Archaeological and Anthropological Sciences

, Volume 11, Issue 7, pp 3459–3475 | Cite as

Ancient mitochondrial DNA and population dynamics in postclassic Central Mexico: Tlatelolco (ad 1325–1520) and Cholula (ad 900–1350)

  • Ana Y. Morales-ArceEmail author
  • Geoffrey McCafferty
  • Jessica Hand
  • Norma Schmill
  • Krista McGrath
  • Camilla SpellerEmail author
Original Paper


The past composition and genetic diversity of populations from Central Mexico during the Postclassic period (ad 900–1520) are still little understood. Two of the largest centres of ancient groups, Tlatelolco and Cholula, declined after European conquest and questions about their relationships with other Central Mexican cities and ritual activities have been debated. Tlatelolco was a Mexica group that practiced the Quetzalcoatl cult and human sacrifice, including the sacrifice of children, while Cholula was considered the main pilgrimage centre and multiethnic city during the Postclassic. This study analysed the mitochondrial DNA control region of 28 human skeletal samples to estimate the genetic affinities of individuals buried at Tlatelolco and Cholula. Amelogenin analysis and whole genome sequencing (WGS) were also applied to determine the sex of the 15 Tlatelolco subadults from sacrificial contexts. Networks, PCoA and Nei genetic distances were calculated to compare Tlatelolco and Cholula haplotypes with available ancient haplotype data from Mesoamerican groups and the two borderland areas, Paquimé and Greater Nicoya. Mitochondrial haplogroups were characterized for 11 of the 15 samples from Tlatelolco (73%) and 12 samples out of 13 from Cholula (92%), revealing the presence of four distinct Amerindian mitochondrial lineages at Tlateloloco, A (n = 6; 55%), B (n = 2; 18%), C (n = 1; 9%) and D (n = 2; 10%); and three lineages in Cholula, A (n = 5; 42%), B (n = 5; 42%) and C (n = 2; 16%). Statistical analysis of the haplotypes, haplogroup frequencies and Nei genetic distances showed close affinity of Tlatelolco’s subadults with ancient Mexica (Aztecs) and closer affinities between Cholula and the Xaltocan of the Basin of Mexico. Sex determination of Tlatelolco subadult sacrifice victims revealed that 83% were females, in contrast to previous studies of subadult sacrificial patterns at the site. Together, these results demonstrate the multi-ethnic nature of religious and economic centres in Postclassic Central Mexico.


Mesoamerica Human sacrifice Mitochondrial DNA Genetic distance Haplogroups Sex determination 



The authors thank Dirección de Antropología Física, INAH; INAH-Tlatelolco and INAH-Puebla for providing information and permissions to conduct this study. We give special thanks to MSc. Jose Antonio Pompa y Padilla and MSc. Ma. Elena Salas Cuesta† who selected the Tlatelolco samples and sent them for genetic analysis to the University of Calgary. Also, we thank the archaeologists Carlos Cedillo Ortega and Martha Adriana Saenz Serdio, for providing information and selecting samples from Cholula for this research. Likewise, we thank Salvador Guilliem Arroyo, who provided information about the samples obtained from Tlatelolco. Finally, we thank to Adam K. Benfer for making the map for this article.

Author contributions were as follows: AYMA, NS and CS designed the research. AYMA, JH and KM performed the experiments. AYMA, JH and CS analysed the data. GM, CS and NS provided materials and resources. AYMA wrote the paper, with input from the other co-authors.


This work was supported by the University Research Grants seed grant from the University of Calgary, and by BioArch, University of York.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

12520_2018_771_MOESM1_ESM.xlsx (13 kb)
ESM 1 Results of whole genome sequencing of Tlatelolco subadults. (XLSX 13 kb)
12520_2018_771_MOESM2_ESM.docx (762 kb)
ESM 2 (DOCX 762 kb)


  1. Abdi HH (2007) The Bonferonni and Šidák corrections for multiple comparisons. Encycl Meas Stat 1:1–9. Google Scholar
  2. Aguirre Samudio AJ, Gonzales Sobrino BZ, Alvarez-Sandoval BA et al (2016) Genetic history of the classic period of teotihuacan’s burials in Central Mexico. Rev Argentina Antropol Biológica 19.
  3. Álvarez-Sandoval BA, Manzanilla LR, González-Ruiz M, Malgosa A, Montiel R (2015) Genetic evidence supports the multiethnic character of Teopancazco, a neighborhood Center of Teotihuacan, Mexico (AD 200-600). PLoS One 10:e0132371. CrossRefGoogle Scholar
  4. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147CrossRefGoogle Scholar
  5. Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48CrossRefGoogle Scholar
  6. Broda de Casas J (1971) Las fiestas aztecas de los dioses de la lluvia una reconstruccion segun las fuentes del siglo XVI. Rev Esp Antropol Am 6:245–327. Google Scholar
  7. Buikstra JE, Ubelaker DH (1994) Standards for data collection from human skeletal remains: proceedings of a seminar at the Field Museum of Natural History. Arkansas Archeological Survey Research Series, FayettevilleGoogle Scholar
  8. Carballo DM (2016) Urbanization and religion in ancient Central Mexico. Oxford University Press, New YorkCrossRefGoogle Scholar
  9. Carmack RM, Gasco J, Gossen GH (2007) The legacy of Mesoamerica : history and culture of a native American civilization, second. Pearson Prentice Hall, New JerseyGoogle Scholar
  10. Carrasco P (1971) Los barrios antiguos de Cholula. In: Castro Morales E (ed) Estudios y Documentos de la Region de Puebla-Tlaxcala Vol.III. Instituto Poblano de Antropologi e Historia, Mexico , pp 9–88Google Scholar
  11. Davies N (1977) The Toltecs until the fall of Tula. University of Oklahoma Press, NormanGoogle Scholar
  12. De La Cruz I, Gonzalez-Oliver A, Kemp BMM et al (2008) Sex identification of children sacrificed to the ancient Aztec rain gods in Tlatelolco. Curr Anthropol 49:519–526. CrossRefGoogle Scholar
  13. de Sahagún B, Garibay KAM, de Bustamante CM (1975) Historia general de las cosas de Nueva España. x, 1093Google Scholar
  14. Dudar JC, Waye JS, Saunders SR (2003) Determination of a kinship system using ancient DNA, mortuary practice, and historic records in a upper Canadian pioneer cemetery. Int J Osteoarchaeol 13:232–246. CrossRefGoogle Scholar
  15. Duran FD (1971) Book of the gods and rites and the ancient calendar. University of Oklahoma Press, NormanGoogle Scholar
  16. Elwess NL, Kopp M, Lavioe E et al (2015) Analysis of ancient mitochondrial DNA within the Tipu Maya collection. Internet J Biol Anthropol 8:1–7. Google Scholar
  17. ESDIS N (2017) Moderate resolution imaging spectroradiometer (MODIS) terra corrected reflectance (true color), 30 m resolution, 3rd December 2017. In: NASA Worldview. Greenbelt, Maryl. Earth Obs. Syst. Data Inf. Syst. (EOSDIS), Earth Sci. Data Inf. Syst. Proj. Flight Proj. Dir. Goddard Sp. Flight Cent. (GSFC), Natl. Aeronaut. Sp. Ad. . Accessed 18 Dec 2017
  18. Fortes GG, Paijmans JLA (2015) Analysis of whole mitogenomes from ancient samples. Methods Mol Biol 1347:179–195. CrossRefGoogle Scholar
  19. Fowler WR (1989) The cultural evolution of ancient Nahua civilizations: the Pipil-Nicarao of Central America. University of Oklahoma Press, OklahomaGoogle Scholar
  20. Ginolhac A, Rasmussen M, Gilbert MTP, Willerslev E, Orlando L (2017) mapDamage : testing for damage patterns in ancient DNA sequences. Bioinformatics 27(15):2153–2155. CrossRefGoogle Scholar
  21. Gonzales Rul F (1996) Tlatelolco a traves de los tiempos 50 anos despues (1944–1994) Tomo II Etnohistoria. Instituto Nacional de Antropologia e Historia, MexicoGoogle Scholar
  22. Gonzales Torres Y (2001) Sacrifice and ritual violence. In: Carrasco D (ed) The Oxford encyclopedia of mesoamerican cultures. Oxford University Press, MexicoGoogle Scholar
  23. González-Martín A, Gorostiza A, Regalado-Liu L, Arroyo-Peña S, Tirado S, Nuño-Arana I, Rubi-Castellanos R, Sandoval K, Coble MD, Rangel-Villalobos H (2015) Demographic history of indigenous populations in Mesoamerica based on mtDNA sequence data. PLoS One 10(8):e0131791. CrossRefGoogle Scholar
  24. González-Oliver A, Márquez-Morfín L, Jiménez JC, Torre-Blanco A (2001) Founding Amerindian mitochondrial DNA lineages in ancient Maya from Xcaret, Quintana Roo. Am J Phys Anthropol 116:230–235CrossRefGoogle Scholar
  25. Guilliem Arroyo S (2016) Reporte de muestras de Tlatelolco. Mexico D.FGoogle Scholar
  26. Guillien Arroyo S (1999) Ofrendas a Ehecatl-Quetzalcoatl en Mexico-Tlatelolco. Proyecto Tlatelolco, 1987–1996. Instituto Nacional de Antropologia e Historia, MexicoGoogle Scholar
  27. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  28. Hansen HB, Damgaard PB, Margaryan A, Stenderup J, Lynnerup N, Willerslev E, Allentoft ME (2017) Comparing ancient DNA preservation in petrous bone and tooth cementum. PLoS One 12(1):e0170940. CrossRefGoogle Scholar
  29. Hirth KG (1996) Political economy and archaeology: perspectives on exchange and production. J Archaeol Res 4(3):203–239CrossRefGoogle Scholar
  30. Hofreiter M, Paijmans JLA, Goodchild H, Speller CF, Barlow A, Fortes GG, Thomas JA, Ludwig A, Collins MJ (2015) The future of ancient DNA: technical advances and conceptual shifts. BioEssays 37:284–293. CrossRefGoogle Scholar
  31. Jonsson H, Ginolhac A, Schubert M et al (2013) mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29:1682–1684. CrossRefGoogle Scholar
  32. Juárez Martín A (2002) Parentesco Biológico entre los pobladores prehispánicos de Cholula, mediante el análisis molecular de sus restos óseos. Escuela Nacional de Antropología e Historia, MexicoGoogle Scholar
  33. Katzenberg MA, Oetelaar G, Oetelaar J, Fitzgerald C, Yang D, Saunders SR (2005) Identification of historical human skeletal remains : a case study using skeletal and dental age , history and DNA. Int J Osteoarchaeol 15:61–72. CrossRefGoogle Scholar
  34. Kemp BM, Reséndez A, Román Berrelleza JA et al (2005) An analysis of ancient Aztec mtDNA from Tlatelolco: pre-Colombian relations and the spread of Uto-Aztecan. In: Reed DM (ed) Genetic approaches to the past. Center for archaeological investigations. Southern Illinois University, Illinois, pp 22–47Google Scholar
  35. Kubler G (1968) La traza colonial de Cholula. Estud Hist Novahispana:111–127Google Scholar
  36. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760. CrossRefGoogle Scholar
  37. Lind M (2012) The kingdom and pilgrimage center of Cholula. In: Fields VM, Pohl JMD, Lyall VI, de Avila Blomberg A (eds) Children of the Plumed Serpent: Art and ritual in Mesoamerica’s Late Antiquity. Los Angeles County Museum of Art, Los Angeles, p 256Google Scholar
  38. Livi-Bacci M (2006) The depopulation of hispanic America after the conquest. Popul Dev Rev 32:199–232. CrossRefGoogle Scholar
  39. Lopez Austin A (2001) Aztec. In: The Oxford encyclopedia of Mesoamerican cultures. Oxford University Press, New York, pp 68–72Google Scholar
  40. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220Google Scholar
  41. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal 17:10–12Google Scholar
  42. Mata-Míguez J, Overholtzer L, Rodríguez-Alegría E, Kemp BM, Bolnick DA (2012) The genetic impact of Aztec imperialism: ancient mitochondrial DNA evidence from Xaltocan, Mexico. Am J Phys Anthropol 149:504–516. CrossRefGoogle Scholar
  43. McCafferty G (1996) Reinterpreting the great pyramid of Cholula, Mexico. Anc Mesoamerica 7:1–17. CrossRefGoogle Scholar
  44. McCafferty G (2001) Cholula. In: The Oxford encyclopedia of Mesoamerican cultures. Oxford University Press, New York, pp 202–205Google Scholar
  45. McCafferty G (2007) So what else is new? A Cholula centric perspective on lowland/Highland interaction during the classic/Postclassic transition. In: Kowalski JK, Kristan-Graham C (eds) Twin Tollans: Chichen Itza, Tula, and the Epiclassic to early Postclassic Mesoamerican world. Dumbarton Oaks, Washington, DC, pp 449–481Google Scholar
  46. Mccafferty G (2015) The Mexican legacy in Nicaragua , or problems when data behave badly. 25:110–118.
  47. McCafferty GG, Dennett CL (2013) Ethnogenesis and hybridity in proto-historic Nicaragua. Archaeol Cult Mix 191Google Scholar
  48. McCafferty G, Steinbrenner L (2005) The meaning of the Mixteca-Puebla style stylistic tradition on the southern periphery of Mesoamerica: the view from Nicaragua. In: Waters-Rist A, Cluny C, Mcnamee C, Steinbrenner L (eds) 33rd annual Chacmool conference. The Arqueological Association of the University of Calgary, Calgary, pp 282–292Google Scholar
  49. Merriwether DA, Reed DM, Ferrell RE, Ferrel RE (2006) Ancient and contemporary mitochondrial DNA variation in the Maya. In: Whittington SL, Reed DM (eds) Bones of the Maya: Studies of Ancient Skeletons. University of Alabama Press, Tuscaloosa, pp 208–217Google Scholar
  50. Meyer M, Kircher M (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc 5:1–11. Google Scholar
  51. Morales-Arce AY, Hofman CA, Duggan AT, Benfer AK, Katzenberg MA, McCafferty G, Warinner C (2017a) Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico. Sci Rep 7:18100. CrossRefGoogle Scholar
  52. Morales-Arce AY, Snow MH, Kelley JH, Anne Katzenberg M (2017b) Ancient mitochondrial DNA and ancestry of Paquime inhabitants, Casas Grandes (A.D. 1200-1450). Am J Phys Anthropol 163:616–626. CrossRefGoogle Scholar
  53. Motolinía T (1950) History of the Indians of New Spain. The Cortés Society, BerkeleyGoogle Scholar
  54. Muller F (1973) La extensionk arqueologica de Cholula a traves del tiempo. Comunicaciones:19–22Google Scholar
  55. Nei M (1972) Genetic distance between populations. Am Nat 106:283–292Google Scholar
  56. Nichols DL, Pool CA (2012) The Oxford handbook of Mesoamerican archaeology. Oxford University Press, OxfordCrossRefGoogle Scholar
  57. O’Rourke DH, Raff JA (2010) The human genetic history of the Americas: review the final frontier. Curr Biol 20:R202–R207CrossRefGoogle Scholar
  58. Ochoa-Lugo MI, Muñoz M de L, Pérez-Ramírez G et al (2016) Genetic affiliation of pre-Hispanic and contemporary Mayas through maternal linage. Hum Biol 88:136–167. CrossRefGoogle Scholar
  59. Orozco y Berra M (1960) Historia antigua y de la conquista de Mexico, vol. 4. Editorial Porrúa, MexicoGoogle Scholar
  60. Paddock J (1987) Cholula en Mesoamerica. Notas Mesoamericanas 10:21–68Google Scholar
  61. Parson W, Gusmão L, Hares DR, Irwin JA, Mayr WR, Morling N, Pokorak E, Prinz M, Salas A, Schneider PM, Parsons TJ, DNA Commission of the International Society for Forensic Genetics (2014) DNA Commission of the International Society for forensic genetics: revised and extended guidelines for mitochondrial DNA typing. Forensic Sci Int Genet 13:134–142. CrossRefGoogle Scholar
  62. Patterson T, Vaughn Kelso N (2017) Cross blended hypso with relief, water, drains, and ocean bottom, 1:10 raster. Version 3.2.0. In: Nat. Earth. Free Vectors Raster Map Data. Accessed 18 Dec 2017
  63. Peakall R, Smouse PE (2006) GENALEX 8: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295CrossRefGoogle Scholar
  64. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics 28:2537–2539. CrossRefGoogle Scholar
  65. Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetic software for exact tests and ecumenicism. J Hered 86:248–249CrossRefGoogle Scholar
  66. Roman Berrelleza JA (1991) A study of skeletal material from Tlatelolco. In: Carrasco D (ed) To change place: Aztec ceremonial landscapes. University Press of Colorado, Niwot, pp 9–19Google Scholar
  67. Rousset F (2008) Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resour 8:103–106. CrossRefGoogle Scholar
  68. Saenz Serdio MA, Cedillo Ortega C (2016) Informe parcial para el procesamiento de muestras de ADN mitocondrial antiguo en el Laboratorio de la Universidad de Calgary. Cholula, PueblaGoogle Scholar
  69. Schubert M, Ginolhac A, Lindgreen S, Thompson JF, Al-Rasheid KAS, Willerslev E, Krogh A, Orlando L (2012) Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13:178CrossRefGoogle Scholar
  70. Sharer RJ, Traxler LP (2006) The ancient Maya, 6th edn. Stanford University Press, StanfordGoogle Scholar
  71. Skoglund P, Storå J, Götherström A, Jakobsson M (2013) Accurate sex identification of ancient human remains using DNA shotgun sequencing. J Archaeol Sci 40:4477–4482. CrossRefGoogle Scholar
  72. Smith ME (1984) The Aztlan migrations of the Nahuatl chronicles: myth or history? Ethnohistory 31:153–186CrossRefGoogle Scholar
  73. Smith ME (2008a) The Aztec empire. In: Brumfield EM, Feinman GM (eds) The Aztec world. Abrams, New York, pp 121–136Google Scholar
  74. Smith ME (2008b) Aztec city-state capitals. University Press of Florida, GainesvilleGoogle Scholar
  75. Smith ME, Berdan FF (2003) Postclassic Mesoamerica. In: Smith ME, Berdan FF (eds) The Postclassic Mesoamerican world. The University of Utah Press, pp 3–13Google Scholar
  76. Solórzano Navarro E (2006) De La Mesoamérica Prehispanica a la Colonial: La huella del DNA antiguo. Universidad Autonoma de BarcelonaGoogle Scholar
  77. Stoneking M (2000) Hypervariable sites in the mtDNA control region are mutational hotspots. Am J Hum Genet 67:1029–1032CrossRefGoogle Scholar
  78. Tsukamoto K, Inomata T, Campiani A et al (2014) Mesoamerican plazas : arenas of community and power. University of Arizona Press, TucsonCrossRefGoogle Scholar
  79. Vågene ÅJ, Campana MG, Robles García NM, et al (2017) Salmonella enterica genomes recovered from victims of a major 16th century epidemic in Mexico. bioRxivGoogle Scholar
  80. van Oven M (2015) PhyloTree build 17: growing the human mitochondrial DNA tree. Forensic Sci Int Genet Suppl Ser 5:e392–e394CrossRefGoogle Scholar
  81. van Oven M, Kayser M (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30:E386–E394. CrossRefGoogle Scholar
  82. van Zantwijk R (1985) The aztec arrangement: the social history of pre-Spanish Mexico. University of Oklahoma Press, Norman, OklahomaGoogle Scholar
  83. Warinner C, García NR, Spores R, Tuross N (2012) Disease, demography, and diet in early colonial New Spain: investigation of a sixteenth-century Mixtec cemetery at Teposcolula Yucundaa. Lat Am Antiq 23:467–489CrossRefGoogle Scholar
  84. Willermet C, Edgar HJH, Ragsdale C, Aubry BS (2013) Biodistances among Mexica, Maya, Toltec, and Totonac groups of central and coastal Mexico. Chungara, Rev Antropol Chil 45:447–460Google Scholar
  85. Yang DY, Eng B, Waye JS, Dudar JC, Saunders SR (1998) Technical note: improved DNA extraction from ancient bones using silica-based spin columns. Am J Phys Anthr 105:539–543.<539::AID-AJPA10>3.0.CO;2-1 CrossRefGoogle Scholar
  86. Yang DY, Liu L, Chen X, Speller CF (2008) Wild or domesticated: DNA analysis of ancient water buffalo remains from North China. J Archeol Sci 35:2778–2785. CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Center for Evolution and MedicineArizona State UniversityTempeUSA
  2. 2.Department of Anthropology and ArchaeologyUniversity of CalgaryCalgaryCanada
  3. 3.BioArCh, Department of ArchaeologyUniversity of YorkYorkUK
  4. 4.Gen Assoc AHS Researcher, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
  5. 5.Department of AnthropologyUniversity of British ColumbiaVancouverCanada

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