Ancient genomes reveal insights into ritual life at Chichén Itzá

Abstract

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^1-4. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population's genetic ties to other Mesoamerican groups, remain unanswered². Here we present genome-wide data obtained from 64 subadult individuals dating to around AD 500-900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes⁵, but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.

Fig. 1. Geographical context for the groups analysed and biological relatedness in the chultún.

a, Location of the Maya region in the Americas. b, Geographical locations of Chichén Itzá and Tixcacaltuyub in the Yucatan Peninsula. c, Stratigraphy for the chultún and the adjacent cave in which the burial was found (adapted from ref. ). d, Location of the chultún within the archaeological site of Chichén Itzá and its relation to El Castillo (adapted from ref. ). Modern roads are marked in light grey; the chultún abuts an airport runway. e, Genetic pairwise mismatch rate (PMR) for child pairs in the chultún identifies 11 close relative pairs (hollow diamonds), including two pairs of monozygotic twins (highlighted in grey). A low overall PMR for unrelated individuals (black triangles) confirms low genetic diversity in the population; only pairs with PMR < 0.20 are visualized in the plot. See Supplementary Fig. 2 for individual annotations.

Fig. 2. Genetic similarities between Chichén Itzá, Tixcacaltuyub and present-day and ancient American Indigenous groups.

a, PCA showing ancient Chichén Itzá (YCH) individuals and present-day Tixcacaltuyub (TIX) in a worldwide PCA plot. b,c, Admixture analyses showing the clustering from k = 4 for YCH, TIX and different continental genetic sources (b) and the clustering for the newly produced samples at k = 8 (lowest cross-validation errors), with a more comprehensive list of Indigenous American populations (c). d,e, Outgroup F₃ statistics in the form f₃(Mbuti; YCH, X) where X are present-day groups from the Americas (d) and published ancient groups and individuals (e). High similarities are indicated by warmer colours; low similarities by darker colours. f,g, Outgroup F₃ statistics in the form f₃(Mbuti; TIX, X) where X are present-day groups from the Americas (f) and published ancient groups and individuals (g). High similarities are indicated by warmer colours, low similarities by darker colours. A list for the populations/individuals used in these analyses can be found in the Supplementary Information: source populations for the population genetics analyses.

Fig. 3. Evidence for selection in the HLA region.

a–c, Pattern of non-overlap associations for the genes in the HLA region as measured by F*_adj (heatmaps on the left) and the difference between those observed amounts of non-overlap and randomized allelic associations, in units of standard deviation (heatmaps on the right), for ancient Mayans from Chichén Itzá (YCH) (a), present-day Mayans from Tixcacaltuyub (TIX) (b) and present-day Lacandon Mayans from Chiapas (southeast Mexico) (c). d, Manhattan plots of genome-wide LSBL values for YCH (top) and TIX (bottom). HLA loci are shown in red. Top 0.1% (red line) and 0.5% (blue line) of all statistics are indicated.

Extended Data Fig. 1. F4 test of the form f₄(Mbuti, YCH; test, TIX).

Values are plotted (circle) with their corresponding error bars (in purple). For all tested populations, the value of the test is positive, indicating that YCH And TIX shared more alleles between them than to any of the Native American populations tested.

Extended Data Fig. 2. A graphical representation for the locus-specific branch lengths comparisons.

The variables x, y and z, (representing either YCH vs. Iberians from Spain and Han from China, or TIX vs. Iberians and YCH, to independently test for selection) are calculated using pairwise F_ST distances, d_AB, d_BC and d_AC, where x = (d_AB + d_AC – d_BC)/2, y = (d_AB +d_BC – d_AC)/2, z = (d_AC + d_BC – d_AB)/2 and A, B and C are the three populations under consideration.