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Beneath the surface of present-day western Honduras lie the ruins of Copán—an archaeological site that once stood as a vital city in the classic Maya world, situated at the crossroads between Central and South America.

of seven individuals from the area, including a potential royal and a sacrificial burial, revealed that the people of classic Copán had genetic similarities with late archaic (5,600–3,700 years ago) populations, later Maya groups, and modern Maya communities in Mexico. This study published in Current Biology found signs of a dramatic decline—but not complete disappearance—of the Maya population around 1200 years ago.

Copán became home to humans as early as the Early Preclassic period (before ~1000 BCE) with the migration of small farming communities to the region. Over the next few centuries, it witnessed the rise of monumental architecture and Maya-style inscriptions by the early classic period (circa 300–400 CE).

Then came the dawn of a new political era with the establishment of a royal dynasty by the first king, K'inich Yax K'uk' Mo', an outsider who assumed power in 426/427 CE and relocated to Copán. Throughout the dynasty's 400-year reign, the city remained a hub of political, economic, and ceremonial activity, housing both elite and commoner residential areas.

A popular theory suggests that the Copán kingdom was formed when Maya elites migrated into the region and integrated with the non-Maya populations that originally inhabited the city. The rich archaeological and historical records from the area tell a similar tale. However, scientists believe that having direct genetic data from Copán could help sharpen this picture by allowing more precise tracing of genetic ancestry, migration patterns, and demographic changes.

For this study, the researchers collected petrous bones (a part of the skull) from 16 individuals from two archaeological projects: Programa Integral de Conservación del Parque Arqueológico Copán (PICPAC) and Proyecto Arqueológico Copán (PROARCO).

DNA was successfully extracted from the samples, but only seven of them yielded sufficient material for further analysis. Among them, five individuals were recovered from separate architectural structures, most of which lacked notable wealth indicators. One, however, received the highest wealth designation and was buried in a royal-style tomb—likely a member of the ruling dynasty. Nearby, another individual with no wealth indicators and a score of "0" was interpreted as a sacrificial offering.

The newly sequenced genomes were then compared with ancient and modern American genomes, revealing a strong genetic continuity in the Maya region from the late archaic period to the present day. The data indicated the presence of a local population since the late archaic and a gene flow (6.1% ± 2.6%) from highland Mexican populations during the early-to-middle classic period, supporting the idea of population movement and cultural integration during the time frame.

The DNA evidence also pointed to a sharp population decline approximately 1,200 years ago due to major droughts and social instability during the 9th to 11th centuries. This timeline perfectly coincided with the beginning of the collapse of the classic Maya civilization.

The researchers note that this study offers a new perspective, suggesting the enduring persistence of local ancestry in the Maya region while also highlighting the broader mobility beyond the conventional boundaries of the Maya territory.

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