). 2006. Regiones indígenas de México. Mexico, MX: Comisión Nacional para el Desarrollo de los Pueblos Indígenas, United Nations Development Programme.
   Google Scholar
• Chakraborty, R. 1990. Mitochondrial DNA polymorphism reveals hidden heterogeneity within some Asian populations. American Journal of Human Genetics 47:87–94.
   PubMed Web of Science ®Google Scholar
• Cook, S. F., and W. W. Borah. 1971. Essays in population history: Mexico and the Caribbean 1. Berkeley: University of California Press.
   Google Scholar
• Cook, S. F., and W. W. Borah. 1974. Essays in population history: Mexico and the Caribbean 2. Berkeley: University of California Press.
   Google Scholar
• Cramaussel, C. 2004. Relaciones entre la Nueva Vizcaya y la provincia de Michoacán. Relaciones 100 (25):173–203.
   Google Scholar
• Cummings, M. P., S. P. Otto, and J. Wakeley. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Molecular Biology and Evolution 12 (5):814–22.
   PubMed Web of Science ®Google Scholar
• Denevan, W. 1992. The pristine myth. The landscape of the Americas in 1492. Annals of the Association of American Geographers 82 (3):369–85. doi:10.1111/j.1467-8306.1992.tb01965.x.
   Web of Science ®Google Scholar
• Ewens, W. J. 1972. The sampling theory of selectively neutral alleles. Theoretical Population Biology 3:87–112. doi:10.1016/0040-5809(72)90035-4.
   PubMed Web of Science ®Google Scholar
• Excoffier, L., G. Laval, and S. Schneider. 2005. Arlequin ver. 3.0. An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1:47–50.
   PubMed Web of Science ®Google Scholar
• Gerhard, P. 1972. A guide to the historical geography of New Spain. Cambridge: Cambridge University Press.
   Google Scholar
• Gerhard, P. 1979. The southeast frontier of New Spain. Princeton, NJ: Princeton University Press.
   Google Scholar
• Gerhard, P. 1982. The north frontier of New Spain. Princeton, NJ: Princeton University Press.
   Google Scholar
• Gorostiza, A., V. Acunha-Alonzo, L. Regalado-Liu, S. Tirado, J. Granados, D. Sámano, H. Rangel-Villalobos, and A. González-Martín. 2012. Reconstructing the history of Mesoamerican populations through the study of the mitochondrial DNA control region. PloS One 7 (9):e44666. doi:10.1371/journal.pone.0044666.
   Google Scholar
• Guardado-Estrada, M., E. Juárez-Torres, I. Medina-Martinez, A. Wegier, A. Macías, G. Gómez, F. Cruz-Talonia, et al. 2009. A great diversity of Amerindian mitochondrial DNA ancestry is present in the Mexican mestizo population. Journal of Human Genetics 54:695–705. doi:10.1038/jhg.2009.98.
   PubMed Web of Science ®Google Scholar
• Harvey, P. H., and M. D. Pagel. 1991. The comparative method in evolutionary biology. Oxford: Oxford University Press.
   Google Scholar
• INALI (Instituto Nacional Indigenista). 2008, January. Catálogo de las lenguas indígenas nacionales: Variantes lingüísticas de México con sus autodenominaciones y referencias geoestadísticas. Diario Oficial de la Federación. 31–78, 1–96, 1–112.
   Google Scholar
• INEGI (Instituto Nacional de Estadística y Geografía). 2011. Censos de Población y Vivienda. Mexico, MX. Available online at: http://www.inegi.org.mx/
   Google Scholar
• Jáuregui, J. 2004. La región cultural del Gran Nayar como ‘campo de estudio etnológico’. Mexico, MX: Instituto Nacional Indigenista.
   Google Scholar
• Karafet, T. M., F. L. Mendez, M. B. Meilerman, P. A. Underhill, S. L. Zegura, and M. F. Hammer. 2008. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Research 18:830–38. doi:10.1101/gr.7172008.
   PubMed Web of Science ®Google Scholar
• Kemp, B. M., A. González-Oliver, R. S. Malhi, C. Monroe, K. B. Schroeder, J. McDonough, G. Rhett, et al. 2010. Evaluating the farming/language dispersal hypothesis with genetic variation exhibited by populations in the Southwest and Mesoamerica. Proceedings of the National Academy of Sciences USA 107:6759–64. doi:10.1073/pnas.0905753107.
   PubMed Web of Science ®Google Scholar
• López Austin, A., and L. López Luján. 1996. El pasado indígena. Mexico, MX: El Colegio de México, Fondo de Cultura Económica.
   Google Scholar
• Malhi, R. S., M. Holly, H. M. Mortensen, J. A. Eshleman, B. M. Kemp, J. G. Lorenz, F. A. Kaestle, J. R. Johnson, C. Gorodezky, and D. G. Smith. 2003. Native American mtDNA prehistory in the American Southwest. American Journal of Physical Anthropology 120:108–24. doi:10.1002/ajpa.10138.
   PubMed Web of Science ®Google Scholar
• Martínez-Cortés, G., J. Salazar-Flores, J. Haro-Guerrero, R. Rubi-Castellanos, J. Velarde Félix, J. Muñoz-Valle, M. López-Casamichana, et al. 2013. Maternal admixture and population structure in Mexican-Mestizos based on mtDNA haplogroups. American Journal of Physical Anthropology 151:526–37. doi:10.1002/ajpa.v151.4.
   PubMed Web of Science ®Google Scholar
• Martinez-Marignac, V. L., A. Valladares, E. Cameron, A. Chan, A. Perera, R. Globus-Goldberg, N. Wacher, et al. 2007. Admixture in Mexico City: Implications for admixture mapping of Type 2 diabetes genetic risk factors. Human Genetics 120:807–19. doi:10.1007/s00439-006-0273-3.
   PubMed Web of Science ®Google Scholar
• Mendizábal, M. O. de. 1946. La demografía mexicana. Época Colonial 1519–1810. Demografía Colonial del Siglo XVI, 1519–1599. In Obras Completas 3, ed. M. O. de. Mendizábal, 307–35. Mexico, MX: Talleres Gráficos de la Nación.
   Google Scholar
• Merriwether, D. A., S. Houston, S. Iyengar, R. Hamman, J. M. Norris, S. M. Shetterly, M. Ilyas Kamboh, and R. E. Ferrell. 1997. Mitochondrial versus nuclear admixture estimates demonstrate a past history of directional mating. American Journal of Physical Anthropology 102:153–59.
   PubMed Web of Science ®Google Scholar
• Moctezuma Zamarrón, J. L. 1991. Las lenguas indígenas del noroeste de México: Pasado y Presente. In El Noroeste de México y sus culturas étnicas: Seminario de etnografía “Fernando Cámara Barbachano,” ed. D. Gutiérrez, and J. Gutiérrez, 125–36. Mexico, MX: Instituto Nacional de Antropología e Historia.
   Google Scholar
• Monroe, C., B. M. Kemp, and D. G. Smith. 2013. Exploring prehistory in the North American southwest with mitochondrial DNA diversity exhibited by Yumans and Athapaskans. American Journal of Physical Anthropology 150:618–31. doi:10.1002/ajpa.22237.
   PubMed Web of Science ®Google Scholar
• Nalda, E. 2005. Clásico Terminal (750–1050 d.C) y Posclásico (1050–1550 d.C.) en el área maya: Colapso y reacomodos. Arqueología Mexicana 13 (76):30–39.
   Google Scholar
• Oropeza, K. 2007. “Los indios chinos” en la Nueva España: La inmigración de la Nao de china 1565–1700. Ph.D. diss., Centro de estudios históricos, El colegio de México.
   Google Scholar
• Ouweneel, A., and R. Hoekstra. 1998. Las tierras de los pueblos de indios en el altiplano de México, 1560–1920. Una aportación teórica interpretativa. Mexico, MX and Amsterdam, The Netherlands: Cuadernos 1. Centre for Latin American Research and Documentation.
   Google Scholar
• París Pombo, M. D. 1999. Racismo y nacionalismo: La construcción de identidades excluyentes. Política Y Cultura (Universidad Autónoma Metropolitana) 12:53–76.
   Google Scholar
• Peñaloza-Espinosa, R. I., D. Arenas-Aranda, R. M. Cerda-Flores, L. Buentello-Malo, G. González-Valencia, J. Torres, B. Álvarez, et al. 2007. Characterization of mtDNA haplogroups in 14 Mexican indigenous populations. Human Biology 79 (3):313–20. doi:10.1353/hub.2007.0042.
   PubMed Web of Science ®Google Scholar
• Reff, D. 1991. Disease, depopulation and culture change in northwestern New Spain, 1518–1764. Salt Lake City: University of Utah Press.
   Google Scholar
• Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (12):1572–74. doi:10.1093/bioinformatics/btg180.
   PubMed Web of Science ®Google Scholar
• Salazar-Flores, J., R. Dondiego-Aldape, R. Rubi-Castellanos, M. Anaya-Palafox, I. Nuño-Arana, L. M. Canseco-Ávila, G. Flores-Flores, et al. 2010. Population structure and paternal admixture landscape on present-day Mexican-mestizos revealed by Y-STR haplotypes. American Journal of Human Biology 22:401–09. doi:10.1002/ajhb.21013.
   PubMed Web of Science ®Google Scholar
• Sandoval, K., L. Buentello-Malo, R. Peñaloza-Espinosa, H. Avelino, A. Salas, F. Calafell, and D. Comas. 2009. Linguistic and maternal genetic diversity are not correlated in native Mexicans. Human Genetics 126:521–31. doi:10.1007/s00439-009-0693-y.
   PubMed Web of Science ®Google Scholar
• Sandoval, K., A. Moreno-Estrada, I. Mendizabal, P. A. Underhill, M. Lopez-Valenzuela, R. Peñaloza-Espinosa, M. Lopez-Lopez, et al. 2012. Y-chromosome diversity in native Mexicans reveals continental transition of genetic structure in the Americas. American Journal of Physical Anthropology 148:395–405. doi:10.1002/ajpa.v148.3.
   PubMed Web of Science ®Google Scholar
• Silva-Zolezzi, I., A. Hidalgo-Miranda, J. Estrada-Gil, J. C. Fernandez-Lopez, L. Uribe-Figueroa, A. Contreras, E. Balam-Ortiz, et al. 2009. Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico. Proceedings of the National Academy of Sciences USA 106:8611–16. doi:10.1073/pnas.0903045106.
   PubMed Web of Science ®Google Scholar
• Templeton, A. R. 2013. Biological races in humans. Studies in History and Philosophy of Biological and Biomedical Sciences 44:262–71. doi:10.1016/j.shpsc.2013.04.010.
   PubMedGoogle Scholar
• Torroni, A., T. G. Schurr, M. F. Cabell, M. D. Brown, J. V. Neel, M. Larsen, D. G. Smith, C. M. Vullo, and D. C. Wallace. 1993. Asian affinities and continental radiation of the four founding native American mtDNAs. American Journal of Human Genetics 53:563–90.
   PubMed Web of Science ®Google Scholar
• Torroni, A., T. G. Schurr, C. C. Yang, E. J. Szathmary, R. C. Williams, M. S. Schanfield, G. A. Troup, et al. 1992. Native American mitochondrial DNA analysis indicates that the Amerind and the Nadene populations were founded by two independent migrations. Genetics 130:153–62.
   PubMed Web of Science ®Google Scholar
• Urteaga, A., and P. Stefani. 1994. Descripción de la situación actual de la población indígena en la Sierra Tarahumara. In Derechos Culturales y derechos indígenas en la Sierra Tarahumara, ed. L. González, S. Gutiérrez, P. Stefani, M. Urías, and A. Urteaga, 17–21. Chihuahua, Mexico: Universidad Autónoma de Ciudad Juárez.
   Google Scholar
• Valdés, L. M. 2001. Los indios en el tercer milenio. Ciencias 60–61:128–32.
   Google Scholar
• Watterson, G. A. 1978. The homozygosity test of neutrality. Genetics 88:405–17.
   PubMed Web of Science ®Google Scholar
• Wichmann, S. 1995. The relationship among the Mixe-Zoquean languages of Mexico. Salt Lake City: University of Utah Press.
   Google Scholar
• Zambardino, R. A. 1980. Mexico’s population in the sixteenth century: Demographic anomaly or mathematical illusion? Journal Interdiscipl Historical 11:1–27. doi:10.2307/202984.
   Web of Science ®Google Scholar
• Zegura, S. L., T. M. Karafet, L. A. Zhivotovsky, and M. F. Hammer. 2004. High-resolution SNPs and microsatellite haplotypes point to a single, recent entry of native American Y chromosomes into the Americas. Molecular Biology and Evolution 21 (1):164–75. doi:10.1093/molbev/msh009.
   PubMed Web of Science ®Google Scholar