At Vanderbilt University, John Anthony Capra, an evolutionary genomics professor, has been combining high-powered computation and a medical records databank to learn what a Neanderthal heritage — even a fractional one — might mean for people today.
We spoke for two hours when Dr. Capra, 35, recently passed through New York City. An edited and condensed version of the conversation follows.
-Let’s begin with an indiscreet question. How did contemporary people come to have Neanderthal DNA on their genomes?
-He replied: “we hypothesize that roughly 50,000 years ago, when the ancestors of modern humans migrated out of Africa and into Eurasia, they encountered Neanderthals. Mating must have occurred then, and later.”
One reason we deduce this is because the descendants of those who remained in Africa — present day Africans — don’t have Neanderthal DNA.
What does that mean for people who have it?
At my lab, we’ve been doing genetic testing on the blood samples of 28,000 patients at Vanderbilt and eight other medical centers across the country. Computers help us pinpoint where on the human genome this Neanderthal DNA is, and we run that against information from the patients’ anonymized medical records. We’re looking for associations.
What we’ve been finding is that Neanderthal DNA has a subtle influence on risk for disease. It affects our immune system and how we respond to different immune challenges. It affects our skin. You’re slightly more prone to a condition where you can get scaly lesions after extreme sun exposure. There’s an increased risk for blood clots and tobacco addiction.
To our surprise, it appears that some Neanderthal DNA can increase the risk for depression; however, there are other Neanderthal bits that decrease the risk. Roughly 1 to 2 percent of one’s risk for depression is determined by Neanderthal DNA. It all depends on where on the genome it’s located.
Was there ever an upside to having Neanderthal DNA?
It probably helped our ancestors survive in prehistoric Europe. When humans migrated into Eurasia, they encountered unfamiliar hazards and pathogens. By mating with Neanderthals, they gave their offspring needed defenses and immunities.
That trait for blood clotting helped wounds close up quickly. In the modern world, however, this trait means greater risk for stroke and pregnancy complications. What helped us then doesn’t necessarily now.
Did you say earlier that Neanderthal DNA increases susceptibility to nicotine addiction? Yes. Neanderthal DNA can mean you’re more likely to get hooked on nicotine, even though there were no tobacco plants in archaic Europe.
We think this might be because there’s a bit of Neanderthal DNA right next to a human gene that’s a neurotransmitter implicated in a generalized risk for addiction. In this case and probably others, we think the Neanderthal bits on the genome may serve as switches that turn human genes on or off.
Aside from the Neanderthals, do we know if our ancestors mated with other hominids? We think they did. Sometimes when we’re examining genomes, we can see the genetic afterimages of hominids, which haven’t even been identified yet.
MORE REPORTING ON HUMAN ORIGINS
A few years ago, the Swedish geneticist Svante Pääbo received an unusual fossilized bone fragment from Siberia. He extracted the DNA, sequenced it and realized it was neither human nor Neanderthal. What Pääbo found was a previously unknown hominid he named Denisovan, after the cave where it had been discovered. It turned out that Denisovan DNA can be found on the genomes of modern Southeast Asians and New Guineans.
Have you long been interested in genetics?
Growing up, I was very interested in history, but I also loved computers. I ended up majoring in computer science at college and going to graduate school in it; however, during my first year in graduate school, I realized I wasn’t very motivated by the problems that computer scientists worked on.
Fortunately, around that time — the early 2000s — it was becoming clear that people with computational skills could have a big impact in biology and genetics. The human genome had just been mapped. What an accomplishment! We now had the code to what makes you, you, and me, me. I wanted to be part of that kind of work.
So I switched over to biology. And it was there that I heard about a new field where you used computation and genetics research to look back in time — evolutionary genomics.
There may be no written records from prehistory, but genomes are a living record. If we can find ways to read them, we can discover things we couldn’t know any other way.
Not long ago, the two top editors of The New England Journal of Medicine published an editorial questioning “data sharing,” a common practice where scientists recycle raw data other researchers have collected for their own studies. They labeled some of the recycling researchers, “data parasites.” How did you feel when you read that?
I was upset. The data sets we used were not originally collected to specifically study Neanderthal DNA in modern humans. Thousands of patients at Vanderbilt consented to have their blood and their medical records deposited in a “biobank” to find genetic diseases.
Three years ago, when I set up my lab at Vanderbilt, I saw the potential of the biobank for studying both genetic diseases and human evolution. I wrote special computer programs so that we could mine existing data for these purposes.
That’s not being a “parasite.” That’s moving knowledge forward. I suspect that most of the patients who contributed their information are pleased to see it used in a wider way.
What has been the response to your Neanderthal research since you published it last year in the journal Science?
Some of it’s very touching. People are interested in learning about where they came from. Some of it is a little silly. “I have a lot of hair on my legs — is that from Neanderthals?”
But I received racist inquiries, too. I got calls from all over the world from people who thought that since Africans didn’t interbreed with Neanderthals, this somehow justified their ideas of white superiority.
It was illogical. Actually, Neanderthal DNA is mostly bad for us — though that didn’t bother them.
As you do your studies, do you ever wonder about what the lives of the Neanderthals were like?
It’s hard not to. Genetics has taught us a tremendous amount about that, and there’s a lot of evidence that they were much more human than apelike.
They’ve gotten a bad rap. We tend to think of them as dumb and brutish. There’s no reason to believe that. Maybe those of us of European heritage should be thinking, “Let’s improve their standing in the popular imagination. They’re our ancestors, too.’”
Source: Claudia Dreifus
We spoke for two hours when Dr. Capra, 35, recently passed through New York City. An edited and condensed version of the conversation follows.
-Let’s begin with an indiscreet question. How did contemporary people come to have Neanderthal DNA on their genomes?
-He replied: “we hypothesize that roughly 50,000 years ago, when the ancestors of modern humans migrated out of Africa and into Eurasia, they encountered Neanderthals. Mating must have occurred then, and later.”
One reason we deduce this is because the descendants of those who remained in Africa — present day Africans — don’t have Neanderthal DNA.
What does that mean for people who have it?
At my lab, we’ve been doing genetic testing on the blood samples of 28,000 patients at Vanderbilt and eight other medical centers across the country. Computers help us pinpoint where on the human genome this Neanderthal DNA is, and we run that against information from the patients’ anonymized medical records. We’re looking for associations.
What we’ve been finding is that Neanderthal DNA has a subtle influence on risk for disease. It affects our immune system and how we respond to different immune challenges. It affects our skin. You’re slightly more prone to a condition where you can get scaly lesions after extreme sun exposure. There’s an increased risk for blood clots and tobacco addiction.
To our surprise, it appears that some Neanderthal DNA can increase the risk for depression; however, there are other Neanderthal bits that decrease the risk. Roughly 1 to 2 percent of one’s risk for depression is determined by Neanderthal DNA. It all depends on where on the genome it’s located.
Was there ever an upside to having Neanderthal DNA?
It probably helped our ancestors survive in prehistoric Europe. When humans migrated into Eurasia, they encountered unfamiliar hazards and pathogens. By mating with Neanderthals, they gave their offspring needed defenses and immunities.
That trait for blood clotting helped wounds close up quickly. In the modern world, however, this trait means greater risk for stroke and pregnancy complications. What helped us then doesn’t necessarily now.
Did you say earlier that Neanderthal DNA increases susceptibility to nicotine addiction? Yes. Neanderthal DNA can mean you’re more likely to get hooked on nicotine, even though there were no tobacco plants in archaic Europe.
We think this might be because there’s a bit of Neanderthal DNA right next to a human gene that’s a neurotransmitter implicated in a generalized risk for addiction. In this case and probably others, we think the Neanderthal bits on the genome may serve as switches that turn human genes on or off.
Aside from the Neanderthals, do we know if our ancestors mated with other hominids? We think they did. Sometimes when we’re examining genomes, we can see the genetic afterimages of hominids, which haven’t even been identified yet.
MORE REPORTING ON HUMAN ORIGINS
A few years ago, the Swedish geneticist Svante Pääbo received an unusual fossilized bone fragment from Siberia. He extracted the DNA, sequenced it and realized it was neither human nor Neanderthal. What Pääbo found was a previously unknown hominid he named Denisovan, after the cave where it had been discovered. It turned out that Denisovan DNA can be found on the genomes of modern Southeast Asians and New Guineans.
Have you long been interested in genetics?
Growing up, I was very interested in history, but I also loved computers. I ended up majoring in computer science at college and going to graduate school in it; however, during my first year in graduate school, I realized I wasn’t very motivated by the problems that computer scientists worked on.
Fortunately, around that time — the early 2000s — it was becoming clear that people with computational skills could have a big impact in biology and genetics. The human genome had just been mapped. What an accomplishment! We now had the code to what makes you, you, and me, me. I wanted to be part of that kind of work.
So I switched over to biology. And it was there that I heard about a new field where you used computation and genetics research to look back in time — evolutionary genomics.
There may be no written records from prehistory, but genomes are a living record. If we can find ways to read them, we can discover things we couldn’t know any other way.
Not long ago, the two top editors of The New England Journal of Medicine published an editorial questioning “data sharing,” a common practice where scientists recycle raw data other researchers have collected for their own studies. They labeled some of the recycling researchers, “data parasites.” How did you feel when you read that?
I was upset. The data sets we used were not originally collected to specifically study Neanderthal DNA in modern humans. Thousands of patients at Vanderbilt consented to have their blood and their medical records deposited in a “biobank” to find genetic diseases.
Three years ago, when I set up my lab at Vanderbilt, I saw the potential of the biobank for studying both genetic diseases and human evolution. I wrote special computer programs so that we could mine existing data for these purposes.
That’s not being a “parasite.” That’s moving knowledge forward. I suspect that most of the patients who contributed their information are pleased to see it used in a wider way.
What has been the response to your Neanderthal research since you published it last year in the journal Science?
Some of it’s very touching. People are interested in learning about where they came from. Some of it is a little silly. “I have a lot of hair on my legs — is that from Neanderthals?”
But I received racist inquiries, too. I got calls from all over the world from people who thought that since Africans didn’t interbreed with Neanderthals, this somehow justified their ideas of white superiority.
It was illogical. Actually, Neanderthal DNA is mostly bad for us — though that didn’t bother them.
As you do your studies, do you ever wonder about what the lives of the Neanderthals were like?
It’s hard not to. Genetics has taught us a tremendous amount about that, and there’s a lot of evidence that they were much more human than apelike.
They’ve gotten a bad rap. We tend to think of them as dumb and brutish. There’s no reason to believe that. Maybe those of us of European heritage should be thinking, “Let’s improve their standing in the popular imagination. They’re our ancestors, too.’”
Source: Claudia Dreifus
