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Ancient DNA Reveals African Origins of Enslaved Individuals in Caribbean

NEW YORK (GenomeWeb) – An analysis of ancient DNA is providing a closer look at the ancestry and geographic origins of African individuals exploited by the transatlantic slave trade.

As detailed this week in the Proceedings of the National Academy of Sciences, an international team led by investigators in Denmark, the Netherlands, and the US enriched and sequenced ancient DNA that was extracted from the remains of three African individuals from a 17th century burial site on the Caribbean island of Saint Martin.

After verifying the African ancestry of the remains, the team used genotyping data for individuals from 11 present-day populations in sub-Saharan Africa to more precisely tease apart the ancient individuals' origins. The results suggest one of the individuals belonged to a Bantu-speaking population from northern Cameroon, while the other two shared genetic features with non-Bantu populations in Nigeria and Ghana.

"These three individuals were buried together and may have even arrived on the same vessel, the same ship," co-first author Hannes Schroeder, a researcher affiliated with the University of Copenhagen's Centre for Geogenetics and Leiden University, told GenomeWeb. "Yet they were genetically very distinct, they probably had different genetic backgrounds, and were maybe even speaking different languages."

More generally, he explained, the proof-of-principle study underscores the potential of using genomic data as a historical record or a type of archive. "You can use this data to start to answer historical questions," Schroeder said, noting that it can be applied to a wide range of sites and contexts, even in places where DNA preservation may be subpar.

The remains tested for the current study were discovered in around 2010 during a construction project. Researchers and archeologists suspected the individuals, who were buried some time between 1660 and 1688, had been born in Africa based on the presence of characteristic dental modifications that were common to some African cultures at the time.

"The remains themselves, obviously, gave no indication that they were enslaved," Schroeder noted. "But from the context, from the date, and from the fact that they had these dental modifications and were African, it's pretty clear that they were probably victims of the slave trade."

The team's first crack at doing shotgun sequencing on DNA from the samples came up short due to the fragmented, degraded, and deaminated nature of the genetic material. While that was no surprise given the Caribbean's toasty environment, it did present challenges when trying to directly apply next-generation sequencing to DNA extracted from the samples.

To get around those problems, the researchers enriched for ancient DNA using whole genome in-solution and capture (WISC) with the MYbait human genome kit, each of which rely on the use of biotinylated RNA probes to nab human DNA from the ancient libraries, Schroeder explained.

After preparing enriched libraries for each sample and sequencing them with the Illumina HiSeq 2000, the researchers compared the resulting sequences to one another and to panels of existing genome and/or genotyping information for individuals from present-day populations around the world.

Since the genome sequences generated from the ancient samples were still somewhat patchy, that involved comparisons with genotyping data for more than 850 global individuals from the Human Genome Diversity Cell Line Panel as well as comparisons with whole-genome sequences for individuals from 11 present-day populations.

Once they verified African ancestry for the ancient Caribbean samples, the researchers turned to genotyping data for more than 150 individuals from relevant African populations to tease apart more specific ancestry patterns.

Their results suggest that the female individual clustered with non-Bantu speaking populations currently found in Nigeria and Ghana, as did one of the male individuals. The other male shared ancestry with present-day Bantu-speaking groups in northern Cameroon.

Likewise, Schroeder noted that the latter individual carried Y chromosome sequences that fit that region, Schroeder noted, and belonged to a mitochondrial haplogroup that is common in northern Cameroon but rare in other parts of Africa.

"These two separate or independent indicators pointed at this one part of Cameroon as a potential place of origin," Schroeder said. That finding is consistent with historical records indicating that slaves brought to European trading posts in coastal regions of Africa came from more inland sites.

Because findings from the study represent only a few individuals, Schroeder emphasized that it is difficult to generalize the results for insights into the ancestry of the millions of individuals enslaved during the slave trade.

Schroeder and his collaborators are currently studying DNA from remains found at the African Burial Ground of New York. They are also looking at other locations relevant to the slave trade and/or Caribbean history through a research network called EUROTAST.