Ancient genomes reveal demographic trajectories during the Classic Maya period

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Abstract: Copán was a major capital at the southeasternmost extreme of the Classic Maya civilization, serving as a crossroads connecting Central and South America. In 426/427 CE, the city witnessed the establishment of a royal dynasty, which endured for approximately 400 years. Despite extensive historical and archaeological records, there remains limited information regarding the genetic profile of people who resided in Copán. Here, we present genomes from seven Classic Copán individuals, including a potential member of the ruling dynasty and an accompanying sacrificial burial. Our analysis shows that the population associated with the Classic Copán culture forms a genetic cluster with the Late Archaic population from Belize, as well as with the Terminal Classic Maya from Chichén Itzá, the Colonial Maya from Campeche, and present-day Maya, all from Mexico. Using Late Archaic Belize as a source of local ancestry, we identify an influx of ancestry associated with highland Mexican populations from the Early-to-Middle Classic period onward, underscoring the role of gene flow in the formation of the Classic Maya state. Estimates of effective population size suggest a decline at the end of the Classic period, when Classic Maya civilization experienced widespread destabilization and collapse.