DNA Profiling an Ancient Person

As well as following the way populations have changed and migrated, we can use modern genetic techniques to really get to know an individual body as long as it’s preserved well...
25 April 2010

Interview with 

Professor Eske Willerslev, University of Copenhagen


Diana -   As well as following the way populations have changed and migrated, we can use modern genetic techniques to really get to know an individual body as long as it's preserved well enough.  Professor Eske Willerslev is from the University of Copenhagen.  Where he's the leader of an ancient DNA and evolution group.  So Eske, can you tell us what are the problems about getting ancient DNA samples?

Eske -   Well, I think it varies a lot.  The problems, or the magnitude of the problems, actually varies a lot from one specimen or one type of specimen to another.  But obviously, one of the biggest problems you have when you're looking at ancient human remains is due to contamination with modern human DNA, because many of these specimens have been handled by humans without protective gloves or anything like that.  And also the reagents that you're buying have all been produced by humans so we can actually have traces of modern human DNA in there.

Artists Impression of Diana -   So how do you get around that?  How can you avoid that contamination?

Eske -   I think that in the last few years we've actually seen a revolution within ancient human genetics in the sense that some new technological breakthroughs have happened that makes it possible for one thing, getting very, very short pieces of DNA out of the specimens.  And the thing is that the copy number of a certain piece of DNA in indigenous DNA actually increases tremendously if you go shorter and shorter in terms of the DNA you try to retrieve.  So that makes a huge, huge difference. Basically, if you go short enough, you can almost swamp the contaminant DNA by the indigenous DNA.  Additionally, you can say the knowledge we have gained about how DNA gets damaged through time can also provide evidence to what extent you're working with indigenous DNA or are suffering from contamination.  So some of these breakthroughs really means a lot.  Another thing is that if you're working with specimens from another ethnic group for example, let's say specimens that had been in Britain, stored in Britain but comes from non-British people.  Well then there's actually ways to, you can say, distinguish the DNA you have from being European to some other ethnic groups.  So there is ways around it.

Diana -   So you're using these shorter pieces.  But can you then sequence it in the same way that you sequence fresh DNA?

Eske -   Yeah.  In fact, you can.  I mean, with these second generation high throughput sequencing platforms that have appeared over the last few years, there you can actually sequence ancient DNA in the same way as you can with modern DNA.  Of course, there are some issues you don't have with modern DNA.  For example, if you have a bone specimen you know, it's full of bacteria for example, additional to any modern human contamination that must have penetrated the bone.  And therefore, a lot of what you get out when you do what we call shotgun sequencing will in fact be microbial DNA from such a specimen while from a modern sample, you know, 99 point something percent of the DNA would be human.  So it's more demanding to deal with ancient DNA certainly.

Diana -   And probably a bit more expensive.  But tell us about Inuk, the guy you studied.  What did you have to work on there?

Eske -   Yeah.  There we worked on ancient hair.  So it's hair from a 4,000-year-old individual.  And hair is actually a really good source of ancient DNA in the sense that it's not porous like bone and therefore, neither modern human contamination or microbial contamination over the years penetrates very far into the hair, and all the contamination is on the surface.  So it's quite easy to clean the hair samples from contamination, [compared to] others like bones for example that are porous and where the contamination penetrates very deep.  So, from that point of view, it was reasonably easy to actually sequence the majority of the genome, the complete genome of this individual.

Diana -   And once you've done that, what did you find out about him?

The excavation at which Inuk's remains were foundEske -   Well that was actually quite interesting and I think it shows some of the power of using ancient DNA.  First of all, the only thing that people have actually found from this culture,  which was the first people who settled in the new world arctic - Alaska, Canada and Greenland,  is in fact a few pieces of hair and four small pieces of human bone.  And that's all we know biologically about these individuals.  By sequencing the genome of this person we could show he is a male.  We could also show he had brown skin and dark eyes.  We could see he had a tendency to baldness for example, so he probably died quite young because it was a fair amount of hair we found from this guy.  We could also see dry ear wax.  We could see that he was genetically adapted to living in cold temperatures although his people hadn't been there for a very long time.  We could see what blood type this individual had.  We could say something about his body's stature, that he had relatively low surface area compared to body mass and stuff like that.  So you know, there was a quite a number of phenotypic traits that we can actually retrieve from the genome but additionally to that, we could actually see that he came from a migration that had been independent of those migrations that resulted in present day Inuit  - people in the new world Arctic.  And also independent of that migration or those migrations, giving way to contemporary native Americans.

We actually found evidence of a previously unrecognized migration from the old world into the new world happening some times around 5,500 years ago.

Diana -   That seems a bit more recent than previous estimates have been put.  So you know that's definitely independent because of the date?

Eske -   Well, it's definitely independent and it's earlier than you can see in that migration that they raise to present Inuits or Eskimos, if you want.  Culturally they're only around a thousand years or a little bit more than thousand years old.  But the thing is, we could see that this guy is actually more closely related to people in north-eastern Siberia than he is to either Inuits or to native Americans.

Diana -   All that from a few pieces of hair.  Thanks, Eske.  That's Eske Willerslev on what we can learn from seemingly insignificant remains provided there are some DNA.


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