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Ancient DNA Speaks Today

May 5, 2009

Neanderthal

German scientists have mapped out the Neanderthal genome. Image by Ryan Somma.

By Dennis McCarthy

CSI: Miami and CSI: New York are among the hottest shows on television these days, and forensics is fast becoming the profession of choice among the preteen set. If you develop an appetite for these shows, you quickly assume that DNA is the Rosetta Stone—to every crime, to every forensics mystery—and if the forensics specialist can just get a DNA sample, the pieces of the puzzle practically fall into place.

For one DNA expert at UT Knoxville, however, DNA asks more questions than it answers; and that’s the way she likes it. Graciela Cabana is not a forensics specialist, although working on the same campus with the world-famous Anthropological Research Facility—popularly known as the Body Farm—means that forensic work is part of her job description. She’s an assistant professor in the anthropology department and she uses DNA, often ancient DNA, to study human evolution, patterns of migration among humans, the impact of genetic knowledge on group identity, and, occasionally, recent cadavers. Quest recently spoke with her about her research.

Q: Tell me a little about your background.

A: I grew up in Northern California, in the Bay area. I went to Berkeley, majoring in political science with a minor in French. Like a lot of people, I didn’t know what I’d do when I graduated. Before graduation, however, I had to take a course in a natural science, and a friend suggested an introductory course in physical anthropology. One week into the course, I was hooked. It was one of the few times in my undergraduate career that I was excited about a course—I actually wanted to read the textbook.

I talked with my anthropology professor, and he outlined a career path for me. I got into graduate school at the University of Michigan, and that’s where my real education began.

Q: Did you get your Ph.D. at Michigan?

A: Yes. I wrote my dissertation on ancient DNA, working on 4,000-year-old Chinchorro mummies from Chile. These mummies are the oldest known intentional mummies in the world. The Chinchorro people mummified their dead from about 4,000 to about 7,000 years ago, so some of these mummies are a couple of millennia older than Egyptian mummies.

There’s a longstanding question in prehistoric anthropology about changes in culture over time: Were the changes caused by immigrants replacing the local inhabitants or did the local inhabitants emulate the cultural practices of other people with whom they came in contact? I developed a simulation model to try to get an answer to this question. I discovered that the question is much more complex than I had originally thought. I developed tools that will aid future research to distinguish among various biological processes—including migration—that may account for cultural change.

Q: The DNA you used in your dissertation study was 4,000 years old. How far back in time can you go and still get viable DNA?

A: It depends upon the conditions, of course, but pretty far back. Animals preserved in peat or ice occasionally have intact DNA. A recent article in Nature magazine reported that German scientists have roughly mapped out the genome of a Neanderthal specimen that is nearly 40,000 years old, and scientists have worked out most of the genome of woolly mammoths of a similar age.

Some researchers claim to have gotten DNA out of 20-million-year-old magnolia leaves buried in clay at the bottom of lakes, and from even earlier-aged insects caught in amber—just like the insects that helped replicate the velociraptors and other dinosaurs in Jurassic Park. Others claim to have revived 250-million-year-old bacteria from salt deposits. These dates are controversial; contamination is always an issue. Neanderthal bones, for example, have often been handled extensively and have modern DNA stuck to them. The short answer to your question is that we don’t know what the outer limits of DNA survival are.

DNA expert Graciela Cabana

DNA expert Graciela Cabana.

Q: Have you looked at your own DNA?

A: Oh, yes. My family is from Argentina, which has a strong Italian heritage, and my family has Italian roots. So whenever I thought about my Argentine ancestry, I’d picture myself in a Tuscan café drinking cappuccinos.

My dad’s mom grew up in a convent, however, and we didn’t know anything about her side of the family. There’s a particular genetic test you can run through the maternal side, looking at genetic markers on mitochondria. Children receive nuclear DNA from both parents, but their mitochondrial DNA comes only from the mother. When I ran the mitochondrial DNA test on my father—my grandmother had passed away by then—it showed that my grandmother had indigenous genes. Before I sampled my family’s DNA, I knew the tests might uncover indigenous genes, and I assumed such a discovery wouldn’t be a big deal for me. But it was. Knowing I had indigenous ancestry changed my attitude about being Argentine. It made me feel more rooted in the country and its history.

When I realized how these genetic results had affected me, I became curious about how genetic ancestry tests affect others. A colleague at the University of Oregon and I conducted a pilot study with 16 Argentineans. We did family trees for the pilot group, and we found that families related most strongly to the most recent immigrants. Interestingly, the people who lacked indigenous genes seemed to feel more like interlopers and not quite as much Argentine. Does this mean that people who have an indigenous heritage have stronger ties to Argentina? Eventually, I hope to have an answer to this question.

Q: What else are you working on?

A: I’m working on a variety of demographic questions in South America. I’m looking at population movements for all periods—the recent past, 1,000 years ago, and 10,000 years ago. Most anthropologists think that people have been in South America for about 15,000 years. There are a few sites in the Americas, however, that are controversial and may be older—Monte Verde in Chile, for example. Some claim that Monte Verde has been occupied for 35,000 to 40,000 years, but most don’t accept those figures. We’ll see. Maybe someone will come up with strong evidence to support a longer period of human occupation.

Earlier studies looked at the diversity of groups in the Amazon and to the west of the Andes and concluded that two distinct groups migrated into South America at different times. One of the assumptions in this theory is that the environment of the Amazon is not conducive to large population densities: people coming into the region necessarily lived in small, relatively isolated groups. But we’re learning more and more from archaeology, and this seems to not always have been the case. So is this two-wave scenario justified? Right now, I’m working on alternative theories to explain the data, but it’s too early to report any results.

I’m also looking at the relationship between skeletal bones and the underlying genetics, to see if the bones themselves give an accurate picture of the genetic makeup. Prehistorians routinely study skeletal bones. Sometimes those bones contain DNA, but many times they don’t, depending on how old they are, where they’ve been, and what kinds of conditions they’ve been subjected to. Ancient DNA opens up a new avenue of research. Scientists studying skeletal morphology assume that their results mirror the underlying genetics. When my labs are finished, I’ll be able to compare the genetics to the morphology to see how well they correspond.

Q: You just said, “When my labs are finished.” Are you building a lab now?

A: Three labs, actually. One is a standard DNA lab, one is for ancient DNA, and the third is for forensic analysis. The ancient DNA and forensic labs are clean labs, with filtered air entering them. Workers in the clean labs will wear bunny suits so they won’t drag in DNA from the outside or shed their own DNA in the lab. Initially, we were going to build only two labs, but because of all the forensic work done here, we decided to build a forensic lab as well. We didn’t want to do forensic work in the same lab that we’ll be doing ancient DNA work. The contamination risk is too high.

Q: Do you ever watch the CSI shows on television? I’ve wondered how realistic they are.

A: I couldn’t tell you. I don’t have a TV and have never seen any of them.

Q: What do you see in your future?

A: Ancient DNA analysis is practically a virgin field, populated by a very small community. There may be 10 established labs in anthropology departments, and probably twice that many people. There are also a few people outside university anthropology departments who work with ancient DNA.

I have a lifetime of study ahead. And since those of us working with ancient DNA are defining the parameters of our profession, we can do almost anything we want. There’s so much to learn. I’ll always have more questions than answers. That’s what’s so exciting about this research.

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