Bustamante is co-author of a paper describing the research. It will be published online March 9 in the Proceedings of the National Academy of Sciences. The lead authors of the study are Hannes Schroeder, PhD, a molecular anthropologist from the University of Copenhagen, and Stanford postdoctoral scholar Maria Avila-Arcos, PhD. The research was initiated in Denmark, and the senior author of the study is Thomas Gilbert, PhD, of the University of Copenhagen.

Bustamante is well-known for his studies of the ethnic background of native Mexicans and Caribbean dwellers, as well as for using genomics to study the patterns of human migration from North Africa to southern Europe.

This project has taught us that we cannot only get ancient DNA from tropical samples, but that we can reliably identify their ancestry.

“Several years ago, we were part of the team that sequenced the genome of Otzi, the iceman, and we were able to show that the people alive today that most closely match him genetically are Sardinians,” said Bustamante. “This incredible precision was possible because we, as a community, had invested lots of resources in understanding patterns of DNA variation in Europe. I started to talk about the ‘Otzi rule,’ or the idea that we should be able to do for all people alive today what we can do for a 5,000-year-old mummy. However, few skeletons today are as well-preserved as Otzi, and not all are of European background.”

In the centuries of the Atlantic slave trade, the largest forced migration in history, more than 12 million enslaved Africans were shipped to the New World to work on plantations in eastern South America, the Caribbean, and portions of the eastern and southern United States. Although some records were kept detailing the slaves’ departure from West and Central African ports, they are often incomplete. Furthermore, it is impossible to tell from the shipping records where in Africa individuals originated.

Researchers could tell from the skeletons found in the Zoutsteeg area that the three people were between 25 and 40 years old when they died in the late 1600s. The skulls of each also bore teeth that had been filed down in patterns characteristic of certain African groups. But this alone wasn’t enough to pinpoint where the individuals originated on the African continent.

Getting DNA from tooth roots

Schroeder and Avila-Arcos isolated DNA from the tooth roots of each of the skeletons. Although the tooth roots are relatively protected from the elements and from external contamination with unrelated genetic material, the DNA was very poorly preserved and highly fragmented — likely due to the centuries of hot, humid conditions the skeletons had endured. Initial DNA sequencing efforts rendered short stretches of highly damaged DNA.

The researchers turned to the whole-genome capture technique developed by study co-author Meredith Carpenter, PhD, a postdoctoral scholar in the Bustamante laboratory, to fish out snippets of ancient DNA from the mixture. The approach exposes the DNA sample to a genome-wide panel of human-specific RNA molecules to which the degraded DNA in the sample can bind. The effect is somewhat like stirring a pile of iron-rich dirt with a powerful magnet to isolate the metal from the soil, and it allowed the researchers to concentrate the ancient DNA for more efficient sequencing.

They then used a different technique called principal component analysis to compare the DNA sequences of the enslaved Africans with a reference panel of 11 West African populations to identify the distinct ethnic groups from which each individual likely originated. The findings illuminate a tumultuous period of time in the Americas and may provide insight into subsequent population patterns and perceived ethnic identities.

This makes us reflect on two things: the dynamics of the trans-Atlantic slave trade within Africa, and how this dramatic, ethnic mingling may have influenced communities and identities in the Americas.

“We were able to determine that, despite the fact that the three individuals were found at the same site, and may even have arrived on the same ship, they had genetic affinities to different populations within Africa,” said Avila-Arcos. “They may have spoken different languages, making communication difficult. This makes us reflect on two things: the dynamics of the trans-Atlantic slave trade within Africa, and how this dramatic, ethnic mingling may have influenced communities and identities in the Americas.”

Other Stanford authors are graduate student David Poznik and former postdoctoral scholar Martin Sikora, PhD.

The research was supported by the Danish National Research Foundation, the Directorate General for Research and Innovation of the European Commission, the European Research Council, the U.S. National Science Foundation, the Swiss National Science Foundation, the National Institutes of Health (grant numbers 5F32HG007342 and K99GM104158), a Leverhulme Early Career Fellowship, the Ministerio de Ciencia e Innovacin, the Plan Galego IDT, the Sistema Universitario Gallego-Modalidad REDES, the Xunta de Galicia, the Lundbeck Foundation and the Danish Council for Independent Research.

Bustamante is the founder of IdentifyGenomics LLC, and is on the scientific advisory board of Personalis Inc. and Ancestry.com, as well as the medical advisory board of InVitae. Carpenter is now the chief scientific officer at IdentifyGenomics.

Information about Stanford’s Department of Genetics, which also supported the work, is available at http://genetics.stanford.edu.