A photo of a skeleton on a black background
A photo of a skeleton on a black background

Ancient DNA Boom Underlines a Need for Ethical Frameworks

The field of ancient DNA, which combines archaeology and anthropology with cutting-edge genetics, is requiring scientists to have frank conversations about when research is justified and who it benefits.

amanda heidt
Amanda Heidt

Amanda is an assistant editor at The Scientist, where she oversees the Scientist to Watch, Foundations, and Short Lit columns. When not editing, she produces original reporting for the magazine and website. Amanda has a master's in marine science from Moss Landing Marine Laboratories and a master's in science communication from UC Santa Cruz.

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Jan 27, 2022

ABOVE: The remains of Kennewick Man Chip Clark, Smithsonian Institution

In 1996, two college students waded into Washington State’s Columbia River, keen to watch the day’s hydroplane races. Roughly 10 feet from shore, however, one of the students stumbled upon something even more attention-grabbing: a human skull, which radiocarbon dating would soon reveal was roughly 8,500 years old, one of the oldest ever found in the Americas. Over several trips, archaeologists pieced together a nearly complete skeleton consisting of more than 300 bones, referred to thereafter as the Ancient One or Kennewick Man.

The discovery of Kennewick Man was a boon for scientists interested in the peopling of the Americas, but it also kicked off a decades-long saga pitting a group of eight researchers against the US Army Corp of Engineers—who oversaw the land where the skeleton had been found and alerted nearby tribes—and at least four local Indigenous groups. At stake was the final judgement over who could claim ownership of the remains and, by extension, the information contained within. 

All of that hinged on the narrative surrounding how the skeleton came to lie along the riverbank in the first place. Early on, the archeologist who recovered the remains, James C. Chatters, interpreted the skull’s morphology and the presence of nearby 19th century tools as evidence that he might be looking at an early European settler. This idea was supported by certain “Caucasoid” features, including the shape of the skull, he tells The Scientist, but notes that it “was not immediately clear when he came from” and that the term was meant only as a descriptor, and not as an identification. When radiocarbon dating showed the man to be much older, Chatters was legitimately stumped. “All my life, I’ve been looking for this person,” he says, in reference to his career studying early North American history. “I finally caught up with him, and he turned around and was not who I expected him to be. And so the question is why?”

But by suggesting that Kennewick Man may have been European (later assessments also likened him to ancient Polynesians or the Ainu people of Japan), Chatters was undermining the claim of Indigenous groups that the remains belonged to them under the Native American Graves Protection and Repatriation Act (NAGPRA), which stipulates that remains must be given to a tribe if it can prove the individual was culturally related. An interim court ruling in 2004 denied repatriation under NAGPRA, and in a contentious move, scientists were given access to the bones, resulting in numerous papers and a 2014 book. (Chatters was not part of the lawsuit, but did ultimately study the remains and published his own book in 2002.)

Paulette Steeves, an Indigenous (Cree-Métis) archaeologist at Algoma University in Canada, was a student in the lab of the well-regarded osteologist Jerome Rose at the University of Arkansas when the controversy first began. Rose was one of several experts called on to analyze the remains, and his findings were at odds with those of Chatters and other notable anthropologists. As Steeves explains, Rose thought the remains resembled a Native American from the Great Plains. “Archaeologists are very aware of the power of the past, . . . and they immediately tried to disenfranchise Kennewick Man from the local Indigenous communities,” she says, adding that “I had no doubt because of the time and where it was found that this was an Indigenous person.”

KENNEWICK MEN: The decades-long struggle to trace Kennewick Man’s origins spawned several facial reconstructions imagining what he may have looked like in life. Anthropologist James C. Chatters worked with sculptor Thomas McClelland, a teacher at Chatters’s daughter’s junior college, on the first bust (left) in 1998 using what is known as the Manchester method. To recreate a face from a skull, the pair analyzed muscle attachment points on the remains and coupled them with measurements of tissue thickness in living peoples averaged across several populations. They avoided adding hair, which can introduce cultural bias, Chatters says. Later recreations include a version for a cover of Time Magazine by visual artist Kam Mak in 2006; a bust crafted by a team of artists for the Smithsonian Institute in 2014 (bottom); and two reconstructions commissioned by Indigenous (Cree-Métis) Algoma University archaeologist Paulette Steeves in 2018 (one by forensic artist Marcia K. Moore and another by Steeves’s student, Saskia Van Walsum, both of whom were given minimal identifying information; top left and right respectively), among others.
Left: James C. Chatters; Top Left: Marcia K. Moore; Top Right: Saskia Van Walsum (courtesy of Paulette Steeves); Bottom: Brittney Tatchell, Smithsonian Institution

Ultimately, modern DNA technology resolved the case. In 2015, researchers definitively linked the Kennewick Man to Indigenous tribes based on a complete genome sequenced from a hand bone. The man’s remains were returned to a coalition of Columbia Basin tribes, and his burial at an undisclosed location in February 2017 attracted more than 200 tribal members. The victory was meaningful, Steeves says, but extracted a great price. “Genetics . . . obviously showed later on that this person definitely was linked to those tribal communities and he was buried, but for how many years did [they] suffer? That’s the kind of damage that researchers and archaeologists and geneticists can do.”

Chatters, for his part, mourns what the remains could have taught scientists and descendent communities about their heritage. His professional argument against repatriation, he says, was never about denying local tribes ownership, but instead was borne out of a refusal by others to “let [Kennewick Man] tell his story and tell us who he was.” The burial, while cathartic for many, means that researchers can no longer turn to Kennewick Man to answer important historical questions. “We’re burning the library, and it’s going to be a tremendous loss.”

The story of Kennewick Man was especially well-publicized, but it’s not the only example of ethically fraught work carried out on ancient humans. Indeed, several incidents over the past decade have served as flashpoints between scientists and the living descendants of ancient people. The rapid pace at which ancient DNA (aDNA) research is advancing—referred to by some as a “gold rush” on aDNA—is forcing scientists in the field, from archaeologists to geneticists, to confront the ethical implications of their work. Sampling for aDNA often leads to the irreversible destruction of human remains, for example, and may generate sensitive information about living people. Who decides what research should move forward, and who has ownership over the products of that work? 

“We really should be questioning the underlying ethics, because some research can be extractive and exploitative,” says Keolu Fox, an Indigenous (Native Hawaiian) genomic anthropologist at the University of California, San Diego, adding that this rush to sequence ancient samples has raised the bar of discovery, such that more and more genomes are now required to get published. “We have created an engine that we have to fuel, and people do unethical things when their career and their livelihood is on the line.”

That engine, by many metrics, continues to pick up speed. Prior to 2010, no one had sequenced a complete genome from an ancient human, while today, that tally tops 6,000. A single paper, published in Nature in December 2021, sequenced genomes from 793 individuals, requiring collaborations among hundreds of scientists. 

We have a responsibility as curators, but also as researchers, to do research that is ethically bound and ethically responsible.

—Victoria Gibbon, University of Cape Town

The reason for this scramble is that the genetic information captured in nuclear DNA, unlocked from ancient samples using cutting-edge technology, has the potential to elucidate everything from how many canoes Native Hawaiians may have used to traverse the Pacific to how early humans, Neanderthals, and Denisovans intermixed. “Prior to ancient DNA, we had a number of tools . . . but it’s like a whole new line of evidence just appeared,” says Jakob Sedig, an archaeology postdoc in David Reich’s aDNA laboratory at Harvard University. “It’s the equivalent of a detective working on a crime scene in the 1950s when DNA wasn’t available versus today.”

Setting a standard in the field

With so many people flocking to aDNA-based research, some researchers “felt that the situation was ripe to produce a scenario in which somebody could violate ethical guidance, wittingly or not, because they didn’t exist,” Mary Prendergast, an anthropologist and archaeologist at Rice University, tells The Scientist. The pandemic, she adds, provided a “meaningful pause . . . to reflect on where the field is going in the future.”

At least two sets of ethical recommendations pertaining to aDNA research have been published since COVID-19 first stymied anthropological and archeological field work in 2020, beginning with a piece in the American Journal of Human Genetics (AJHG) in August of that year. Katrina Claw, an Indigenous (Diné/Navajo) genomicist at the University of Colorado’s Anschutz Medical Campus and a coauthor on the paper, says that the field lacked codified principles, even if conversations were happening. “We thought, given the current state of ancient DNA research and the push to sequence samples, that it was very timely.”

The guidelines published by Claw and her colleagues focus on North America, where Indigenous groups continue to suffer the lingering effects of biocolonialism, or the commandeering of biological resources from an Indigenous people without compensation. Many of their recommendations center around building relationships with living descendants to design co-produced research with a clear benefit to the communities providing the samples. In her work studying genes that determine how quickly drugs are metabolized, members of Indigenous tribes dictate the research priorities. “Sometimes this results in a research project that we can do collaboratively,” Claw says. “Other times, it doesn’t result in anything except getting to know people.”

Discussions followed in the paper’s wake, including among members of the Reich lab, one of the most influential in the aDNA space. Sedig, the lab’s ethics and outreach officer, says that shortly after its publication, “we had collaborators and colleagues from other parts of the world reaching out to us and saying that [the AJHG study], while important, . . . just doesn’t work in the country where I work.” In response, the group decided to organize a workshop with more than 60 researchers representing 31 countries “to come together and talk about it,” Sedig says.

Conclusions from the workshop, which was held virtually in November 2020, were published last year in Nature. Many of the issues first highlighted in the AJHG piece were reflected in this global set of recommendations, including the need to minimize the damage to human remains and adhere closely to local regulations.

A Tale of Two Guidelines

When compared side-by-side, the two sets of guidelines—one published in AJHG in 2020 by Penn State anthropologist and law professor Jennifer K. Wagner and colleagues, and another published in Nature in 2021 by Harvard University geneticist Songül Alpaslan-Roodenberg along with more than 60 coauthors—have many similarities. For instance, both note the importance of planning ahead for how data will be managed and of beginning a study with a clearly outlined set of research questions to minimize destructive sampling. The two papers differ in their emphasis on community engagement, however. While the Nature paper does recommend forging relationships with community stakeholders, it acknowledges that this particular issue is one that is not always practical. In some countries, identifying as a minority or Indigenous group can be dangerous for all involved, while in others, Indigeneity may refer more to political or social marginalization than a long-term identity tied to a region. 

AJHG , 2020Nature, 2021
Formally consult with communities.Ensure that all regulations are followed in the places where they work and from which the human remains derived.
Address cultural and ethical considerations.Prepare a detailed plan prior to beginning any study.
Engage the community and support capacity building.Engage with stakeholders from the beginning of a study and ensure respect and sensitivity to other stakeholder perspectives.
Develop plans to manage data and report results.Minimize damage to human remains.
Develop plans for long-term responsibility and stewardship.Ensure that data are made available following publication to allow critical re-examination of scientific findings. 

The Nature paper also discussed access to data derived from aDNA, concluding that open policies are often democratizing and therefore ethical. According to attendees, this point stirred contention during the meeting, as many Indigenous communities prefer to retain ownership of their genetic information to avoid repeating historical misuses by researchers, such as a case in which Arizona State University researchers collected DNA from members of the Havasupai tribe to study diabetes but went on to use the samples in a number of other studies that had not been consented to. As a scientist, Jakob Sedig, an archaeology postdoc in David Reich’s aDNA laboratory at Harvard University, says that he recognizes these concerns but believes that, at a minimum, “data needs to be made available to researchers so that it can be tested for replication.”

But since the publication of both sets of guidelines, arguments have erupted—both in private and in print—about certain aspects of the proposed recommendations.

Several Indigenous researchers who spoke to The Scientist say they were excluded from the workshop that led to the guidelines presented in Nature and accuse the overseeing labs of exacerbating a power imbalance that minimizes minority scientists who have been vocal about these issues for years. “It’s really clear how they cite us, and they talk about our work, but we weren’t included in any of the conversations,” Claw says. Fox echoes that “there’s nothing novel or new in their paper besides the fact that [the workshop organizers are] white.”

Sedig, in response to some of these criticisms, acknowledges that his group was aware of Claw’s paper; it was noted at the workshop as being “important and very relevant for North America.” But in order to find common ground on an international scale, he tells The Scientist, the workshop was structured to include aDNA practitioners conducting their work primarily in other countries who had yet to have their voices heard. “Our goal wasn’t to purposefully exclude [Claw and her North American colleagues], we just really wanted to provide a venue for people that hadn’t had a chance to comment about ethics in the field that are really actively involved with ancient DNA,” he says.

Rice University’s Prendergast, a coauthor on the Nature paper who attended the workshop, says that as a scientist who collaborates with geneticists on aDNA-based research in Africa—a region that has traditionally been exploited with respect to its anthropological resources—she did find the conversations helpful in assessing the global state of knowledge. Africa doesn’t have any aDNA laboratories, meaning that researchers almost always collaborate with colleagues overseas, some of whom might not understand the particular challenges of the work. The meeting provided a forum to highlight those issues, Prendergast says. “Something that is really apparent . . . is that there’s just huge discrepancies between the Global North and South [in terms of] infrastructure, funding support, and training for research.” As a result of colonialism, she adds, remains have also often been taken to other countries. “I think you have to have that colonial legacy always at the forefront of your mind as you’re doing this research.”

Growing pains

Groups led by largely Indigenous scholars, including the National Science Foundation–funded aDNA Ethics and the South Dakota-based Native BioData Consortium (NBDC), voiced their concerns shortly after the Nature paper’s publication. The aDNA Ethics team, of which Claw is a member, published a joint response, and members of NBDC, including cofounder Krystal Tsosie and Fox, who serve on the board, published a correspondence in Nature

Speaking to The Scientist, Tsosie, an Indigenous (Diné/Navajo) geneticist and bioethicist at Vanderbilt University, notes that what she finds particularly egregious is the fact that “ancient DNA researchers are effectively writing their own rules and their own ethical guidelines that protect their right to access the data,” when ownership should ultimately lie with the community stakeholders, including descendants, according to existing data governance principles.

Ancient DNA researchers are effectively writing their own rules and their own ethical guidelines that protect their right to access the data.

—Krystal Tsosie, Vanderbilt University

Debra Harry, an Indigenous (Numu) associate professor of gender, race, and identity at the University of Nevada, Reno, who teaches students about their genetic rights, also takes issue with what she sees as a broader sense of ownership and entitlement over the direction that research involving Indigenous people often takes. While the AJHG paper suggested bringing stakeholders into the research process as equal partners, the Nature paper was less explicit about this point. While it acknowledged that researchers must accept a negative answer if not all groups agree with the research, it subsequently states that “once a consensus to proceed has been reached, professional scientific ethics requires that researchers are able to pursue their work up to the point of publication without requiring further approval.” 

Not allowing Indigenous groups to have an ongoing dialogue around consent and the research process, Harry notes, reignites old traumas. “Ancient DNA is a really sensitive field of study that is nearly impossible to agree with as an Indigenous person,” she says. “At the end of the day, I think . . . the rights of individuals to free and fully informed consent trump the interests of any researcher. It’s a further extension of that colonial process to have researchers believe they have a right to access these ancient remains, to control them, to do study on them.”

See “Steps to End ‘Colonial Science’ Slowly Take Shape

Prendergast says she “respectfully disagree[s]” with the idea that researchers are rubber-stamping their own work. Ethics guidelines in many disciplines, she notes, are established by practitioners in that field, and the fact that they did struggle so much to reach a consensus shows that researchers are mindful of the ethical implications of their work and how they might improve. “This is a starting point for a conversation about what additional work needs to be done depending on where you are in the world.”

A long road ahead

Moving forward, researchers spoke of the need to update NAGPRA, which was first passed in 1990 before the advent of modern sequencing technology. While the law protects cultural and biological remains, it says nothing about what should be done with data, or about human information gleaned from sources such as soil or gut microbes. “I personally would love to see a complete makeover that reflects the potential of many, many, many of these technologies,” Fox says. “We’re not really addressing data as a resource.”

Victoria Gibbon, a biological anthropologist at the University of Cape Town (UCT) in South Africa, has grappled with these hypotheticals since 2016, when she took over as curator of the UCT human skeletal repository, where she oversees research requests to access the repository’s samples. “We have a responsibility as curators, but also as researchers, to do research that is ethically bound and ethically responsible, something that we could stand for if we were questioned,” she says.

In the past five years, she has overhauled how UCT assesses aDNA research proposals—an example, she says, of how she hopes this process might be done at other universities or in countries with less stringent guidelines. To access remains housed in the repository (itself a renaming from the UCT human skeletal collection, which Gibbon felt connoted commoditization and ownership), researchers must complete a series of steps. In addition to securing a permit from the country’s heritage resource agency, a project must also be approved both by a South African human ethics board and by Gibbon’s repository committee, which includes biological anthropologists, human biologists, archaeologists, geneticists, and clinical anatomists. UCT also requires a shipping permit and a material transfers agreement outlining the rules and regulations for the destruction of biological products following the work (to avoid genetic material sitting in freezers overseas for decades, Gibbon says), a clear communication of who stewards the data, whether it will be open access, and whether and when the specimens or the resulting data should return to South Africa.

University of Cape Town (UCT) biological anthropologist Victoria Gibbon in the UCT human skeletal repository. Over the last five years, Gibbon has overhauled the requirements for scientists to access specimens for ancient DNA research.
University of cape town

“It gives you an idea of who is actually doing ethical practice in their labs,” Gibbon says of the protocol, noting that so far, she’s the only researcher who has completed applications (for her projects, she steps aside as curator and lets a colleague oversee her applications). “I had people who applied to work on the repository to do ancient DNA, but . . . when we said they would need to have a materials transfer agreement and informed consent, along with a human ethics review, [they] withdrew their application and never reapplied.”

One certainty is that the next generation of scientists will need better training to bridge the gap between archaeology, anthropology, and genetics. While some researchers argue that the divide between these different camps is sometimes trumped-up for drama, others point to fundamental differences in how young scientists are trained in these specialties. Algoma University’s Steeves wasn’t able to find a single archaeology program in the Americas that required students to take a class on Indigenous history, for example, and Prendergast notes that “many geneticists are not taking courses on archaeological history.”

Instilling a reverence and respect for ancient ancestors in emerging ancient DNA scientists—moving away from the gold rush mentality—will also go a long way towards disincentivizing research that can lead to ethical violations, experts say. “It’s a profound responsibility, and one that scares the shit out of me,” Fox says, but adds that as of late, “there is a change in the tide and an attention to detail around these issues. Frankly, I think that people are going to take this a lot more seriously now, because we’ve had this row. It’s a good thing, ultimately.”

Clarification (February 3): This article has been updated to reflect that Keolu Fox was specifically referring to the workshop organizers when he said “they're white.” The Scientist regrets any confusion.