Ancient genomes reveal insights into ritual life at Chichén Itzá.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
12 Jun 2024
12 Jun 2024
Historique:
received:
30
03
2023
accepted:
02
05
2024
medline:
13
6
2024
pubmed:
13
6
2024
entrez:
12
6
2024
Statut:
aheadofprint
Résumé
The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (AD 600-1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica
Identifiants
pubmed: 38867041
doi: 10.1038/s41586-024-07509-7
pii: 10.1038/s41586-024-07509-7
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2024. The Author(s).
Références
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).
pubmed: 31294838
doi: 10.1002/ajpa.23879
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).
doi: 10.1017/S0956536101122066
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).
Dahlin, B. H. Climate change and the end of the Classic period in Yucatán. Resolving a paradox. Anc. Mesoam. 13, 327–340 (2002).
doi: 10.1017/S0956536102132135
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).
doi: 10.1017/S0956536110000179
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).
doi: 10.1017/S0956536116000377
Puleston, D. E. An experimental approach to the function of Classic Maya chultuns. Am. Antiq. 36, 322–335 (1971).
doi: 10.2307/277717
Brady, J. & Layco, W. Maya cultural landscapes and the subterranean: assessing a century of chultun research. Int. J. Archaeol. 6, 46–55 (2018).
doi: 10.11648/j.ija.20180601.16
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).
doi: 10.4236/ad.2018.61001
Ardren, T. Empowered children in Classic Maya sacrificial rites. Child. Past 4, 133–145 (2011).
doi: 10.1179/cip.2011.4.1.133
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).
pubmed: 29335577
doi: 10.1038/s41559-017-0446-6
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).
Fellows Yates, J. A. et al. Reproducible, portable and efficient ancient genome reconstruction with nf-core/eager. PeerJ 9, e10947 (2021).
pubmed: 33777521
pmcid: 7977378
doi: 10.7717/peerj.10947
Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015).
pubmed: 26595274
pmcid: 4918750
doi: 10.1038/nature16152
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).
pubmed: 34002224
pmcid: 8476174
doi: 10.1093/molbev/msab147
Fu, Q. et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553–559 (2013).
pubmed: 23523248
pmcid: 5036973
doi: 10.1016/j.cub.2013.02.044
Lamnidis, T. C. et al. Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe. Nat. Commun. 9, 5018 (2018).
pubmed: 30479341
pmcid: 6258758
doi: 10.1038/s41467-018-07483-5
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).
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).
doi: 10.1016/S0185-2574(14)70325-9
Kennett, D. J. et al. Early isotopic evidence for maize as a staple grain in the Americas. Sci. Adv. 6, eaba3245 (2020).
pubmed: 32537504
pmcid: 7269666
doi: 10.1126/sciadv.aba3245
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).
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).
doi: 10.1016/j.jas.2012.10.029
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).
doi: 10.1016/0305-4403(89)90068-X
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).
doi: 10.1007/BF02221075
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).
doi: 10.1007/s10814-016-9098-3
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).
pubmed: 30415837
pmcid: 6327247
doi: 10.1016/j.cell.2018.10.027
Reich, D. et al. Reconstructing Native American population history. Nature 488, 370–374 (2012).
pubmed: 22801491
pmcid: 3615710
doi: 10.1038/nature11258
Kennett, D. J. et al. South-to-north migration preceded the advent of intensive farming in the Maya region. Nat. Commun. 13, 1530 (2022).
pubmed: 35318319
pmcid: 8940966
doi: 10.1038/s41467-022-29158-y
Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).
pubmed: 22960212
pmcid: 3522152
doi: 10.1534/genetics.112.145037
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).
pubmed: 27654912
pmcid: 5161557
doi: 10.1038/nature18964
Schraiber, J. G. Assessing the relationship of ancient and modern populations. Genetics 208, 383–398 (2018).
pubmed: 29167200
doi: 10.1534/genetics.117.300448
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).
pubmed: 11596002
doi: 10.1002/ajpa.1118
Ochoa-Lugo, M. I. et al. Genetic affiliation of pre-Hispanic and contemporary Mayas through maternal lineage. Hum. Biol. 88, 136–167 (2016).
pubmed: 28162001
doi: 10.13110/humanbiology.88.2.0136
Mizuno, F. et al. Characterization of complete mitochondrial genomes of indigenous Mayans in Mexico. Ann. Hum. Biol. 44, 652–658 (2017).
pubmed: 28724311
doi: 10.1080/03014460.2017.1358393
Bodner, M. et al. The mitochondrial DNA landscape of modern Mexico. Genes 12, 1453 (2021).
pubmed: 34573435
pmcid: 8467843
doi: 10.3390/genes12091453
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).
pubmed: 25254375
pmcid: 4177621
doi: 10.1371/journal.pgen.1004572
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).
pubmed: 30568240
pmcid: 6300600
doi: 10.1038/s41467-018-07748-z
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).
pubmed: 31735679
doi: 10.1016/j.cub.2019.09.076
Shriver, M. D. et al. The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. Hum. Genom. 1, 274 (2004).
doi: 10.1186/1479-7364-1-4-274
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).
pubmed: 26715629
doi: 10.1093/molbev/msv334
Auton, A. et al. A global reference for human genetic variation. Nature 526, 68–74 (2015).
pubmed: 26432245
doi: 10.1038/nature15393
Amorim, E. et al. Genetic signature of natural selection in first Americans. Proc. Natl Acad. Sci. USA 114, 2195–2199 (2017).
pubmed: 28193867
doi: 10.1073/pnas.1620541114
Villalobos-Comparán, M. et al. The FTO gene is associated with adulthood obesity in the Mexican population. Obesity 16, 2296–2301 (2008).
pubmed: 18719664
doi: 10.1038/oby.2008.367
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).
pubmed: 34454619
pmcid: 8403373
doi: 10.1186/s40101-021-00259-9
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).
pubmed: 25839936
doi: 10.1016/j.gene.2015.03.065
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).
pubmed: 34597392
doi: 10.1093/molbev/msab290
Kofler, R. & Schlötterer, C. Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies. Bioinformatics 28, 2084–2085 (2012).
pubmed: 22635606
pmcid: 3400962
doi: 10.1093/bioinformatics/bts315
Lindo, J. et al. A time transect of exomes from a Native American population before and after European contact. Nat. Commun. 7, 13175 (2016).
pubmed: 27845766
pmcid: 5116069
doi: 10.1038/ncomms13175
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).
pubmed: 24225852
pmcid: 3845180
doi: 10.1073/pnas.1304218110
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).
pubmed: 20129981
pmcid: 2871849
doi: 10.1098/rspb.2009.2033
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).
pubmed: 32094421
pmcid: 7039995
doi: 10.1038/s41598-020-58897-5
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).
pubmed: 31722398
Gómez-Casado, E. et al. Origin of Mayans according to HLA genes and the uniqueness of Amerindians. Tissue Antigens 61, 425–436 (2003).
pubmed: 12823766
doi: 10.1034/j.1399-0039.2003.00040.x
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).
pubmed: 11120931
doi: 10.1086/317940
Dunstan, S. J. et al. Variation at HLA-DRB1 is associated with resistance to enteric fever. Nat. Genet. 46, 1333–1336 (2014).
pubmed: 25383971
pmcid: 5099079
doi: 10.1038/ng.3143
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).
pubmed: 521665
doi: 10.1111/j.1744-313X.1979.tb00684.x
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).
pubmed: 32406916
pmcid: 7319546
doi: 10.1093/nar/gkaa379
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).
pubmed: 20418488
pmcid: 2893805
doi: 10.1093/hmg/ddq173
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).
pubmed: 34233476
pmcid: 8664085
doi: 10.1161/ATVBAHA.120.315391
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).
pubmed: 32329554
doi: 10.1002/ajhb.23426
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).
doi: 10.2307/25063087
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).
pubmed: 9590521
doi: 10.1002/(SICI)1096-8644(199805)106:1<1::AID-AJPA1>3.0.CO;2-W
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).
pubmed: 15500972
doi: 10.1016/j.femsle.2004.09.011
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).
pubmed: 10954969
pmcid: 1044288
doi: 10.1017/S0025727300066746
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).
doi: 10.2307/202984
Crosby, A. W. Virgin soil epidemics as a factor in the aboriginal depopulation in America. William Mary Q. 33, 289–299 (1976).
pubmed: 11633588
doi: 10.2307/1922166
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).
pubmed: 32094538
pmcid: 7186082
doi: 10.1038/s41559-020-1106-9
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).
pubmed: 32651014
doi: 10.1016/j.humimm.2020.06.008
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).
doi: 10.32776/revbiomed.v11i4.248
Patch, R. W. Sacraments and disease in Mérida, Yucatán, Mexico, 1648–1727. Historian 58, 731–743 (1996).
doi: 10.1111/j.1540-6563.1996.tb00971.x
Potter, D. F. Prehispanic architecture and sculpture in Central Yucatan. Am. Antiq. 41, 430–448 (1976).
doi: 10.2307/279010
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).
doi: 10.1017/S095653610314103X
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).
doi: 10.1002/oa.2874
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).
pubmed: 24364037
pmcid: 3858009
doi: 10.1155/2013/705862
Brown, T. A., Nelson, D. E., Vogel, J. S. & Southon, J. R. Improved collagen extraction by modified Longin method. Radiocarbon 30, 171–177 (1988).
doi: 10.1017/S0033822200044118
Stuiver, M. & Polach, H. A. Discussion reporting of
doi: 10.1017/S0033822200003672
Reimer, P. J. et al. The IntCal20 Northern Hemisphere radiocarbon age calibration curve (0–55 cal kBP). Radiocarbon 62, 725–757 (2020).
doi: 10.1017/RDC.2020.41
Ramsey, C. B. & Lee, S. Recent and planned developments of the program OxCal. Radiocarbon 55, 720–730 (2013).
doi: 10.1017/S0033822200057878
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).
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).
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).
doi: 10.1006/jasc.1998.0387
van Klinken, G. J. Bone collagen quality indicators for palaeodietary and radiocarbon measurements. J. Archaeol. Sci. 26, 687–695 (1999).
doi: 10.1006/jasc.1998.0385
DeNiro, M. J. Postmortem preservation and alteration of in vivo bone collagen isotope ratios in relation to palaeodietary reconstruction. Nature 317, 806–809 (1985).
doi: 10.1038/317806a0
Rohland, N. & Hofreiter, M. Comparison and optimization of ancient DNA extraction. Biotechniques 42, 343–352 (2007).
pubmed: 17390541
doi: 10.2144/000112383
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).
pubmed: 24019490
pmcid: 3785785
doi: 10.1073/pnas.1314445110
Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007).
pubmed: 17715061
pmcid: 1976210
doi: 10.1073/pnas.0704665104
Gansauge, M.-T. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8, 737 (2013).
pubmed: 23493070
doi: 10.1038/nprot.2013.038
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).
pubmed: 32612278
doi: 10.1038/s41596-020-0338-0
Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 5, pdb.prot5448 (2010).
doi: 10.1101/pdb.prot5448
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).
doi: 10.1098/rstb.2013.0624
Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182–189 (2009).
pubmed: 19182786
pmcid: 2663421
doi: 10.1038/nbt.1523
Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad Sci USA 110, 2223–2227 (2013).
pubmed: 23341637
pmcid: 3568306
doi: 10.1073/pnas.1221359110
Fu, Q. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015).
pubmed: 26098372
pmcid: 4537386
doi: 10.1038/nature14558
Barquera, R. et al. Origin and health status of first-generation Africans from early Colonial Mexico. Curr. Biol. 30, 2078–2091 (2020).
pubmed: 32359431
doi: 10.1016/j.cub.2020.04.002
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).
pubmed: 34294811
pmcid: 8298398
doi: 10.1038/s41598-021-94491-z
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).
pubmed: 11237011
doi: 10.1038/35057062
Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2009).
doi: 10.1093/bioinformatics/btp698
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).
pubmed: 23613487
pmcid: 3694634
doi: 10.1093/bioinformatics/btt193
Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinf. 15, 356 (2014).
doi: 10.1186/s12859-014-0356-4
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).
pubmed: 10508508
doi: 10.1038/13779
Weissensteiner, H. et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58–W63 (2016).
pubmed: 27084951
pmcid: 4987869
doi: 10.1093/nar/gkw233
Vianello, D. et al. HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment. Hum. Mutat. 34, 1189–1194 (2013).
pubmed: 23696374
doi: 10.1002/humu.22356
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).
pubmed: 19617889
pmcid: 3159387
doi: 10.1038/nprot.2009.97
Szolek, A. et al. OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics 30, 3310–3316 (2014).
pubmed: 25143287
pmcid: 4441069
doi: 10.1093/bioinformatics/btu548
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).
pubmed: 11543903
doi: 10.1016/S0198-8859(01)00298-1
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).
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).
pubmed: 28809135
doi: 10.1017/S0031182017001159
Wang, P. et al. Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinf. 11, 568 (2010).
doi: 10.1186/1471-2105-11-568
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).
pubmed: 16767078
doi: 10.1038/nbt1215
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).
pubmed: 35383854
pmcid: 9021733
doi: 10.1093/molbev/msac073
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).
pubmed: 20445096
pmcid: 3024022
doi: 10.1073/pnas.0914618107
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
pubmed: 19648217
pmcid: 2752134
doi: 10.1101/gr.094052.109
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).
pubmed: 32499399
doi: 10.1126/science.aba8697
Nakatsuka, N. et al. A paleogenomic reconstruction of the deep population history of the Andes. Cell 181, 1131–1145 (2020).
pubmed: 32386546
pmcid: 7304944
doi: 10.1016/j.cell.2020.04.015
Scheib, C. L. et al. Ancient human parallel lineages within North America contributed to a coastal expansion. Science 360, 1024–1027 (2018).
pubmed: 29853687
doi: 10.1126/science.aar6851
Fernandes, D. M. et al. A genetic history of the pre-contact Caribbean. Nature 590, 103–110 (2021).
pubmed: 33361817
doi: 10.1038/s41586-020-03053-2
John, L. et al. The genetic prehistory of the Andean highlands 7000 years BP though European contact. Sci. Adv. 4, eaau4921 (2018).
doi: 10.1126/sciadv.aau4921
Capodiferro, M. R. et al. Archaeogenomic distinctiveness of the Isthmo-Colombian area. Cell 184, 1706–1723 (2021).
pubmed: 33761327
pmcid: 8024902
doi: 10.1016/j.cell.2021.02.040
Moreno-Mayar, J. V. et al. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature 553, 203–207 (2018).
pubmed: 29323294
doi: 10.1038/nature25173
Moreno-Mayar, J. V. et al. Early human dispersals within the Americas. Science 362, eaav2621 (2018).
pubmed: 30409807
doi: 10.1126/science.aav2621
Rasmussen, M. et al. The ancestry and affiliations of Kennewick Man. Nature 523, 455–458 (2015).
pubmed: 26087396
pmcid: 4878456
doi: 10.1038/nature14625
Schroeder, H. et al. Origins and genetic legacies of the Caribbean Taino. Proc. Natl Acad. Sci. USA 115, 201716839 (2018).
doi: 10.1073/pnas.1716839115