The Bioethical Considerations of Archaeogenomic Studies

by SARAH KIM

Sarah Kim is a fourth-year at the University of Chicago majoring in Biological Sciences. Outside of classes, she works at UChicago Medicine as an Oncology Clinical Trials Assistant and Pharmacokinetics Coordinator. Sarah also plays for UChicago’s womxn’s rugby team, and is an executive board member of Korean Students Organization. She hopes to work as a clinical research coordinator after graduation. In her spare time, she enjoys writing poems, watching movies, and solving chess puzzles.

In February of 2017, a 14-member team of anthropologists, geneticists, and archaeologists from the American Museum of Natural History (AMNH) excavated numerous ancestral remains from a burial site in Chaco Canyon, New Mexico. This excavation was part of a larger endeavor to research the ancient Puebloans, a Native American civilization whose cultural influence spread across the Four Corners of the American Southwest during its peak from 850 to 1250 AD.1 The presence of thousands of shell beads and turquoise jewelry within the burial site suggested that these remains belonged to elite members of society.2 The research team successfully extracted and sequenced ancient DNA from each entombed individual, and found that everyone buried at Chaco Canyon shared a common mitochondrial DNA (mtDNA) lineage. Since mtDNA is only inherited maternally, the geneticists confirmed that the elite status of the Puebloans was also matrilineally inherited. Six of the individuals had sufficient DNA preservation to have their genomes mapped, leading to identification of mother-daughter and grandmother-grandson relationships amongst them.2

After publishing their work in scientific journals and discussing their research within academic circles, the AMNH team anticipated support from the surrounding Native American communities. Believing their research would be welcomed as evidence for modern Pueblo and Diné (Navajo) claims of descent from the ancient Chacoans, the AMNH team was unprepared for the dismay of the Native communities, who felt that the dignity of their ancestors and the sacredness of Chaco Canyon had been severely violated.

Other established researchers also condemned the project. “In recent decades, archaeologists have been working hard to build trusting, collaborative relationships with our Indigenous colleagues,” stated Ruth Van Dyke, a professor of anthropology at Binghamton University. “Any research that fails to respect Native rights and sensibilities can only undermine this progress”.2

In the United States, the Native American Graves Protection and Repatriation Act (NAGPRA) regulates outside interference with Native American ancestral remains and objects. NAGPRA mandates all federal agencies and museums to engage with “any tribal group that may have cultural affiliations” with any Native American historical artifacts of interest, and to “repatriate ancestral remains and objects” to any Native American or Indigenous community once a direct cultural relationship can be established.3 However, NAGPRA does not explicitly specify the manner in which this engagement or consultation must occur: a simple notification to the Native leaders of any excavation or transfer of their ancestral artifacts may technically fulfill the consultation requirement, even if no mutual agreement or exchange has occurred. Due to the ambiguity of this policy, the researchers escaped legal punishment. Nevertheless, many prominent tribal leaders, as well as other archaeologists and scientists, felt that the concealment of the Chaco Canyon excavation project, and the subjection of these individual remains to highly destructive chemical processes for sequencing, was highly unethical and disrespectful to the Pueblo and Diné tribes near Chaco Canyon.

To extract and analyze DNA from ancient human remains, each sample must undergo highly destructive processes. First, samples of DNA can be taken by sawing cross-sectional pieces out of the skeletal remains sample. Then the process involves crushing the pieces into powder, immersing the powder in a series of organic solvents, and centrifuging the mixtures to isolate the DNA samples.4 Ancient oral microbiomes can also be extracted from ceramic artifacts, or even dental calculus, which is calcified dental plaque and mineral buildup. In fact, bacteria typically found in the upper respiratory tract and the digestive system can be extracted from dental calculus dating back several millennia.5

Initial attempts to sequence ancient genetic material in the 1980s were successful, but highly inefficient. The first prominent method was Sanger sequencing. Sanger sequencing involves attaching free-floating DNA bases to different colored fluorescent tags, then sequencing a sample of DNA by observing the color of light emitted. Before the first complete human genome was compiled and sequenced in 2003, scientists had no reference DNA to compare these ancient samples to.6 This made it exceptionally difficult to detect and separate genuine ancient DNA from modern DNA (possibly from cross-contamination during collection), and only one base pair could be sequenced at a time. However, the emergence of a more advanced sequencing method called nextgeneration sequencing (NGS), as well as the compilation of the world’s first entire human genome, revolutionized the field of genetic sequencing.

NGS can sequence multiple (up to one million) DNA fragments simultaneously per run. Compared to Sanger sequencing, NGS is way more efficient and cost-effective.7 It is capable of whole-genome sequencing as well as targeted sequencing that focuses only on a specific region of the DNA. The two main targeted NGS methods are hybridization capture and polymerase chain-reaction (PCR) amplification.4

In hybridization capture, DNA is heated in solution until it denatures, or, unravels. It is then randomly sheared at various points in the sample. The DNA fragment solution is then washed over a hybridization capture sensor, which has “baits” made of complementary DNA that are specific to the region of interest. The appropriate DNA fragments then bind onto the sensor, and residual DNA is flushed out to unveil any overlapping pieces. Multiple cycles of hybridization are carried out to ensure accuracy and adequate amounts of data.

In PCR amplification, fragments of genomic double-stranded DNA are unraveled into single strands and treated with primers, before being bathed in a solution of free-floating DNA segments that are complementary to the region of interest. The free bases then bind onto the single-stranded DNA in their corresponding order, doubling the number of DNA fragments in the solution. The background DNA fragments are flushed out so that only the DNA of interest remains. Multiple cycles of PCR amplification can lead to a pool of available fragments to sequence. Compared to hybridization, although PCR amplification has quicker turnaround time and costs less per run, it is less sensitive and can only accommodate a limited number of targets.4 Depending on the size of the gene panel, different methods are suited for different studies. If an ancient DNA research project involves many different genes that need to be tagged in a sample, hybridization would be preferred. However, if only one gene of interest is involved in a study, then PCR would be much more efficient.

In 2021, a committee of archaeological and bioanthropological scientists from over 31 countries convened to draft a set of universal guidelines that ensured ancient DNA research remains sustainable and ethical.8 These scientists advised that archaeogenomic research teams should follow, but critically examine NAGPRA’s outlined regulations before proceeding with fieldwork or destructive analysis on ancestral remains and other culturally significant artifacts. Research teams must also prepare a detailed plan to be presented to the appropriate governing board of research before proceeding.

Another guideline suggested by this committee was to make all resulting data accessible and publishable. This applies to cases where sequencing data for certain genes or reference genomes from previous biobank studies may already be available, eliminating the need to conduct repeated ancient DNA extraction. There is only a finite number of skeletal samples in the world (the real number of available samples is unknown due to the lack of a formal documentation system). These remains contain a plethora of ancient DNA that we can learn from, but they also hold great historical and cultural significance. Because these remains cannot be reconstructed after use in genomic studies, it is imperative that researchers minimize destructive harm to samples during analytic research.

Advancements in genetic sequencing technology have enabled anthropologists, archaeologists, and geneticists to unveil groundbreaking findings in the study of ancient cultures and civilizations. However, conducting these projects without regard for upholding ethical standards in research may unintentionally cause more harm to the involved communities rather than allow them to benefit from the research, as seen in the removal of ancestral remains by the AMNH in Chaco Canyon. Although research teams often evade punishment for these ethical violations due to the ambiguity of legal policy in this field, meaningful consultation or discussion of these research studies with tribal leaders and local Native American communities should be encouraged, or perhaps required. In fact, researchers themselves may benefit from learning a given sample’s significance, as they would acquire a greater understanding of the sociocultural context of the samples.

Often, ancient DNA studies reflect a hierarchical dynamic between genetic sequencing and archaeological interpretations, hailing the former as a “true” revelation of history and discrediting the latter as a discipline prone to imprecision and inaccuracy. In truth, both fields are self-encompassing on their own, and simultaneously rely on each other to uncover the past. Another pressing concern among archaeologists is that a genetics-based approach to history may offer “sanitized versions of the past” that perpetuate misleading Eurocentric views and avoid engagement with violent experiences.10 Without placing both fields on equal footing, these studies may unintentionally project a historical narrative ridden with antiquated ideologies.

Archaeogenomics, ideally, should transform into a more conscientious field to Native American communities when conducting fieldwork or sequencing ancient DNA. Research teams can avoid future incidents reminiscent of that of Chaco Canyon, and take both the interests of scientists and of Native American communities into account.

References

1. Cortez, Amanda et al. “An Ethical Crisis in Ancient DNA Research: Insights From the Chaco Canyon Controversy as a Case Study.” Journal of Social Archaeology, vol. 21 (2), 2021, pp. 157-178.

2. Balter, Michael. “Ancient DNA Yields Unprecedented Insights into Mysterious Chaco Civilization.” Scientific American, 2017. https:// www.scientificamerican.com/article/ancient-dna-yields-unprecedented-insights-into-mysterious-chaco-civilization.

3. United States, House of Representatives. U.S. Code 25 Ch. 32, Native American Graves Protection and Repatriation Act.1990. U.S. Government Printing Office. https://uscode.house.gov/view.xhtml?path=/prelim@title25/chapter32&edition=prelim.

4. Samorodnitsky, Eric et al. “Evaluation of Hybridization Capture vs. Amplicon-Based Methods for Whole-Exome Sequencing.” Human Mutation, vol 36 (9), 2015, pp. 903-14.

5. Daley, Jim. “Ancient ‘Chewing Gum’ Reveals a 5,700-Year-Old Microbiome.” Scientific American, 2019. https://www.scientificamerican. com/article/ancient-chewing-gum-reveals-a-5-700-year-old-microbiome1/

6. “Human Genome Project Completion: Timeline.” National Human Genome Research Institute, https://www.genome.gov/humangenome-project/timeline.

7. Knapp, Michael and Michael Hofreiter. “Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives.” Genes (Basel), vol 1 (2), 2010, pp. 227-43. doi: 10.3390/genes1020227.

8. Alpaslan-Roodenberg, Söngul et al. “Ethics of DNA Research on Human Remains: Five Globally Applicable Guidelines.” Nature, vol. 599 (7883), 2021, pp. 41-46.

9. Arbuckle, Benjamin and Zoe Schwandt. “Ancient Genomes and West Eurasian History.” Science, vol 377 (6609), 2022, pp. 922-923. doi: 10.1126/science.add9059.

10. Furlong, Rebecca. “Waking the Dead: Sequencing Archaic Hominin Genomes.” Nature, 2021, https://www.nature.com/articles/d42859020-00112-6.