March 7, 2012

Gorilla genome offers insights into great ape and human evolution

UW Health Sciences/UW Medicine

A lowland gorilla at Seattle's Woodland Park Zoo.

The gorilla is the last genus of the living great apes to have its genome decoded. While confirming that our closest relative is the chimpanzee, the team showed that much of the human genome more closely resembles the gorilla than it does the chimpanzee genome.

This is the first time scientists have been able to compare the genomes of humans and all three living great apes: chimpanzees, gorillas and orangutans. This study provides a new perspective on human origins and is an important resource for research into human evolution and biology, as well as for gorilla biology and conservation.

Researchers at the Wellcome Trust Sanger Institute in the United Kingdom led the study, with contributions from several other institutions, including the University of Washington.

“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 the gorilla, the largest living primate,” said 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 gorilla genome assembly was compared with other great apes, including the orangutan.

Alice Gray

The gorilla genome assembly was compared with other great apes, including the orangutan.

“This finding suggests a quite rapid process of speciation and explains why it is so difficult to differentiate the three species in a very important period of our evolution,”  said Dr. Tomas Marques, who worked on this project when he was a postdoctoral student at the University of Washington and Howard Hughes Medical Institute genome science lab of Dr. Evan Eichler. “We noticed that the reconstruction of human evolution is more complex than we had anticipated.”

The researchers also called attention to fact that ear shape is one of the few external physical traits in which humans look more like gorilla than chimps.

In all three species, genes relating to sensory perception, hearing and brain development showed accelerated evolution, particularly so in humans and gorillas.

The external gorilla ear not only resembles the human ear, but the genes for hearing perception also show similarities.

Alice Gray

The external gorilla ear not only resembles the human ear, but the genes for hearing perception also show similarities.

“The study of certain categories of genes, such as those linked to hearing perception, shows that they seemed to evolved more rapidly in humans and gorillas in parallel,” said Marques. The finding is new and unusual, he said, because some of these genes had been previously linked to aspects of behavior thought to be intrinsically human.

The research team’s observations were consistent with studies showing a major role for adaptive modifications in sensory perception and brain development in hominines (great apes and human-like creatures), such as a genetic basis for blood flow modifications allowing for larger brains.

Gorillas have a gene to make a protein for the leathery texture of their knuckle pads. Gorillas often drag their knuckles when they walk.

Alice Gray

Gorillas have a gene to make a protein for the leathery texture of their knuckle pads. Gorillas often drag their knuckles when they walk.

Other genes comparatively examined were those possibly related to growth hormones, sperm function, and defense against viruses.

The researchers also mentioned that, in several cases, a genetic variation thought to cause disease in humans was associated with a normal state in gorillas.  Striking examples, they said, were variants linked to dementia and dangerously enlarged hearts in humans.

This paper 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 a long 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.

The researchers also noticed greater genetic diversity in the western versus the eastern lowland genetic samples.  This finding is consistent with the smaller population of eastern lowland gorillas, which is merely one-tenth of the 200,000 estimated living western lowland gorillas.

Two young gorillas at play. Understanding the biology of this endangered species may help protect future generations.

Alice Gray

Two young gorillas at play. Understanding the biology of this endangered species may help protect future generations.

“Because it manifests in genetic diversity, this disparity must have existed for many millennia, and cannot have resulted solely from the current pressure of human activity in central Africa or recent outbreaks of the Ebola virus,” the authors surmised.

In the Middle Miocene epoch many kinds of great apes lived throughout Europe, Asia and Africa.

Since then, the authors note, the story of great ape evolution has told of fragmentation and extinction. People are the only remnant of the genus Homo. All of the other human-like primates vanished.

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 provides new information about human evolution, but also highlights the importance of protecting and conserving the full diversity of the few remaining great ape species, the researchers said.

“As well as teaching us about human evolution,” the authors wrote, “the study of great apes connects us to a time when our existence was more tenuous, and in so doing, teaches us the importance of protecting and conserving
these remarkable species.”

What do we see in ourselves in looking at the great apes?

Alice Gray

What do we see in ourselves in looking at the great apes?

“Our research completes the genetic picture for overall comparisons of the great apes,” said 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 paleontologists 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.”

The UW’s role in this project was to use previous knowledge of the great ape genomes to assess the quality of the gorilla genome assembly, especially in the more complex regions that are difficult to annotate. The UW researchers also applied their experience in studying the composition of structural variations in the gorilla genome to other great apes and humans, and to comparing the rates of variations among gorillas and humans.

The Nature report is titled, “Insights into hominid evolution from the gorilla genome sequence.”

In addition to Marques and Eichler, other present and recent UW researchers on the project were Dr. LaDeana W. Hillier, UW assistant professor of genome sciences, and former postdoctoral student Dr. Can Alkan. Hillier’s primary role was organizing the whole gorilla genome shotgun sequence assembly into ordered and oriented gorilla chromosomes. The Eichler lab helped with analyzing duplicated sequences within the gorilla genome and comparing gorilla DNA sequences with those in the human and other great ape genomes.