Whole-genome analysis offers clarity about remains of 36 enslaved Africans in 18th-century Charleston

The City of Charleston, South Carolina, has been on a quest to better understand the remains of 36 people, described collectively as “the Ancestors,” since their chance discovery a decade ago in the city’s center.  

In 2020, a team from the University of Pennsylvania and the nonprofit Gullah Society, whose mission was to reclaim African and African American burial sites around Charleston, made progress by sequencing the Ancestors mitochondrial DNA (mtDNA). That group included Ade Ofunniyin, Joanna Gilmore, and La’Sheia Oubré from the Gullah Society, along with Theodore Schurr, a professor in Penn’s Department of Anthropology; Raquel Fleskes, then a Penn graduate student and now a University of Connecticut postdoctoral fellow; and others.

The research—a community-initiated and community-engaged study today called the Anson Street African Burial Ground (ASABG) project—showed that most of the individuals had originated in Charleston or sub-Saharan Africa and, given the burial ground’s location, had likely been enslaved. At the time, that work was the largest DNA study of its kind. It was also unique in its aim to involve the community from the start, guided by the questions and concerns of the people directly affected by what the researchers might find. 

A new Proceedings of the National Academy of Sciences paper expands on those initial results, this time getting more granular and precise. Through whole-genome sequencing, the researchers confirmed that most of the people had West African or West Central African genetic ancestry and were genetically male. Beyond that, the ASABG team verified that just one mother-child pair was related. The researchers say that, taken as a whole, these findings significantly increase what’s known about African diversity in colonial America.

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“All the work we have done has been directed toward learning more about the experiences of the Ancestors and by extension the experiences of enslaved African Americans at that time,” Schurr says. “The community in Charleston has been the driving force behind this work, as its members wanted to know who the Ancestors were and what their life histories were like.”

In fact, the project grew out of feedback from the community, prompting the Gullah Society to advocate for the 2019 reinterment of the remains on the original grounds where they had been discovered and for a scientific inquiry centered around answers sought by the local African American community. Schurr and Fleskes joined the project in 2018. “Our aim has always been to do science that doesn’t objectify these remains but rather tries to restore personhood to them,” says Fleskes.

With permission from the community, she, Schurr, and the other ASABG team members started by analyzing mitochondrial DNA, the genetic material inherited from the female line alone and a frequent jumping off point for research of this type, given its abundance, size, and the fact that it’s often well-preserved. That examination revealed broad strokes about the individuals’ background and demography but couldn’t go as deep as whole-genome sequencing would. Archival maps and subsequent bone analysis led the researchers to conclude that the remains belonged to enslaved people.

“Those findings generated a great deal of interest from the community, which encouraged us to continue this work,” Schurr says.

As a next step, the team conducted a more extensive analysis, using data from 18 low-coverage genomes. “With ancient DNA research, the DNA you’re able to extract isn’t in the same form as for a living person. It’s broken up, fragmented,” Schurr says. “We want high coverage, which means 10, 20, 50 copies of the complete genome. In this case, the amount we had was small, so we call that low coverage, yet it was still adequate to complete these kinds of analyses.”

In conjunction with material from the Trans-Atlantic Slave Trade Database, these data provided greater clarity on the Ancestors’ genetic history. Specifically, the researchers found that nine had DNA that aligned closely with populations from Gabon in West Central Africa, and nine had DNA that lined up with reference populations in Ghana, the Ivory Coast, Sierra Leone, and the Gambia. In addition, of 27 individuals for which the researchers could analyze genetic sex, 21 were chromosomal males.

To verify what the researchers had determined with their initial mitochondrial DNA analysis, they also looked at 31 uniparental haplotypes, including both mtDNA and Y chromosomes, that are passed down from just one parent each generation, according to Schurr. “They represent a unique part of the genome inherited in a singular kind of way,” he says. From these data, they confirmed the connection between one mother-child pair and strengthened their hypothesis about the remains’ genetic origins; of 27 individuals analyzed, 24 displayed genetic characteristics also found in contemporary African and African American populations.

“We’ve also been able to confirm that at least one of those individuals has a genetic signature that shows mixing with a person of Native descent,” says Schurr. “That’s interesting because the first people enslaved in Charleston were Native Americans. Shortly thereafter, African people were brought to colonial America as forced labor.”

The findings, which align with what the researchers expected they might see, have been shared widely. The team filmed its scientific process in the lab, reported back to the community every few months and held a webinar series to share results. “We wanted to make sure the community members were the first people we talked to,” Fleskes says. “This project is about relationship building, trust building, being transparent in all steps of the research process, and being accountable.”

Schurr says this research can make visible a history that was either previously unknown or has historically been overlooked. For that reason, he and colleagues are creating material about the Ancestors and other aspects of Charleston’s past that they hope the city’s STEM curriculum might eventually incorporate. Schurr says he also thinks the findings have already influenced Charleston to start taking responsibility for its history, through actions like the reinternment of the Ancestors.

“We want to bring views forward that have largely been ignored,” Schurr says, “to help acknowledge that this is not something separate from American history but a part of it.”

Funding for this work came from the National Geographic Society (grants NGS-52378R-18 and NGS-54324E-18); the University Research Foundation of the University of Pennsylvania; the University of Tennessee, Knoxville, Department of Anthropology; the City of Charleston; the Gullah Society Inc.; a Dissertation Completion Fellowship from the University of Pennsylvania; and a National Science Foundation SBE Postdoctoral Research Fellowship (Grant SPRF-FR 2105384).

Theodore Schurr is a professor in the Department of Anthropology in the School of Arts & Sciences at the University of Pennsylvania. He is also a consulting curator in the Physical Anthropology and American sections of the University of Pennsylvania Museum of Archaeology and Anthropology and head of the Laboratory of Molecular Anthropology at Penn.

Raquel Fleskes is a National Science Foundation postdoctoral fellow in the Department of Anthropology at the University of Connecticut. She earned her Ph.D. from Penn in 2021.

Other co-authors on the paper include Graciela S. Cabana of the University of Tennessee; Ade A. Ofunniyin and Joanna K. Gilmore of the Anson Street African Burial Ground Project and the College of Charleston; Chelsey Juarez of California State University, Fresno; Emilee Karcher of the University of California, Davis; and Grant Mishoe and La’Sheia Oubré of the Anson Street African Burial Ground Project.