• Price, T. D., Tiesler, V. & Freiwald, C. Place of origin of the sacrificial victims in the Sacred Cenote, Chichén Itzá, Mexico. Am. J. Phys. Anthropol. 170, 98–115 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Kristan-Graham, C. et al. Twin Tollans: Chichén Itzá, Tula and the Epiclassic to Early Postclassic Mesoamerican World (Dumbarton Oaks, 2007).

  • Beck, L. A. & Sievert, A. K. in Interacting with the Dead: Perspectives on Mortuary Archaeology for the New Millennium (eds Rakita, G. et al.) 290–304 (Univ. Press Florida, 2005).

  • Márquez Morfín, L. & Schmidt, P. in Investigaciones Recientes en el área Maya. Vol. II. Memorias de la XVII Mesa Redonda (1981) 89–104 (Sociedad Mexicana de Antropología, 1984).

  • Coe, M. D. in The Maya Vase Book: A Corpus of Rollout Photographs of Maya Vases (eds Kerr, B. & Kerr, J.) 161–184 (Kerr Associates, 1989).

  • Cobos, R. & Winemiller, T. L. The Late and Terminal Classic-period causeway systems of Chichen Itza, Yucatan, Mexico. Anc. Mesoam. 12, 283–291 (2001).

    Article 

    Google Scholar
     

  • Tiesler, V. in Stone Houses and Earth Lords: Maya Religion in the Cave Context (eds Prufer, K. M. & Brady, J. E.) 341–364 (Univ. Press Colorado, 2005).

  • Miller, V. E. in New Perspectives on Human Sacrifice and Ritual Body Treatments in Ancient Maya Society (eds Tiesler, V. & Cucina, A.) 165–189 (Springer New York, 2007).

  • Graña-Behrens, D., Prager, C. & Wagner, E. The hieroglyphic inscription of the ‘High Priest’s Grave’ at Chichén Itzá, Yucatán, Mexico. Mexicon 21, 61–66 (1999).


    Google Scholar
     

  • Dahlin, B. H. Climate change and the end of the Classic period in Yucatán. Resolving a paradox. Anc. Mesoam. 13, 327–340 (2002).

    Article 

    Google Scholar
     

  • Roys, R. L. The Book of Chilam Balam of Chumayel (Univ. Oklahoma Press, 1967).

  • Tozzer, A. M. Chichen Itza and its Cenote of Sacrifice: A Comparative Study of Contemporaneous Maya and Toltec (Harvard Univ., 1957).

  • Anda, G. D., Tiesler, V. & Zabala, P. in Los Investigadores de la Cultura Maya Vol. 12, 376–386 (Universidad Autónoma de Campeche, 2004).

  • Márquez Morfín, L. in Los Niños Como Actores Sociales Ignorados. Levantando el Velo, una Mirada al Pasado (ed. Márquez Morfín, L.) 253–282 (ENAN-INAH, 2006).

  • Baudez, C.-F. & Latsanopoulos, N. Political structure, military training and ideology at Chichen Itza. Anc. Mesoam. 21, 1–20 (2010).

    Article 

    Google Scholar
     

  • Cagnato, C. Underground pits (chultunes) in the southern Maya lowlands: excavation results from Classic period Maya sites in northwestern Petén. Anci. Mesoam. 28, 75–94 (2017).

    Article 

    Google Scholar
     

  • Puleston, D. E. An experimental approach to the function of Classic Maya chultuns. Am. Antiq. 36, 322–335 (1971).

    Article 

    Google Scholar
     

  • Brady, J. & Layco, W. Maya cultural landscapes and the subterranean: assessing a century of chultun research. Int. J. Archaeol. 6, 46–55 (2018).

    Article 

    Google Scholar
     

  • Prout, M. G. & Brady, J. E. Paleodemographics of child sacrifice at Midnight Terror Cave: reformulating the emphasis of Maya sacrificial practices. Archaeol. Discov. 6, 1–20 (2018).

    Article 

    Google Scholar
     

  • Ardren, T. Empowered children in Classic Maya sacrificial rites. Child. Past 4, 133–145 (2011).

    Article 

    Google Scholar
     

  • MacLeod, B. & Puleston, D. E. in Tercera Mesa Redonda de Palenque (eds Robinson, M. G. & Jeffers, D. C.) 71–77 (Herald Printers, 1978).

  • Moyes, H. & Brady, J. E. in Sacred Darkness: A Global Perspective on the Ritual Use of Caves (ed. Moyes, H.) 151–170 (Univ. Press Colorado, 2014).

  • del Castillo Chávez, O. & Williams-Beck, L. Rituales k’ex al Dios Del Maíz En Chichén Itzá y Mayapán: Una Tradición Ritual Del Clásico al Postclásico (Centro Regional Yucatán del INAH, 2020).

  • Willard, T. A. The City of the Sacred Well (Century, 1926).

  • Arnold, C. & Frost, F. J. T. The American Egypt: A Record of Travel in Yucatan (Hutchinson, 1909).

  • Cucina, A. & Tiesler, V. in The Bioarchaeology of Space and Place (ed. Wrobel, G. D.) 225–254 (Springer, 2014).

  • de Landa, D., Tozzer, A. M. & Bowditch, C. P. Landa’s Relación de Las Cosas de Yucatan: A Translation (Harvard Univ., 1941).

  • Clendinnen, I. Ambivalent Conquests. Maya and Spaniard in Yucatan, 1517–1570 (Cambridge Univ. Press, 2003).

  • Vågene, Å. J. et al. Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nat. Ecol. Evol. 2, 520–528 (2018).

    Article 
    PubMed 

    Google Scholar
     

  • Llamas, B. et al. From the field to the laboratory: controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era. Sci. Technol. Archaeol. Res. 3, 1–14 (2017).


    Google Scholar
     

  • Fellows Yates, J. A. et al. Reproducible, portable and efficient ancient genome reconstruction with nf-core/eager. PeerJ 9, e10947 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Immel, A. et al. Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes. Mol. Biol. Evol. 38, 4059–4076 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fu, Q. et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553–559 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lamnidis, T. C. et al. Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe. Nat. Commun. 9, 5018 (2018).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lamnidis, T. C. pMMRCalculator. GitHub https://github.com/TCLamnidis/pMMRCalculator (2020).

  • Götz, C. M. La alimentación de los mayas prehispánicos vista desde la zooarqueología. An. Antropol. 48, 167–199 (2014).


    Google Scholar
     

  • Herrera Flores, D. A. & Markus Götz, C. La alimentación de los antiguos mayas de la península de Yucatán: consideraciones sobre la identidad y la cuisine en la época prehispánica. Estud. Cult. Maya XLIII, 69–98 (2014).

    Article 

    Google Scholar
     

  • Kennett, D. J. et al. Early isotopic evidence for maize as a staple grain in the Americas. Sci. Adv. 6, eaba3245 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Staller, J. E., Tykot, R. H. & Benz, B. F. in Histories of Maize in Mesoamerica (eds Staller, J. et al.) Ch. 11 (Routledge, 2010).

  • Fernández Souza, L., Toscano, L. & Zimmermann, M. De Maíz y de Cacao: Aproximaciones a la Cocina de las Elites Mayas en Tiempos Prehispánicos. In: Hernández Álvarez, H., et al. Estética y Poder en la Ciencia y la Tecnología, Mérida pp 107–130 (UADY, 2014).

  • Zimmermann, M. Starch grain extraction in lime-plastered archaeological floors. Sci. Technol. Archaeol. Res. 7, 31–42 (2021).


    Google Scholar
     

  • Somerville, A. D., Fauvelle, M. & Froehle, A. W. Applying new approaches to modeling diet and status: isotopic evidence for commoner resiliency and elite variability in the Classic Maya lowlands. J. Archaeol. Sci. 40, 1539–1553 (2013).

    Article 

    Google Scholar
     

  • White, C. D. & Schwarcz, H. P. Ancient Maya diet: as inferred from isotopic and elemental analysis of human bone. J. Archaeol. Sci. 16, 451–474 (1989).

    Article 

    Google Scholar
     

  • Wright, L. E. & White, C. D. Human biology in the Classic Maya collapse: evidence from paleopathology and paleodiet. J. World Prehist. 10, 147–198 (1996).

    Article 

    Google Scholar
     

  • Tykot, R. H. in Archaeological Chemistry Vol. 831 (ed. Jakes, K.) 214–230 (American Chemical Society, 2002).

  • Scherer, A. K. Bioarchaeology and the skeletons of the Pre-Columbian Maya. J. Archaeol. Res. 25, 133–184 (2017).

    Article 

    Google Scholar
     

  • Mansell, E. B., Tykot, R. H., Freidel, D. A., Dahlin, B. H. & Ardren, T. in Histories of Maize: Multidisciplinary Approaches to the Prehistory, Linguistics, Biogeography, Domestication and Evolution of Maize (eds Staller, J. et al.) 173–185 (Elsevier, 2010).

  • Posth, C. et al. Reconstructing the deep population history of Central and South America. Cell 175, 1185–1197 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Reich, D. et al. Reconstructing Native American population history. Nature 488, 370–374 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kennett, D. J. et al. South-to-north migration preceded the advent of intensive farming in the Maya region. Nat. Commun. 13, 1530 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bergström, A. et al. Insights into human genetic variation and population history from 929 diverse genomes. Science https://doi.org/10.1126/science.aay5012 (2020).

  • Mallick, S. et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schraiber, J. G. Assessing the relationship of ancient and modern populations. Genetics 208, 383–398 (2018).

    Article 
    PubMed 

    Google Scholar
     

  • González-Oliver, A., Márquez-Morfín, L., Jiménez, J. C. & Torre-Blanco, A. Founding Amerindian mitochondrial DNA lineages in ancient Maya from Xcaret, Quintana Roo. Am. J. Phys. Anthropol. 116, 230–235 (2001).

    Article 
    PubMed 

    Google Scholar
     

  • Ochoa-Lugo, M. I. et al. Genetic affiliation of pre-Hispanic and contemporary Mayas through maternal lineage. Hum. Biol. 88, 136–167 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Mizuno, F. et al. Characterization of complete mitochondrial genomes of indigenous Mayans in Mexico. Ann. Hum. Biol. 44, 652–658 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Bodner, M. et al. The mitochondrial DNA landscape of modern Mexico. Genes 12, 1453 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ruiz-Linares, A. et al. Admixture in Latin America: geographic structure, phenotypic diversity and self-perception of ancestry based on 7,342 individuals. PLoS Genet. 10, e1004572 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chacón-Duque, J. C. et al. Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance. Nat. Commun. 9, 5388 (2018).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ongaro, L. et al. Evaluating the impact of sex-biased genetic admixture in the Americas through the analysis of haplotype data. Genes 12, 1580 (2021).

  • Ongaro, L. et al. The genomic impact of European colonization of the Americas. Curr. Biol. 29, 3974–3986 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shriver, M. D. et al. The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. Hum. Genom. 1, 274 (2004).

    Article 
    CAS 

    Google Scholar
     

  • Duforet-Frebourg, N., Luu, K., Laval, G., Bazin, E. & Blum, M. G. B. Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data. Mol. Biol. Evol. 33, 1082–1093 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Auton, A. et al. A global reference for human genetic variation. Nature 526, 68–74 (2015).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Amorim, E. et al. Genetic signature of natural selection in first Americans. Proc. Natl Acad. Sci. USA 114, 2195–2199 (2017).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Villalobos-Comparán, M. et al. The FTO gene is associated with adulthood obesity in the Mexican population. Obesity 16, 2296–2301 (2008).

    Article 
    PubMed 

    Google Scholar
     

  • Ortega, P. E. N. et al. Association of rs9939609-FTO with metabolic syndrome components among women from Mayan communities of Chiapas, Mexico. J. Physiol. Anthropol. 40, 11 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lara-Riegos, J. C. et al. Diabetes susceptibility in Mayas: evidence for the involvement of polymorphisms in HHEX, HNF4α, KCNJ11, PPARγ, CDKN2A/2B, SLC30A8, CDC123/CAMK1D, TCF7L2, ABCA1 and SLC16A11 genes. Gene 565, 68–75 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ojeda-Granados, C. et al. Dietary, cultural and pathogens-related selective pressures shaped differential adaptive evolution among Native Mexican populations. Mol. Biol. Evol. 39, msab290 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kofler, R. & Schlötterer, C. Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies. Bioinformatics 28, 2084–2085 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lindo, J. et al. A time transect of exomes from a Native American population before and after European contact. Nat. Commun. 7, 13175 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Penman, B. S., Ashby, B., Buckee, C. O. & Gupta, S. Pathogen selection drives nonoverlapping associations between HLA loci. Proc. Natl Acad. Sci. USA 110, 19645–19650 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Buckee, C. O., Gupta, S., Kriz, P., Maiden, M. C. J. & Jolley, K. A. Long-term evolution of antigen repertoires among carried meningococci. Proc. R. Soc. B 277, 1635–1641 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Barquera, R. et al. Diversity of HLA Class I and Class II blocks and conserved extended haplotypes in Lacandon Mayans. Sci. Rep. 10, 3248 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gonzalez-Galarza, F. F. et al. Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools. Nucleic Acids Res. 48, D783–D788 (2020).

    CAS 
    PubMed 

    Google Scholar
     

  • Gómez-Casado, E. et al. Origin of Mayans according to HLA genes and the uniqueness of Amerindians. Tissue Antigens 61, 425–436 (2003).

    Article 
    PubMed 

    Google Scholar
     

  • Dunstan, S. J. et al. Genes of the class II and class III major histocompatibility complex are associated with typhoid fever in Vietnam. J. Infect. Dis. 183, 261–268 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Dunstan, S. J. et al. Variation at HLA-DRB1 is associated with resistance to enteric fever. Nat. Genet. 46, 1333–1336 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • de Vries, R. R. P., Meera Khan, P., Bernini, L. F., van Loghem, E. & van Rood, J. J. Genetic control of survival in epidemics. J. Immunogenet. 6, 271–287 (1979).

    Article 
    PubMed 

    Google Scholar
     

  • Reynisson, B., Alvarez, B., Paul, S., Peters, B. & Nielsen, M. NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res. 48, W449–W454 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fuchs, K. M. & D’Alton, M. E. in Obstetric Imaging: Fetal Diagnosis and Care (eds Copel, J. A. et al.) 639–641 (Elsevier, 2018).

  • Christenson, A. J. Popol Vuh. Sacred Book of the Quiché Maya People (Transl.) (Univ. Oklahoma Press, 2007).

  • Saturno, W. A., Stuart, D. & Taube, K. in XVIII Simposio de Investigaciones Arqueológicas en Guatemala (eds LaPorte, J. P. et al.) Ch. 60 (Museo Nacional de Guatemala, 2004).

  • Acuña-Alonzo, V. et al. A functional ABCA1 gene variant is associated with low HDL-cholesterol levels and shows evidence of positive selection in Native Americans. Hum. Mol. Genet. 19, 2877–2885 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • León-Mimila, P. et al. Genome-wide association study identifies a functional SIDT2 variant associated with HDL-C (high-density lipoprotein cholesterol) levels and premature coronary artery disease. Arterioscler. Thromb. Vasc. Biol. 41, 2494–2508 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fritz, J., Lopez-Ridaura, R., Choudhry, S., Razo, C. & Lamadrid-Figueroa, H. The association of Native American genetic ancestry and high-density lipoprotein cholesterol: a representative study of a highly admixed population. Am. J. Hum. Biol. 32, e23426 (2020).

    Article 
    PubMed 

    Google Scholar
     

  • Scherer, A. K., Wright, L. E. & Yoder, C. J. Bioarchaeological evidence for social and temporal differences in diet at Piedras Negras, Guatemala. Latin Am. Antiq. 18, 85–104 (2007).

    Article 

    Google Scholar
     

  • Wright, L. E. & Schwarcz, H. P. Stable carbon and oxygen isotopes in human tooth enamel: identifying breastfeeding and weaning in prehistory. Am. J. Phys. Anthropol. 106, 1–18 (1998).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Acuña-Soto, R., Stahle, D. W., Therrell, M. D., Griffin, R. D. & Cleaveland, M. K. When half of the population died: the epidemic of hemorrhagic fevers of 1576 in Mexico. FEMS Microbiol. Lett. 240, 1–5 (2004).

    Article 
    PubMed 

    Google Scholar
     

  • Cook, S. F. & Simpson, L. B. The Population of Central Mexico in the Sixteenth Century Vol. 31 (Univ. California Press, 1948).

  • Marr, J. S. & Kiracofe, J. B. Was the huey cocoliztli a haemorrhagic fever? Med. Hist. 44, 341–362 (2000).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cook, N. Born to Die: Disease and New World Conquest, 1492–1650 (Cambridge Univ. Press, 1998).

  • Cook, S. F. & Borah, W. The Indian Population of Central Mexico, 1531–1610 (Univ. California Press, 1960).

  • Zambardino, R. A. Mexico’s population in the sixteenth century: demographic anomaly or mathematical illusion? J. Interdiscipl. Hist. 11, 1–27 (1980).

    Article 

    Google Scholar
     

  • Crosby, A. W. Virgin soil epidemics as a factor in the aboriginal depopulation in America. William Mary Q. 33, 289–299 (1976).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Crosby Jr, A. W. The Columbian Exchange: Biological and Cultural Consequences of 1492 (Greenwood, 1972).

  • Real Academia de la Historia & del Paso & Troncoso, F. Relaciones Geograficas de La Diocesis de Mexico: Manuscritos de La Real Academia de La Historia de Madrid y Del Archivo de Indias En Sevilla. Anos 1579–1582 (Est. tipografico ‘Sucesores de Rivadeneyra,’ Sevilla, 1905).

  • Viesca, C. in Ensayos Sobre la Historia de las Epidemias en México (eds Florescano, E. & Elsa, M.) 157–165 (Instituto Mexicano del Seguro Social, 1982).

  • Márquez Morfín, L. La sífilis y su carácter endémico en la ciudad de México. Hist. Mex. 64, 1099–1161 (2015).

  • Key, F. M. et al. Emergence of human-adapted Salmonella enterica is linked to the Neolithization process. Nat. Ecol. Evol. 4, 324–333 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Barquera, R. et al. The immunogenetic diversity of the HLA system in Mexico correlates with underlying population genetic structure. Hum. Immunol. 81, 461–474 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • de Buenaventura, J., Guerrero, G., Solís Robleda, G. & Bracamonte y Sosa, P. Historias de la Conquista del Mayab, 1511–1697 (Universidad Autónoma de Yucatán, Facultad de Ciencias Antropológicas, 1994).

  • Góngora-Biachi, R. A. La fiebre amarilla en Yucatán durante las épocas precolombina y colonial. Rev. Bioméd. 11, 301–307 (2000).

    Article 

    Google Scholar
     

  • Patch, R. W. Sacraments and disease in Mérida, Yucatán, Mexico, 1648–1727. Historian 58, 731–743 (1996).

    Article 

    Google Scholar
     

  • Potter, D. F. Prehispanic architecture and sculpture in Central Yucatan. Am. Antiq. 41, 430–448 (1976).

    Article 

    Google Scholar
     

  • Andrews IV, E. W. in Handbook of Middle American Indians: Guide to Ethnohistorical Sources Vol. 13 (ed. Wauchope, R.) 288–330 (Univ. Texas Press, 1964).

  • Andrews, A. P., Andrews, E. W. & Castellanos, F. R. The northern Maya collapse and its aftermath. Anc. Mesoam. 14, 151–156 (2003).

    Article 

    Google Scholar
     

  • Hermes, B. & Calderón, Z. in El Sitio Maya de Topoxté. Investigaciones en una Isla del Lago Yaxhá, Petén, Guatemala (ed. Wurster, W. W.) 66–74 (Verlag Philipp von Zabern, 2000).

  • Milbrath, S. in New Directions in American Archaeoastronomy (Proc. 46th International Congress of Americanists) (ed. Aveni, A. F.) 57–79 (BAR International, 1988).

  • Andrews, E. W. Balankanche, Throne of the Tiger Priest (Middle American Research Institute, 1970).

  • Ubelaker, D. H. Human Skeletal Remains: Excavation, Analysis, Interpretation (Aldine, 1978).

  • Hernández Espinosa, P. O. La Regulación Del Crecimiento de La Población En El México Prehispánico (Instituto Nacional de Antropología e Historia, 2006).

  • Verdugo, C. et al. Implications of age and sex determinations of ancient Maya sacrificial victims at Midnight Terror Cave. Int. J. Osteoarchaeol. 30, 458–468 (2020).

    Article 

    Google Scholar
     

  • Karnes, J. H. et al. Phenome-wide scanning identifies multiple diseases and disease severity phenotypes associated with HLA variants. Sci. Transl. Med. 9, eaai8708 (2017).

  • Fernández-Torres, J., Flores-Jiménez, D., Arroyo-Pérez, A., Granados, J. & López-Reyes, A. HLA-B*40 allele plays a role in the development of Acute Leukemia in Mexican population: a case-control study. BioMed. Res. Int. 2013, 705862 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Brown, T. A., Nelson, D. E., Vogel, J. S. & Southon, J. R. Improved collagen extraction by modified Longin method. Radiocarbon 30, 171–177 (1988).

    Article 
    CAS 

    Google Scholar
     

  • Stuiver, M. & Polach, H. A. Discussion reporting of 14C data. Radiocarbon 19, 355–363 (1977).

    Article 

    Google Scholar
     

  • Reimer, P. J. et al. The IntCal20 Northern Hemisphere radiocarbon age calibration curve (0–55 cal kBP). Radiocarbon 62, 725–757 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Ramsey, C. B. & Lee, S. Recent and planned developments of the program OxCal. Radiocarbon 55, 720–730 (2013).

    Article 
    CAS 

    Google Scholar
     

  • Błaszczyk, D. et al. Social status and diet. Reconstruction of diet of individuals buried in some early medieval chamber graves from Poland by carbon and nitrogen stable isotopes analysis. J. Archaeol. Sci. Rep. 38, 103103 (2021).


    Google Scholar
     

  • Pérez-Ramallo, P. et al. Stable isotope analysis and differences in diet and social status in northern Medieval Christian Spain (9th–13th centuries CE). J. Archaeol. Sci. Rep. 41, 103325 (2022).


    Google Scholar
     

  • Ambrose, S. H. & Norr, L. in Prehistoric Human Bone: Archaeology at the Molecular Level (eds. Lambert, J. B. & Grupe, G.) 1–37 https://doi.org/10.1007/978-3-662-02894-0_1 (Springer, 1993).

  • Richards, M. P. & Hedges, R. E. M. Stable isotope evidence for similarities in the types of marine foods used by late Mesolithic humans at sites along the Atlantic coast of Europe. J Archaeol. Sci. 26, 717–722 (1999).

    Article 

    Google Scholar
     

  • van Klinken, G. J. Bone collagen quality indicators for palaeodietary and radiocarbon measurements. J. Archaeol. Sci. 26, 687–695 (1999).

    Article 

    Google Scholar
     

  • DeNiro, M. J. Postmortem preservation and alteration of in vivo bone collagen isotope ratios in relation to palaeodietary reconstruction. Nature 317, 806–809 (1985).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Rohland, N. & Hofreiter, M. Comparison and optimization of ancient DNA extraction. Biotechniques 42, 343–352 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gansauge, M.-T. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8, 737 (2013).

    Article 
    PubMed 

    Google Scholar
     

  • Gansauge, M.-T. & Meyer, M. in Ancient DNA: Methods and Protocols (eds Shapiro, B. et al.) 75–83 (Springer New York, 2019).

  • Gansauge, M.-T., Aximu-Petri, A., Nagel, S. & Meyer, M. Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA. Nat. Protoc. 15, 2279–2300 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 5, pdb.prot5448 (2010).

    Article 

    Google Scholar
     

  • Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. Phil. Trans. R. Soc. B 370, 20130624–20130624 (2014).

    Article 

    Google Scholar
     

  • Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182–189 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad Sci USA 110, 2223–2227 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fu, Q. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Barquera, R. et al. Origin and health status of first-generation Africans from early Colonial Mexico. Curr. Biol. 30, 2078–2091 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rohrlach, A. B. et al. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe. Sci. Rep. 11, 15005 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming, identification and read merging. BMC Res. Notes 9, 88 (2016).

  • Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2009).

    Article 
    CAS 

    Google Scholar
     

  • Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. MapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinf. 15, 356 (2014).

    Article 

    Google Scholar
     

  • Schiffels, S. sequenceTools. GitHub https://github.com/stschiff/sequenceTools.git (2018).

  • Andrews, R. M. et al. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 23, 147 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Weissensteiner, H. et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58–W63 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vianello, D. et al. HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment. Hum. Mutat. 34, 1189–1194 (2013).

    Article 
    PubMed 

    Google Scholar
     

  • Durinck, S., Spellman, P. T., Birney, E. & Huber, W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat. Protoc. 4, 1184–1191 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Szolek, A. et al. OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics 30, 3310–3316 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cao, K. et al. Analysis of the frequencies of HLA-A, B and C alleles and haplotypes in the five major ethnic groups of the United States reveals high levels of diversity in these loci and contrasting distribution patterns in these populations. Hum. Immunol. 62, 1009–1030 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yunis, E. J. et al. In Encyclopedia of Molecular Cell Biology and Molecular Medicine, Vol. 13 (ed. Meyers, R. A.) pp 192–215 (John Wiley & Sons, 2006).

  • R Core Team. R: A Language and Environment for Statistical Computing https://www.r-project.org/ (Foundation for Statistical Computing, 2021).

  • Benjamini, Y., Kenigsberg, E., Reiner, A. & Yekutieli, D. FDR adjustments of microarray experiments (FDR-AME). MathTauAcIl 1, 1–3 (2005).


    Google Scholar
     

  • Penman, B. S. & Gupta, S. Detecting signatures of past pathogen selection on human HLA loci: are there needles in the haystack? Parasitology 145, 731–739 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, P. et al. Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinf. 11, 568 (2010).

    Article 

    Google Scholar
     

  • Moutaftsi, M. et al. A consensus epitope prediction approach identifies the breadth of murine T(CD8 +)-cell responses to vaccinia virus. Nat. Biotechnol. 24, 817–819 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Di, D., Simon Thomas, J., Currat, M., Nunes, J. M. & Sanchez-Mazas, A. Challenging ancient DNA results about putative HLA protection or susceptibility to Yersinia pestis. Mol. Biol. Evol. 39, msac073 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bryc, K. et al. Genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proc. Natl Acad. Sci. USA 107, 8954–8961 (2010).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schiffels, S. Xerxes CLI software. GitHub https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/xerxes.md (2022).

  • Nägele, K. et al. Genomic insights into the early peopling of the Caribbean. Science 369, 456–460 (2020).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Nakatsuka, N. et al. A paleogenomic reconstruction of the deep population history of the Andes. Cell 181, 1131–1145 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Scheib, C. L. et al. Ancient human parallel lineages within North America contributed to a coastal expansion. Science 360, 1024–1027 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Fernandes, D. M. et al. A genetic history of the pre-contact Caribbean. Nature 590, 103–110 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • John, L. et al. The genetic prehistory of the Andean highlands 7000 years BP though European contact. Sci. Adv. 4, eaau4921 (2018).

    Article 

    Google Scholar
     

  • Capodiferro, M. R. et al. Archaeogenomic distinctiveness of the Isthmo-Colombian area. Cell 184, 1706–1723 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Moreno-Mayar, J. V. et al. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature 553, 203–207 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Moreno-Mayar, J. V. et al. Early human dispersals within the Americas. Science 362, eaav2621 (2018).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Rasmussen, M. et al. The ancestry and affiliations of Kennewick Man. Nature 523, 455–458 (2015).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schroeder, H. et al. Origins and genetic legacies of the Caribbean Taino. Proc. Natl Acad. Sci. USA 115, 201716839 (2018).

    Article 

    Google Scholar
     



  • Source link