Archaeologists Analyze How Diseases Impacted Indigenous Populations in the Americas During Colonial Times

A new study examines the history of smallpox epidemics brought to America by European colonists, the absence of archaeological evidence associated with those epidemics, and whether ancient DNA might offer new insights

When Europeans first arrived in the Americas, they brought many infectious diseases with them that did not exist in the continent before.

One of them was smallpox, a highly contagious and deadly viral disease that spread quickly through Indigenous populations that hadn’t yet developed defenses against it. It is considered one of the most devastating of all the introduced diseases to the Americas, killing an estimated 3 to 4 million people.

A recent paper, published in the Journal of Anthropological Archaeology, and co-authored by anthropologists and archaeologists, including from the Smithsonian Tropical Research Institute (STRI), examines ethnohistoric and archaeological records from across the Americas to understand the nature and magnitude of epidemics caused by these diseases, as well as impacts, both biological and cultural, on Indigenous populations.

It also highlights something puzzling: despite multiple accounts of mass death and depopulation, there are no documented mass or altered burials identified as resulting from smallpox during the colonial period, and no substantial collections of bones, teeth, or skeletal fragments recovered from one place, that could provide more archaeological evidence.

“Disease is a global phenomenon, but evidence for severe epidemic disease in the Americas prior to European arrival is scarce,” says the main author, historical bioarcheologist Alex Garcia-Putnam, who is an assistant professor in the Anthropology Department and the Assistant Director of the Forensic Anthropology Identification and Recovery (F.A.I.R.) Lab at the University of New Hampshire.

Garcia-Putnam’s research first focused on the impacts of disease spread by Spanish colonists on Indigenous populations in Peru. Soon it expanded to other Native populations during the colonial period: the central Great Plains of North America, the Pacific Northwest, and central and South America, including Mexico, the Isthmus of Panama, and Peru. He invited STRI staff scientist Nicole Smith-Guzman, New York University bioarcheologist Thomas Snyder, the State of Washington’s State Physical Anthropologist Guy Tasa, and University of Kansas archaeologist and Pawnee Nation citizen Carlton Shield Chief Gover, to be co-authors, for their ample knowledge of the archaeological and ethnohistoric context covering a broad geography, to better understand the impact on different populations.

“It wasn’t just diseases as biological agents that were affecting people's health. It was also things that were going on socially around them that could make them more vulnerable to disease,” says Smith-Guzman. “This research would help to better understand the complexities and the impact of colonialism on the populations all across the continent.”

For instance, the impact of Spanish colonialism in Panama, a high-traffic area, and its surrounding regions is well-documented. Accounts from Spanish colonists such as Pedrarias Dávila note that smallpox decimated most of the Native populations; and in the oral histories of the Indigenous Guna people of Panama, the ongoing epidemics are mentioned as having played a role in their decision to migrate from the mainland in the Darien province to the islands of the San Blas Archipelago, in the Caribbean coasts of Panama.

“Though they had more than one place of residence to make the most of the land resources when fishing or hunting, and they changed the location of their settlements approximately once a decade, the Guna oral histories do refer to the arrival of the epidemics as a factor for moving,” explains social anthropologist Monica Martinez Mauri of the University of Barcelona, who was not involved in this study.

Yet there is very little evidence of mass or altered burials related to the smallpox epidemic found in any of these regions.

“Mass burial was not an unknown phenomenon to Indigenous societies prior to European arrival, due to warfare or other scenarios, but the Euro-Christian practices that were forced upon Indigenous populations could have impacted how they buried their dead, diseased or otherwise,” the authors say.

One explanation might be that mass burials simply have not been discovered yet by archaeologists. It’s also possible that since so many people were dying at the same time, there was no one left to bury the dead.

“Burial traditions vary for different cultures. It was important to include specialists from across these different areas to know what's a normal burial and what's an altered burial in these places,” points out Smith-Guzman.

Is it possible to tell if someone died of smallpox, especially if it happened a long time ago?

The answer might be in ancient DNA (aDNA): since smallpox is a DNA-based virus, genetic evidence of the pathogen’s presence in human tissue can be found in preserved human teeth, bones, preserved skin and coprolites (preserved fecal matter). The researchers consider one possible future avenue of paleopathological analyses using aDNA to detect viral aDNA and identify people who died of smallpox, which might help identify mass graves dedicated to smallpox victims.

However, since the samples need to be destroyed for aDNA analysis, it presents an ethical issue and requires permission and support from the descendant communities. “Limiting the destruction of human remains is paramount,” Garcia-Putnam adds.

Another challenge of aDNA is obtaining sufficient samples of human tissue for analysis. In Panama and other tropical areas, for example, the soils are often too acidic for preserving pathogen DNA within ancient bone tissues. But areas like Peru and the Pacific Northwest of the U.S. might offer better DNA preservation, if mass burials can be found.

The article ultimately proposes a multidisciplinary approach and criteria to guide future research, including evaluating burials and skeleton assemblages to determine if they were a result of the smallpox epidemics, expanding the research to other impactful diseases—measles, plague, influenza, etc.—and using computer-based modeling to simulate how smallpox spread from community to community.

The authors hope to understand the complexity of health impacts on Indigenous communities during colonial times, including how populations dealt with multiple overlapping epidemic diseases as well as violence, and political, religious and environmental upheavals happening simultaneously.

“It's important to acknowledge that these epidemics have been happening for a long time in our human history, and that they impact more than just human health,” states Smith-Guzman. “Knowing that diseases took a toll on certain communities at specific points in time helps us understand decisions that were made in that culture.”

“Infectious diseases are on the front of everyone’s mind: COVID, Mpox, Ebola, Hantavirus,” Garcia-Putnam states. “And we can and should learn from our global history co-evolving with these pathogens and use those lessons to better guide our present and future.”

About the Smithsonian Tropical Research Institute
Headquartered in Panama City, Panama, STRI is a unit of the Smithsonian Institution. Our mission is to understand tropical biodiversity and its importance to human welfare, to train students to conduct research in the tropics and to promote conservation by increasing public awareness of the beauty and importance of tropical ecosystems. Watch our video, and visit our website, Facebook, X and Instagram for updates.

Garcia-Putnam, Alex, Snyder, Thomas J., Tasa, Guy L., Smith-Guzmán, Nicole E., Chief Gover, Carlton Shield. 2026. Exploring archaeological evidence for historic smallpox epidemics in the Americas, Journal of Anthropological Archaeology, Volume 83, 101778, ISSN 0278-4165, DOI: 10.1016/j.jaa.2026.101778

Vanessa Crooks | Read More

Vanessa Crooks is a bilingual journalist and writer located in Panama City, Panama, working to bring science to all audiences. She is also an illustrator, graphic designer and animator.