One percent of humanity

Human DNA is almost 99% identical to that of the chimpanzee. Which regions of the genome are included in the one percent that makes us human, what are they responsible for and why exactly did they develop differently? And how is it that so little genetic material causes the formation of so many different species?

By: Catherine S. Pollard, Scientific American

Six years ago I had the opportunity to join an international team that was involved in identifying base sequences or DNA "letters" in the genome of the chimpanzee (Pan troglodytes). As a biostatistician who has been interested in human origins for a long time, I wanted to compare the human DNA sequence to that of the animal closest to us today and find the differences.

The result filled me with humility: it turned out that the human DNA is almost 99% identical to that of the chimpanzee. In other words, of the three billion letters that make up the human genome, only 15 million, that is, less than 1%, have changed in the 6 million years since humans and chimpanzees parted ways.

According to the theory of evolution, most of these changes hardly affected our biology, and yet - among the 15 million bases that changed lies the difference between us and the chimpanzees. I was determined to find them. Since then my colleagues and I have made considerable progress in identifying some of the DNA sequences that make us human.

An early surprise

The millions of bases in question constitute only a small proportion of the total genetic load, but their number is still enormous. To make the search easier, I wrote software that will scan the human genome and locate in it the pieces of DNA that have undergone the greatest change since the human and chimpanzee species split from their common ancestor.

Since, for the most part, random genetic mutations are neither harmful nor beneficial to the organism, they accumulate at a uniform rate that reflects the amount of time that has passed since two biological species separated from their common ancestor (many call this rate the "ticking of the molecular clock"). But an accelerated rate of change in a certain region of the genome is a clear sign of positive selection, that is, a situation where a mutation that helps a certain species survive and reproduce has a higher chance of being passed on to future generations. Or in other words, it is likely that the parts of the genome that have changed to a greater extent since the human species and chimpanzees separated are the ones that have shaped man the most.

In November 2004, after months of tweaking and improving the software so that it could run on a large computer cluster at the University of California, Santa Cruz, I finally obtained a file that ranked the sequences that had undergone accelerated change. My instructor, David Hausler, was standing behind me looking at the results, as my eyes rested on the sequence that appeared at the top of the list. It was a 118-base segment known as human accelerated region 1 (HAR1). When I discovered this I looked up what HAR1 was with the University's Genome Browser, a visual tool that uses information found in public databases.

The browser displayed the human HAR1 sequence as well as the same sequence in the chimpanzee, mouse, rat and chicken, all vertebrates whose genomes had already been deciphered by then. It also turned out that in two large scanning experiments, HAR1 activity was detected in two human brain samples, but the scientists had not yet studied the sequence or given it a name. "Giant!" We shouted in perfect coordination, when we realized that the HAR1 sequence may turn out to be part of an active shield in the brain that has not yet been studied.

We won the whole jackpot. It is known that the human brain is very different from the chimpanzee brain, among other things in its size, arrangement and complexity. But the evolutionary and developmental mechanisms that distinguish the human brain have not yet been properly understood. The HAR1 sequence may have shed light on this mysterious facet of human biology.

We spent the next year trying to learn as much as we could about the evolutionary history of the HAR1 sequence by comparing this region of the genome in several species, including 12 other vertebrates whose genomes were mapped at the time.

It soon became clear that until humans appeared, the HAR1 sequence evolved very slowly. There is a difference of only two bases between this sequence in the chicken and that of the chimpanzee, two species whose evolutionary paths diverged about 300 million years ago, in contrast, there is a difference of 18 bases between the human and the chimpanzee, whose paths diverged much less recently. The very fact that the HAR1 sequence remained frozen for hundreds of millions of years shows the importance of its role, and the fact that this sequence underwent a sudden change in humans points to a serious turn that occurred in this role during human development.

In 2005 we got a big hint as to the role of the HAR1 sequence in the brain, when my colleague Pierre van der Hagen from the Free University of Brussels received a test tube of HAR1 copies from our laboratory while visiting Santa Cruz. Using these DNA sequences, he genetically engineered a fluorescent molecular marker that emits light when the HAR1 sequence is activated in living cells, that is, when it is transcribed from DNA to RNA (RNA).

When typical genes are activated in a cell, the first thing the cell makes is a mobile copy of a messenger RNA, and then uses that RNA as a template to make the protein it needs at that moment. Thanks to the fluorescent marking, it was discovered that the HAR1 sequence is active in a type of nerve cells that play an important role in creating patterns and organization during the development phase of the cerebral cortex - the wrinkled outer layer of the brain. When these neurons do not function properly, a serious and even fatal congenital disorder develops: smooth brain syndrome, in which the cerebral cortex lacks its characteristic folds, so that its surface area is much smaller. Dysfunction of these nerve cells is also associated with schizophrenia in adults.

It therefore turns out that the HAR1 sequence is active at exactly the time and place that make it an essential component in the development of a healthy cerebral cortex (other evidence points to an additional role of the sequence in sperm production). However, my colleagues and I have not yet been able to understand exactly how this part of the genetic code affects the development of the cerebral cortex. We have good reason to engage in this with full vigor: it is possible that the burst of changes that has recently hit the sequence has changed our minds considerably.

Clues in language
When we compared whole genomes of other species we were also able to understand why humans are so different from chimpanzees, despite the great similarity between their genomes. In recent years, the genomes of thousands of species (mostly microorganisms) have been mapped. It turns out that the location of the substitutions of bases in DNA is much more important than the number of substitutions in any genome. In other words, you don't need to change many details in the genome to get a new species. The path to the development of man from the common ancestor to man and chimpanzee did not require the speeding up of the entire molecular clock, but rather the creation of rapid changes in areas that would lead to a noticeable difference in the functioning of the organism.

The HAR1 sequence is certainly such a region. So did the FOXP2 gene, in which I identified another rapidly changing sequence. Researchers from the University of Oxford in England discovered that this sequence is related to speech. In 2001, they reported that humans suffering from a mutation in this gene are unable to make the subtle and rapid facial movements necessary for speech, even though they possess the cognitive ability needed to process language.

There are several differences in the typical human sequence compared to the same sequence in the chimpanzee: two base substitutions that changed the protein that the gene encodes, and many more substitutions that probably led to a change in the way, when and where the human body uses this protein.

We also recently discovered when the version of the FOXP2 gene that enables speech first appeared in hominids. In 2007, scientists at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, mapped the FOXP2 gene isolated from a fossil of a Neanderthal man and found that in this extinct human species the gene had already appeared in its modern version, in a way that perhaps allowed him to pronounce words like us.

Estimates of the date of separation of the human and Neanderthal lineages show that the modern version of the FOXP2 gene appeared at least half a million years ago. But the main difference between human language and vocal communication among other species lies not in physical structure, but in cognitive ability, which is often related to brain size. The brains of primates are often larger than expected based on their body size, but the volume of the human brain has increased more than threefold since the time of the common ancestor of humans and chimpanzees. Geneticists are only now beginning to understand this sudden growth.

An example of a gene responsible for brain size in humans and other animals, and which has already been studied in depth, is the ASPM gene. Genetic tests conducted among people with microcephaly, a disease in which the brain is 70% smaller than normal, revealed that the ASPM gene, as well as three other genes: MCPH1, CDK5RAP2 and CENPJ, control brain size.

Recently, researchers at the University of Chicago and the University of Michigan in Ann Arbor have even demonstrated that the ASPM gene underwent several bursts of variation during primate evolution, a pattern indicating positive selection. At least one of these bursts of change occurred in the human lineage after it split from the chimpanzee, so it is possible that it served as an important component in the development of our great brain.

There are other regions of the genome that may have influenced the development of the human brain less directly. The same computer scan that led to the identification of the HAR1 sequence also found 201 other regions whose variation was accelerated in humans, most of which do not code for proteins or even RNA (a parallel study to ours, conducted at the Wellcome Trust Sanger Institute in Cambridge, England, discovered many of the same HAR sequences). These are control sequences that tell the genes when to act.

Surprisingly, more than half of the genes located near those HAR sequences are involved in the development and function of the brain. And as happens with the FOXP2 gene, the products of these genes also participate in the control of other genes. So, despite the relatively small portion of HAR sequences in the entire genome, the mutations that occurred in them could have brought about a profound change in the human brain by influencing the activity of entire gene networks.

Beyond the mind

A lot of effort has been invested in studying the evolution of our sophisticated mind, but there are also scientists who study the development of other aspects of the human body. The HAR2 sequence, a gene control region that ranks second in the list of sequences whose development has been accelerated, is a good example of this.

In 2008, researchers from the American Lawrence Berkeley Laboratory compared the human version of the HAR2 sequence (also known as HACNS1) and a version found in non-human primates. They demonstrated that differences in certain bases allow this sequence to activate genes in the wrist and thumb region during embryonic development, as opposed to an older version present in other primates. This finding is particularly exciting, because it may explain the formal changes that have occurred in the human hand, which allow us to use our hands for the production and use of sophisticated tools.

Besides structural changes, our ancestors also experienced behavioral and physical changes that helped them adapt to different conditions and migrate to new environments. The beginning of the use of fire more than a million years ago, for example, as well as the agricultural revolution 10,000 years ago, allowed us greater access to starchy foods. But cultural changes are not enough to allow us to utilize such energy-rich foods. Our ancestors had to adapt to the new diet also genetically.

A well-known example of this is provided by the changes in the AMY1 gene, which encodes the production of amylase, an enzyme that helps digest starch, in the salivary glands. Multiple copies of this gene appear in the DNA of mammals, and the number of copies varies from species to species and even between different humans. But in general, humans have especially many copies of this gene compared to other primates. Geneticists from the University of Arizona discovered in 2007 that the saliva of people who carry more copies of AMY1 contains more starch, so they can digest more starch. It therefore seems that the evolution of the AMY1 gene is related both to the number of copies of the gene and to specific changes in its DNA sequence.

Another well-known example of nutritional adaptation is related to the gene encoding lactase (LCT), an enzyme that allows mammals to digest lactose, a carbohydrate known as "milk sugar". In most mammalian species, only weanlings are able to digest lactose. But about 9,000 years ago, not long ago in evolutionary terms, changes in the human genome created versions of the LCT gene that also allow adults to digest lactose.

The changes in the LCT gene developed separately in Europe and Africa, and allowed the carriers of the gene in its new version to digest dairy products from domesticated sheep and cattle. Today, the descendants of these ancient shepherds have a greater chance of being able to digest lactose compared to adults who come from other parts of the world, such as Asia and South America, where many suffer from sensitivity to milk because the ancient version of the gene still exists in their bodies.

It is known that the LCT gene continues to develop in humans today, but it is not the only one. In the chimpanzee genome project, we were able to identify 15 additional genes that are currently in the process of moving away from the version that worked well in our ape ancestors and other mammals, but in modern humans is associated with diseases such as Alzheimer's and cancer.

Some of these diseases affect only humans, or occur in humans at a higher rate than in other primates. Scientists are currently investigating the functions in which these genes are involved, and trying to understand why their ancient versions are involved in human disorders. These studies could help doctors identify patients who are at a higher risk of developing these deadly diseases, hopefully leading to a cure for the plague as well as discovering new treatments for them.

To her and a thorn in her

Man, like any biological species, has always defended himself against diseases in order to pass on his genetic load. Particularly clear evidence of this struggle is found in the immune system. When researchers look for positive selection in the human genome, the most obvious candidates are vaccine-related genes. It is no wonder that evolution is so busy improving these genes: in the absence of antibiotics and vaccines, it is likely that the obstacle that an individual will face trying to transfer his genetic load to the next generation is a deadly infection that could harm him before the end of his fertile years.

Another factor that accelerates the development of the immune system is the adaptation of the disease agents themselves to it, which leads to an evolutionary arms race between microorganisms and the animals that suffer from them.

These struggles leave their mark on our DNA. This is especially true for retroviruses, such as the AIDS virus, HIV, which survive and multiply by inserting their genetic material into our DNA. The human genome is multiplied by dozens of copies of short retroviral DNA, many of which belong to viruses that caused diseases millions of years ago and that no longer exist.

Over time, the retroviral sequences accumulate random mutations, just like any other sequence, so that the resulting different copies are similar, but not identical. If we check the degree of variation between the copies, we can use the molecular clock technique to date the original retroviral infection. The scars left by these ancient infections can also be seen in the genes of our immune system, which have had to change frequently to adapt to combat the ever-changing retrovirus.

The PtERV1 virus is one such ancient found species. In modern man, a protein called TRIM5α is used to prevent the retrovirus PtERV1 and its like from growing. The genetic evidence indicates that chimpanzees, gorillas and prehistoric humans suffered from the PtERV1 plague that hit Africa four million years ago.

To understand how different primates reacted to this virus, researchers at the Fred Chinson Cancer Research Center in Seattle used the many copies of PtERV1 that underwent random mutations in the chimpanzee genome to reconstruct the original genetic sequence and recreate the ancient retrovirus. They then performed experiments to determine how successfully the TRIM5α gene could limit the activity of the resurrected virus.

Their results show that one change in the human TRIM5α gene likely allowed our ancestors to fight the PtERV1 virus more successfully than our primate cousins ​​(it is possible that other changes in the human TRIM5α gene evolved in response to similar retroviruses). In other primates, other changes in the TRIM5α gene appear, in a way that probably reflects the struggles in which their own ancestors defeated the virus.

Defeating one type of retrovirus does not necessarily guarantee success in the fight against other retroviruses. Although the mutations in the TRIM5α gene helped us survive the PtERV1 plague, the same mutations make it really difficult for us to fight the AIDS virus. This finding helps researchers understand why HIV causes AIDS in humans, but not in other primates. If so, it turns out that evolution can go one step forward and two steps back, and the same is true in scientific research. We have identified many exciting candidates for explaining the genetic basis of unique human traits, but in most cases we know only the most basic facts about these genetic sequences. The gaps in our knowledge are particularly deep in non-protein coding regions such as HAR1 and HAR2.

These sequences, which are unique to humans and develop in an accelerated manner, outline the way for further research. The plot of the process of us becoming human will probably not focus on our building blocks, the proteins, but on the new way in which evolution assembled these building blocks in the body by creating permutations in the timing of the activation of various genes. Experimental and computational studies are currently being conducted in thousands of laboratories around the world, and promise to clarify for us what is happening in that percentage of the genome, which distinguishes us from chimpanzees.

Catherine S. Pollard is a biostatistician at the University of California, San Francisco. The full article was published in Scientific American magazine - Israel

How is man different?

• The sequence HAR1 - active in the brain, probably having a decisive role in the development of the cerebral cortex, an especially large organ in humans. Probably also related to sperm production
• The sequence FOXP2 - helps in pronouncing words, thus enabling speech in the modern man
• The sequence AMY1 – helps digest starch, which probably helped early humans to use new types of food
• The HAR2 sequence - activates genes that control the development of the wrist and thumb, in such a way that it is probably possible for the human hand to produce and use sophisticated tools
• The LCT sequence - enables the digestion of lactose in adults, thus raising the milk products from sheep and cattle to the status of a basic food

On the same topic on the science website

• On the origin of religion and why chimpanzees are smarter than humans
• Human evolution continues
• A scientist from the Weizmann Institute participates in the decoding of the chimpanzee genome - the difference from humans is 1.2%