Ancient pre-Hispanic genome sequencing reveals a ‘ghost’ ancestry

Genome biologists achieved a major feat by isolating ancient DNA from excavated pre-Hispanic individuals in modern-day Mexico. Genome sequencing of this pre-Hispanic ancient DNA revealed a ‘ghost’ ancestry, meaning ancestry not found in present-day Mexican populations.
Sculpture of a Mexican pre-Hispanic man.
A sculpture of a Mexican pre-Hispanic man.

In ancient Mexico, about 10 centuries ago (between 2500 BCE and 1521 CE), pre-Hispanic civilizations were spread across two main cultural areas:

  1. Aridoamerica in the north, inhabited mainly by hunter-gatherers
  2. Mesoamerica in the central and southern regions, inhabited by agriculturists

During this period, global warming is suggested to have brought long and intense droughts that changed the way these civilisations lived.

A map of present-day Mexico showing pre-Hispanic cultural areas.
Pre-Hispanic Mexico was spread across two main cultural regions - Aridoamerica in the north and Mesoamerica in the central and south.

Did the Aridoamericans invade Mesoamerica?

Archaeological evidence suggested that due to these periods of intense drought, the border between these two cultures moved southwards. This means that at least some Mesoamerican population was replaced by the Aridoamericans. However, these hypotheses are only based on archaeological evidence. No genetic evidence of these ancient population changes was available.

To validate the archaeological evidence, scientists recently embarked upon a project to sequence ancient DNA from the pre-Hispanic period in Mexico 1.

Studying the genetic diversity of the Mesoamerican population across this period would inform scientists of any population changes. So, they first collected archaeological samples from 37 pre-Hispanic individuals excavated from Mesoamerican regions in central Mexico.

Sequencing of DNA from these ancient individuals was difficult. This is because DNA is sensitive to degradation, particularly in hot climates such as that in central Mexico. However, the researchers were able to use 12 of the 37 genomes as they had a good amount of sequencing data. These 12 people lived before and after the global warming period.

Results from the ancient genomes were contrary to what archaeological evidence suggested.

Aridoamericans stayed put

The Mesoamerican genetic makeup stayed consistent before and after the period of climate change. This goes against the idea that Aridoamerican groups replaced the local population in this region.

It suggests that despite long-lasting droughts, Aridoamerican people stayed in their homeland. The researchers think that two reasons might have contributed to this population continuity:

  1. The Aridoamericans preferred the high and humid Sierra Gorda mountain range.
  2. Their main economic activity was cinnabar mining and not agriculture.

A “ghost” ancestry unveiled

The researchers also discovered two distinct genetic ancestries that are not found in present-day Mexican populations.

These two “ghost” genetic ancestries contributed to the pre-Hispanic populations in both Aridoamerican (north) and Mesoamerican (central) populations.

One of these ancestries was previously identified in a present-day population from southern Mexico 2. However, the other one was unknown before this discovery.

The authors acknowledge this confusion. In their paper, they write,

This observation reveals a complex population history in the Americas during the late Pleistoscene that needs to be further characterized. Additional ancestral DNA studies from the Americas could help identify the source of both ghost ancestries, which seemingly contribute to many present-day Indigenous populations from Mexico.


  1. Viridiana Villa-Islas et al., Demographic history and genetic structure in pre-Hispanic Central Mexico. Science. 380, (2023).
  2. J. Víctor Moreno-Mayar et al., Early human dispersals within the Americas. Science. 362, (2018).
Photo of Sampath Amitash Gadi, author at
Sampath AmitashGadi, Ph.D.
Editor at

Sampath works as a DNA researcher at the University of Copenhagen. Right now, he is studying how proteins and protein signaling help with DNA Damage in cells.

twitter iconlinkedin icon