Paleogenomic Insights into the Mitogenomic Composition of an Ancient Urban Neighborhood Near the Puchituk Terminus, Caracol

Mesoamerican archaeology has been instrumental in understanding early urbanism on global and diachronic scales. One of the most important cities shaping our knowledge of Mesoamerican urbanism is the large Maya metropolis of Caracol. Caracol was one of the largest cities of the Classic Maya Period (250-900 CE) and, at its peak, was home to more than 100,000 people. Previous archaeological analyses have demonstrated that residential groups at Caracol shared city-wide commonalities in material culture and mortuary practices. Compared to the city of Teotihuacan in the Basin of Mexico, where dense urban neighborhoods were divided by distinctions in material culture and mortuary treatments, the demographic composition of Caracol at the neighborhood level is less apparent from mortuary analyses alone. In this project, we reconstruct ancient mitogenomes and estimate chromosomal sex to characterize matrilineal relationships among residents of two residential groups near the Puchituk Terminus, located 3 km northeast of the epicenter of Caracol. We extracted ancient DNA from 51 bones of Ancestors who were excavated from the Puchituk area and screened them for the preservation of endogenous ancient DNA (aDNA). For 25 of these extracts, we constructed double-stranded, partial UDG-treated, dual-barcoded, and dual-indexed Illumina genome libraries and enriched them using the myBaits Expert Complete Human Affinities probes targeting more than 2 million nuclear SNPs and the complete mitogenome. Resulting sequence data (N=7) were used to assess matrilineal relationships and estimate the chromosomal sex of individuals interred near Puchituk, providing the first insights into the genomic composition and biological kinship relationships of a neighborhood at Caracol.