7 March 2012
What have we got in common with a Gorilla?
An insight into human evolution from the gorilla genome sequence
Researchers announce today that they have completed the genome sequence for the gorilla - the last genus of the living great apes to have its genome decoded. While confirming that our closest relative is the chimpanzee, the team show that much of the human genome more closely resembles the gorilla than it does the chimpanzee genome.
Dr Aylwyn Scally
PLAYTranscript
The gorilla genome sequence that we've made freely and publicly available is a resource for all scientists, all researchers around the world to use, comes entirely from one individual.
It's a female western lowland gorilla - her name is Kamilah - she lives in San Diego Zoo. And her DNA was sampled and sequenced into short fragments, and then assembled on computers here at the Sanger Institute. And that forms the basis for the sequence assembly.
We sequenced the gorilla genome partly because gorillas are fascinating animals in their own right. They are the largest living primates, they've been an iconic animal ever since they were first discovered and they certainly represent something unique, almost, in the animal kingdom from our perspective.
But obviously the real interest in gorillas is their evolutionary closeness to us. They are the second closest evolutionary cousins to us, after chimpanzees. And so sequencing them, understanding the content of their genome, tells us quite a lot about our own evolution, about the biology of the great apes in general, and how we fit in to that picture of great ape evolution.
If you go back about 15 to 20 million years or so, it was the golden age of apes: the Miocene area. All across Asia and Africa there was just the right kind of open forest environment. There were lots of different species of ape and our ancestors were quite plentiful, as far as we can tell. But, since that time, all kinds of geophysical changes have occurred and the apes, in general, have really fragmented. They've gone into smaller populations, species have gone extinct and what we are left with now - the legacy of the great apes - all the four great ape species are really living in isolated populations mostly in equatorial forests, either in Africa or the orang-utans in south-east Asia. Humans are obviously the exception, in that we are now all over the world and we are living in places where there was no previously... primate was ever possible to live. It's quite likely that, if you go back 100,000 years, our own - the picture of humans - looked quite similar to the way the great apes look now, which is close to extinction.
When you do look at a copy of a gene in human and a copy of a gene in gorilla: some of those genes we actually have some of idea about what they do in humans, there are lots of places where we really don't yet. And one of the reasons that we study other animals is to try to inform us of that. There is an example, a gene that is strongly associated with dementia in humans for which, in all of the gorillas we sequenced, this mutation - this dementia-associated mutation - does exist. And so it is interesting to wonder how can they survive with this, when in humans this is a very bad idea, this is a very bad thing for us. And there are all kinds of possible explanations.
One would be that somewhere else in the genome, in the gorilla genome, there is a compensating change which effectively neutralises the effect of this mutation that we don't have in humans. Humans don't have this compensating change. Or, if we did, it would have other problems.
Another possibility, however, is that simply gorillas live in an environment where this mutation, due to perhaps the things they eat or the things they do, perhaps this mutation doesn't have the effect that it would in humans.
Gorillas are unique in that the two events - the speciation of humans from chimpanzees and the gorilla speciation event - were very close in time. That means that, actually, having this sequence tells us a lot about that really crucial period in our own evolution when diverged from our closest evolutionary cousins.
So, in most places, in about 70 per cent of the genome, humans and chimpanzees look more similar to each other, basically, at the genetic level. But actually the other 30 per cent that's not true. It's either the case that humans are closer to gorillas or chimpanzees are closer to gorillas.
An interesting example is in hearing genes where we can see that, comparing with chimpanzee, humans had shown quite a lot of evolutionary acceleration in these genes. In other words, there were quite a lot of changes that seemed to have an important effect on how human hearing works. And there had been some suggestions, some ideas that that was maybe connected to the development of important things like speech in humans.
But actually, it looks like gorillas share some of these changes too and yet, as far as we can tell, gorillas don't talk to each other. So maybe that isn't the explanation, not that it isn't obviously important - that there aren't important things that have occurred in the hearing of both animals - but, perhaps, not something that is uniquely human.
This is the first time scientists have been able to compare the genomes of all four living great apes: humans, chimpanzees, gorillas and orang-utans. This study provides a unique perspective on our own origins and is an important resource for research into human evolution and biology, as well as for gorilla biology and conservation.
"The gorilla genome is important because it sheds light on the time when our ancestors diverged from our closest evolutionary cousins. It also lets us explore the similarities and differences between our genes and those of gorilla, the largest living primate," says Aylwyn Scally, first author from the Wellcome Trust Sanger Institute. "Using DNA from Kamilah, a female western lowland gorilla, we assembled a gorilla genome sequence and compared it with the genomes of the other great apes. We also sampled DNA sequences from other gorillas in order to explore genetic differences between gorilla species."
The team searched more than 11,000 genes in human, chimpanzee and gorilla for genetic changes important in evolution. Humans and chimpanzees are genetically closest to each other over most of the genome, but the team found many places where this is not the case. 15% of the human genome is closer to the gorilla genome than it is to chimpanzee, and 15% of the chimpanzee genome is closer to the gorilla than human.
Kamilah. [San Diego Zoo]
In all three species, genes relating to sensory perception, hearing and brain development showed accelerated evolution - and particularly so in humans and gorillas.
" The gorilla genome is important because it sheds light on the time when our ancestors diverged from our closest evolutionary cousins. "
Dr Aylwyn Scally
"Our most significant findings reveal not only differences between the species reflecting millions of years of evolutionary divergence, but also similarities in parallel changes over time since their common ancestor," says Dr Chris Tyler-Smith, senior author from the Wellcome Trust Sanger Institute. "We found that gorillas share many parallel genetic changes with humans including the evolution of our hearing. Scientists had suggested that the rapid evolution of human hearing genes was linked to the evolution of language. Our results cast doubt on this, as hearing genes have evolved in gorillas at a similar rate to those in humans."
This research also illuminates the timing of splits between species. Although we commonly think of species diverging at a single point in time, this does not always reflect reality: species can separate over an extended period of time.
The team found that divergence of gorillas from humans and chimpanzees occurred around ten million years ago. The split between eastern and western gorillas was much more recent, in the last million years or so, and was gradual, although they are now genetically distinct. This split is comparable in some ways to the split between chimpanzees and bonobos, or modern humans and Neanderthals.
"Our research completes the genetic picture for overall comparisons of the great apes," says Dr Richard Durbin, senior author from the Wellcome Trust Sanger Institute, "After decades of debate, our genetic interpretations are now consistent with the fossil record and provide a way for palaeontologists and geneticists to work within the same framework.
"Our data are the last genetic piece we can gather for this puzzle: there are no other living great ape genera to study."
Gorillas survive today in just a few isolated and endangered populations in the equatorial forests of central Africa. They are severely threatened and their numbers are diminishing. This research not only informs us about human evolution, but highlights the importance of protecting and conserving the full diversity of these remarkable species.
Notes to Editors
Publication details
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Insights into hominid evolution from the gorilla genome sequence.
Nature 2012;483;7388;169-75
PUBMED: 22398555; PMC: 3303130; DOI: 10.1038/nature10842
Funding
Refer to paper for list of funding agencies.
Participating Centres
Refer to paper for list of participating centres.
The Wellcome Trust Sanger Institute
The Wellcome Trust Sanger Institute is one of the world's leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease.
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The Wellcome Trust
The Wellcome Trust is a global charitable foundation dedicated to achieving extraordinary improvements in human and animal health. We support the brightest minds in biomedical research and the medical humanities. Our breadth of support includes public engagement, education and the application of research to improve health. We are independent of both political and commercial interests.
