Maria Avila of Stanford University explains how researchers identified DNA and solved a slave trade mystery

NSF's Weather or Not!

Maria Avila of Stanford University explains how researchers identified DNA and solved a slave trade mystery

National Science Foundation


Can fossils help solve a slave trade mystery?

Interviewer: Charlie Heck

Interviewee: Maria Avila

Charlie: This is Charlie Heck at the National Science Foundation, co-editor of the Science360 News Service. An estimated 12 million enslaved Africans were shipped to South America, the Caribbean, and the United States in the largest forced migration in history, the Trans-Atlantic Slave Trade. Spanning from the 16th through 19th century, records from this period of the middle passage are often incomplete.  Most focus on vessel and captain names and their home ports, forgetting the millions of humans below deck. NSF-funded researcher Maria Avila, a post-doctoral research fellow in genetics at Stanford University, explains that in this recordkeeping important information has been lost.

Maria: It never quite registered the actual origins of these persons. Like not geographical origins, or ethnic origins, or anything like that. They suddenly became just a number and a lot of their identity was lost this way, and their history and who they were was lost as they were put in ships to America.

Charlie: Avila, with a team of researchers from Stanford and the University of Copenhagen, has been able to fill in the gaps through genetics. They recently used an entirely new process to successfully extract and sequence DNA from the skeletons of three African-born slaves found on the Caribbean Island of St. Maartin. Through this, the team was able to discover new information about slave origins that contradicts common beliefs. I spoke with Avila about this newly developed genetic technique.

Charlie: Pretty exciting stuff! You guys have been able to sequence DNA from the teeth of 300-year-old skeletons. You want to tell us a little bit about it?

Maria: Yes, they're older than 300 years old, the skeletons. And it's not only that they are 300 years old. What's impressive is that they were actually in the Caribbean. So it's like hot and humid environment. And that's very bad for DNA preservation. So the fact that we were able to do that is what's really interesting about this project from the methodological part of the project.

Charlie: Okay, so let's talk a little bit about that. Where exactly where they found, and what are some of the weather conditions like where they were found?

Maria: So three of them were found in the same site in the town of Philipsburg, which is the capital of the Dutch side of St. Maarten. That's a Caribbean Island. It's a beautiful island in the Caribbean, but it is hot and humid throughout the year. So these were actually found during--they were renovating one of the streets. And they were doing these construction work, and they came up across... And, yeah, then they had to call the archaeologist in charge and stop all the construction and put the efforts into more archaeological studies and excavation.

Charlie: So why does the tropical climate make it a little bit more difficult than, say, a frozen climate?

Maria: You mean, why--

Charlie: Yeah, when it comes to dealing with the ancient DNA.

Maria: Well, all the studies we've done on ancient DNA we've-- they have done on samples preserved, like sometimes even thousands of years in ice or in very cold conditions because we know DNA gets fragmented and sometimes it's eaten by bacteria. It's degraded. But when it's in cold conditions that happens frequently. Whereas in hot weather the DNA breaks. It's more prone to break, and it will accumulate certain what we call damage in the DNA so that some of the (basis) in the DNA changes as a result of a chemical reaction. And also that happens more often too when it's under humid conditions and hot conditions. So, actually, this is the first study to do DNA extraction and sequencing of samples preserving these conditions. All the studies you see before, at least at the genomic level, they're from European or like Arctic environment, even like permafrost environment. So none are really there to try samples from these environments before. So we were very happy to show if it's actually possible to do this.

Charlie: Are you guys using new methods or processes for this specific type of climate?

Maria: Yes, actually, that was a key point in the study is that we use this method that is called whole gene in-solution capture, so WISC. And what it does is it enriches the amount of human DNA in a sample. So, for example, when you extract DNA from a tooth or a bone or even hair and it's ancient, it will come with some bacterial or microorganism DNA, its environmental DNA. And only a small fraction will be human. So that's you would be observing, these samples. And we use this method that was developed here in part of the semantic group. I was also an author on the paper. So she developed these methods where you can basically-- it's like building (traits) that are specifically human, so what they do is they fish out only human DNA from this pool of human environmental DNA. So this way we were able to kind of enrich the amount of human DNA in the sample even though it was very degraded. We pull out more human DNA, and then we were able to sequence it and have more data as a result of this.

Charlie: Okay, so going back a little bit more to why this new technique is so important: When we talk about recordkeeping during the Trans-Atlantic slave trade there really isn't much to go on. So why is this new technique so important? And what do you hope to kind of do with this?

Maria: It's very important because, yeah, the recent records, the historical records from the Trans-Atlantic slave trade, it mostly recorded the number of people in Africa and (embarkation?) ports and the number of people disembarking in certain ports in the Caribbean or other places in the Americas beyond the states. It never quite registered the actual origin of this person, not geographical origins or ethnic origins or anything like that. Some just became a number. And a lot of their identity was lost this way and the history and who they were was lost as soon as they were put in the ships to America. So it's very important-- it's kind of a proof of principle study that we hope it can be expanded because the results reveal what we were expecting that the ethnic origins or the first Africans to arrive to the Americas were actually quite diverse. They don't come-- they didn't all come from the exact place where they were embarked in Africa. The origins actually are more in-land, and they were more diverse than some people could think looking at the historical records. So to us it was very important to prove this, that there's a diversity in the first people from Africa to arrive to the Americas.

Charlie: So let's talk about these three skeletons. Male, female? Do we know an age? Where exactly they did come from?

Maria: Yes, so these were three skeletons. And there were two males and one female. And they were between 20 and 40 years old. And they had these very characteristic things in their teeth. So they had certain dental modification patterns that were known to be practiced in Africa. But it's one of the first cultural traditions in a way to be lost after the arrival to the Americas. So just by looking at these dental patterns that was the first striking thing that suggested that these individuals were probably born in Africa just by looking at how they were modified. So the archaeologists noticed that, and then they did another study previous to our where they actually did something called isotope analysis in the teeth. So basically what they do is they compare the patterns of isotopes in the teeth to a reference, a worldwide reference. And those also point to an African origin of these samples. Not with enough resolution because they were in Africa but at least it was proven this way that the individuals were born in Africa. They were brought-- we knew that they were brought as slaves to this island in the Caribbean.

Charlie: So, specifically do we know an area in Africa where these three individuals came from?

Maria: Yes, so we were able-- using a reference analysis of modern populations in Africa, we were able to find what populations in these modern reference sample are more similar to our samples. So for one of the samples, for one of the males, we were able to using markers across the genome and the Y chromosome markers. So that's the chromosome that's inherited from your dad to males only. We were able to trace the origin of this one sample to a place in Cameroon. And it looked very similar to the population that speaks Bantu today. So that's the living population that looks more similar to this particular sample, at least in this reference panel we had access to. And the other two samples, the male and the female, we were able to say they're more similar to populations in Nigeria and Ghana. And these are non-Bantu speakers and populations that are in Ghana and Nigeria nowadays. So those were our main results in terms of tracing the origins of these three samples.

Charlie: OK, so what's next? Are you guys working with other remains? Or kind of what do you see next now that you have this new technique?

Maria: Yes, we actually want to use this technique not only in this context. Of course, we want to expand this context and work in collaboration with the University of Copenhagen, and they're world experts on DNA. So together with them we want to expand our sample sites to study more islands in the Caribbean and maybe some places ideally also in the states. There's a famous site in New York that would be interesting to look at from this perspective, places in Mexico and Brazil even. And we want to go even a bit further back and not only do it with the African slaves but also try to do-- identify the original native population in the Caribbean. So these are tiny populations. So now that we trust these methods and that we know it works we can try to even push it a bit more and go further back in time and study remains from the Caribbean, maybe a thousand years old or samples that pre-date arrival of the Europeans. So that would be really interesting to look at as well.

Charlie: Well, thank you so much for taking the time to chat with us today, Maria.

Maria: Thank you very much. It was a pleasure.

Charlie: That was Maria Avila, Stanford post-doctoral scholar and co-author of the paper "Genome-wide Ancestry of 17th Century Enslaved Africans from the Caribbean." To read more about this genetic research, check out the March 9th edition of the proceedings of the National Academy of Sciences. You can also search our top stories on The music for this interview is "Tempting Secrets," composed by Kevin McCloud and licensed under Creative Commons. I'm Charlie Heck, co-editor of the Science360 news service at the NSF.