Fri March 9, 2012
Gorilla Genome Sheds Light On Human Evolution
Originally published on Fri March 9, 2012 11:11 am
IRA FLATOW, HOST:
This is SCIENCE FRIDAY. I'm Ira Flatow. Camilla is a 300-pound female gorilla in her 30s who lives in the San Diego Zoo. Now, what sets Camilla apart from the rest of the troop is that she became the first gorilla to have its entire genome sequenced.
It took an international dream team of more than 60 researchers four years to decipher Camilla's DNA. The genes of other great apes - humans, chimpanzees, orangutans - have all been decoded. So she is the last. And here's the surprising thing: Scientists say that when they matched up genetic data from the four great apes, they found that we humans have more in common with gorillas than we think.
Dr. Aylwyn Scally was the first author of the research published in Nature and is a postdoctoral fellow at the Wellcome Trust Sanger Institute. He joins us from Hinxton in the U.K. Welcome to SCIENCE FRIDAY.
AYLWYN SCALLY: Hello, thank you.
FLATOW: How difficult was this deciphering?
SCALLY: Well, it was very difficult, partly because we don't get to - once we get the DNA from the gorilla, we didn't - we weren't able just to read that all off in one go. Effectively, what we have, the technology we have for reading DNA sequence breaks it up into very, very short fragments and many, many millions of fragments, in fact.
So putting together a whole genome assembly is really like an enormous jigsaw puzzle, and that's why it took so long.
FLATOW: Dr. Scally, you compared it then to the genomes of other apes and other gorilla species, and what did you find?
SCALLY: Well, we found obviously several things because we wanted to look - make a first look at all the different kind of things that are of interest in a genome. So we looked at evolutionary questions to see what we can say about the divergence of the great apes and how human and the other apes compare with gorilla.
We also looked at various genes all across the gorilla genome to try and see what differences there are from gorillas, chimpanzees and humans, and perhaps what some of the most important, or what things stand out.
FLATOW: Let's talk about where that divergence happens. Tell us what you found from the genome.
SCALLY: Well, the divergence between gorillas and the other two great - so the common ancestor of all four great apes, which includes orangutans, as well as humans, chimpanzees and gorillas, that was about 15 to 20 million years ago, perhaps about 15 million years.
Gorilla diverged then. So orangutan separated around then. Gorilla was then about 10 million years ago, and then there was a period when there was just the ancestors of humans and chimpanzees in one population and then gorillas in a separate one, and then subsequently humans and chimpanzee ancestors also diverged. That was about six million years ago.
FLATOW: So it's erroneous when people say we descended from the chimps. We had a common ancestor. We were not...
SCALLY: That's true. Strictly speaking, none of the animals around that time were either chimpanzee or humans necessarily. They were some sort of common ancestor of the two of them. Chimpanzees in their present form evolved over the six million years since then, as did humans.
FLATOW: 1-800-989-8255 is our number, talking with Dr. Aylwyn Scally about the gorilla genome. Anything surprise that stuck out, surprising to you that stuck out from that?
SCALLY: Well, one interesting thing is the fact that because that speciation time between gorillas and chimpanzees, although it seems like a long time, four million years, actually in evolutionary terms that's relatively short, and that means that some of the ancestry, the mixture of ancestry that was present at the time of gorilla speciation was still there when humans and chimpanzees split.
And what we see that as is in fact this 15 percent figure that you may have mentioned or that people might have seen, which is that humans are actually closer to gorillas in 15 percent of their genome, of the human genome. So overall we're closer to chimpanzees, and 70 percent of our genome is closer to chimpanzees. That's consistent with the speciation of the species tree.
But there are these regions all across the genome where the ancestry is different, and that amounts to 15 percent where humans and gorillas are closest and then another 15 percent where chimpanzees and gorillas are closest.
FLATOW: And did that surprise you, that high number?
SCALLY: Well, that number itself had been estimated from smaller amounts of sequence, just the actual magnitude of that, but what we were able to do is having the whole genome, we're able to see exactly which parts of the genome are affected by this and how - and what is the pattern of ancestry. And that tells us something about this really crucial time in human evolution when we were diverging from the - yeah, essentially just before we diverged from the chimpanzees.
It tells about the size of that population and how stable, to some extent, how much genetic diversity there was and also how strong, how important natural selection was at that time.
FLATOW: What about - speaking of natural selection, does it tell us anything about why our hearing and speech got to be better than the apes, than the gorillas or the chimps?
SCALLY: Well, we certainly - it's very hard to point to genetic changes and say exactly in many cases what's going to happen. But what we can do is look - when we look at the present-day genome sequences and compare those with what we infer about the ancestral state of those sequences, we can work out which of them have changed the most and in particular which have accumulated the most significant changes, changes that actually affect how those genes function and what the proteins they produce look like.
And we call those - and we see that, then we regard that as being genes that accelerated evolution - that have undergone accelerated evolution. And as you say, we do see that in genes associated with hearing and some other genes. What's interesting is the hearing acceleration that we see, which is in parallel in humans and gorillas, it had been seen in accelerated evolution before in humans, and people had suggested or speculated that maybe this was connected with human speech.
But of course if we see a similar parallel acceleration in gorilla, we can't conclude that it was connected with speech because as far as we know, gorillas don't talk to each other.
FLATOW: Well, not in the way - yeah, let's not go there.
(SOUNDBITE OF LAUGHTER)
FLATOW: Let's go to Gary(ph) in D.C. Hi, welcome to SCIENCE FRIDAY.
GARY: Hi, Ira, I'm calling from the District of Columbia, and I wanted to ask about mountain gorillas and lowland gorillas. Which type of gorilla was sequenced, and what's the genetic difference between the two?
SCALLY: Yes, so we sequenced a lowland gorilla, a Western lowland gorilla. So gorillas are actually divided into two species, and we - the gorilla, the female gorilla that we sequenced is a Western lowland gorilla. Mountain gorillas as actually from the Eastern species. In fact, we didn't - so we did also obtain some other gorilla - some data from another individual from an Eastern lowland species, which – Eastern lowland species, which is a closely related subspecies to the mountain gorillas.
So we don't know exactly what the situation is with mountain gorillas, but we can see that in the Eastern species, there are distinct differences. So they definitely look like a separate population that have been - that have diverged about half a million years ago. But they have - they've maintained some sort of genetic contact. They've maybe interbred a little bit since then, and the eastern species is - has a lot less genetic diversity and is undergoing - maybe is starting to suffer from defective inbreeding or may well do if its threatened status continues.
GARY: When will mountain gorillas be sequenced?
SCALLY: Well, there is now some sequence, I think, some sequencing being done. I'm not sure when that will be...
FLATOW: We lost - I think we lost our guest.
(SOUNDBITE OF LAUGHTER)
SCALLY: That was a good question.
FLATOW: Oh, are you still there? OK, I heard a click. I thought you dropped out...
SCALLY: No, no, I'm here.
FLATOW: What sorts of things - can the gorilla genome be useful? I mean, what can you do with it now? Where do you go from here now that you've sequenced it?
SCALLY: Well, yes, it's a major resource for anyone using - who wants to go on and study great ape genetics, obviously, and in particular gorilla genetics. But it's also pretty useful in looking in more detail about the processes that have been involved in human evolution and how we got from our common ancestor with the great apes and humans, as another primate, how we got from there to where we are now.
There's lots of really interesting questions that we'd like to be able to address, and in order to do that, having this comparison with our nearest relatives is a very useful and important thing to have.
FLATOW: Are there any other genome sequences that we need to have, would like to have?
SCALLY: Well, actually, to some extent it depends what time period we're interested in. For that period, you could say that this now sort of completes the picture as far as the branches, the major branches of the great ape family tree are concerned. There are - there's also the bonobo, which is a sort of a sister species of the chimpanzee, and it will be interesting to see when that happens. But by and large, we expect that to be quite similar to chimpanzee in terms of comparison with the other apes.
It would also be interesting to know about further back in time, our origins and the origins of the primates as a whole, and there's lots of other sequencing that would be very interesting to have...
FLATOW: Such as? Which primates would you like...
SCALLY: Well, we could – well, there are, in fact, some projects underway. So the sequence of the gibbon, which is the next - which is also an ape but not a great ape, that would be very interesting to have. And also some of the more distant ones like tarsiers and lemurs, very distantly related primates from ours.
FLATOW: You say - you were talking about how many years it took you. Are there newer tools now than when you started that would speed the process up a bit?
SCALLY: Well, yes, the technology does move on, and so do methods. So it's probably true that there are tools now that have changed and that sequencing has moved on. It's still going to be a very - it's still a very complicated challenge. And actually, one thing that hasn't really gotten any easier is trying to make sense of what you've got.
SCALLY: You can get to the sort of - to a certain level data maybe faster, but you've still got to - there's still a lot of wracking of brains to try and work out what it means.
FLATOW: You know, we now have this $1,000 human genome sequencing idea and processed - we don't have one for the apes yet, I'm guessing.
SCALLY: Well, we don't, but apes are so similar that it would certainly work for them as well.
FLATOW: Well, and as you say, even though we have a $1,000 human genome sequence, it could take another 50 grand to figure out what it all means.
SCALLY: Precisely, yes. Those costs tend not to come down so fast.
FLATOW: Yeah. So when do you think you'll be done with your next project, how soon?
SCALLY: Well, yeah, there's lots of things to carry on looking for. I think we want to look at more detail at that - at other great ape populations today and find out a bit more about what's going on with those species and how it - whether they interbreed and how they've separated from each other.
And we'd also like to find about - a bit more about this separation from chimpanzees that humans underwent six million years ago, how long did that take and maybe what were the actual, some of the evolutionary pressures involved.
FLATOW: Yeah, that's fascinating. And I want to thank you for taking time to be with us, and have a good weekend.
SCALLY: Thank you, it's been great to be on.
FLATOW: You're welcome. Dr. Aylwyn Scally was the first author of the research paper published in Nature. He's a postdoctoral fellow at the Wellcome Trust Sanger Institute. That's in Hinxton, U.K. I understand that's like a suburb of Cambridge. Transcript provided by NPR, Copyright NPR.