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Ancient genomes reveal demographic trajectories during the Classic Maya period

PRJEB88222 Original Paper / DOI2025-05-287 samples (study)

AI interpretationAI-generated

Seven ancient genomes from Copán reveal Classic Maya ancestry and a population decline.

Researchers sequenced seven genomes from Copán, a key Classic Maya city. The individuals genetically cluster with ancient and modern Maya groups. Starting in the Early-to-Middle Classic period, they received ancestry from highland Mexican populations, showing gene flow during state formation. By the end of the Classic period, effective population size dropped, matching the Maya collapse.

Sample interpretation

The study analyzed seven individuals from Copán, including a possible royal dynasty member and a sacrificial burial. Six are culturally Maya. Y-chromosome DNA was resolved for three males: two carry Q-M848 and one Q-MPB016. Mitochondrial DNA shows six distinct lineages: A2, A2-x, A2-x-G16129A!, A2ad, C1c, and C1c4. These markers are typical of Indigenous American populations.

For genealogy enthusiasts

For ancestry enthusiasts, this study shows that Classic Maya populations were not isolated; they mixed with highland Mexican groups. It also links genetic decline to the Maya collapse, offering a deeper context for interpreting Maya-related DNA results.

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.

Samples & Data on TheYtree

7samples on site
3Y haplogroup resolved

Paternal (Y-DNA) Haplogroups

HaplogroupSamples
Q-M848 2
Q-MPB016 1

Maternal (mtDNA) Haplogroups

Sample Highlights More samples →

SampleY-DNAmtDNACulture / Period
CpM13 Q-M848 A2-x Maya· 425–542 CE
CpM12 Q-MPB016 C1c4
CpM11 Q-M848 — Maya· 667–774 CE