Differences between human and Chimpanzee genome are bigger than thought

During the last decade it was commonly accepted that humans and our closest living relatives, chimpanzees, only differed by 1.24 % in our DNA sequences. This discovery shows that this figure is absolutely incorrect and, what is more, may be ten times higher. Nature magazine is to publish this important scientific discovery in a special issue on the occasion of the two hundredth anniversary of Charles Darwin's birth.

Toms Marqus-Bonet, investigador de l'IBE The essential point of the discovery has been the study of segmental duplications; big DNA fragments repeated many times along the genome that were difficult to distinguish until recently. As a result of this difficulty, these fragments were ignored and parts of the genome easier to individualise were studied, leading to a partial view of it.

  Scientists have suspected for a long time that the presence of duplica  tions may be important, but only the systematic study of the segmental duplications of the whole genome of four primate species (macaques, orangutans, chimpanzees and humans) has allowed the advance published at Nature. Thus, it has been possible not only to elaborate the first species-specific catalogue of these regions of the genome, but also to quantify much better the existing differences between different species and understand at which moment of the evolution of our lineage there appeared things that would help to understand many unique diseases of our species.

Toms Marqus-Bonet, researcher on the Marie Curie exchange programme in the Evolutionary Biology Institute (IBE) - a mixed research centre of the Universitat Pompeu Fabra and the CSIC - has coordinated the international team that, directed by Evan E. Eichler, from Washington University (Seattle, USA) and in collaboration with Arcadi Navarro (ICREA-IBE Barcelona), has made this important scientific discovery.

Humans and primates are qualitatively different 

It must be highlighted that the identified duplicated regions of the genome represent qualitatively different evolutive innovations. The differences with which scientists had been working until now were changes (mutations) in the DNA sequence that codified for genes shared by all primates. It was like having two different editions of the same book.

 Arcadi Navarro, investigador de l'Institut de Biologia Evolutiva (UPF-CSIC)The differences studied by researchers at IBE are radical differences in each species' library: they are complete collections of books that some organisms have and others don't. They are unique differences for each species.

Segmental duplications are fragments of the genome from thousands to millions of nucleotides long which, due to very complex molecular mechanisms, have been duplicated. This is to say that, at certain moments of evolution, multiple copies were made and gradually inserted in different parts of the genome. As duplications can be very big, they may contain complete genes many times over. Copies of these genes that are, in principle, identical, could specialise (by acquiring little mutations) until they become completely different from each other.

That is how most unique genes from a particular species are generated: by duplication and later specialisation. All these new genes can perform new functions that, of course, will be exclusive to the species which has these genes.

Toms Marqus and Arcadi Navarro have said that "we also know that duplications predispose the genome to reorganize itself, to experience great structural changes (as if we made different constructions with Lego bricks) and this can result in certain diseases (such as autism, schizophrenia or mental retardation). Duplication of genes doesn't mean anomaly, but variation and innovation. Innovations that, depending on the case, can be favoured by natural selection or become pathological".

A specialization that started six million years ago

Another important aspect of the investigation is that it has succeeded in dating the period in which there were most duplications.

It was 8-12 million years ago, just before the separation of the lineages of humans and chimpanzees (which took place approximately six million years ago), which implies that all the genes that had just appeared have gradually acquired new characteristics in the course of the six million years that humans and chimpanzees have been evolutively separate.

Researchers have stated that "it is maybe thanks to this radical type of mutation that humans succeeded in adapting ourselves to our environment. Maybe it is in this wide ocean of differences where we have to look for the ‘humanity genes' or the genes that cause certain diseases typical of our species. We still don't know, but we are working on it".

The research line opened up by this important work is to find out which are the regions of the genome that differ between different individuals of the same species and study some specific cases in detail.

This figure shows how human, chimpanzee and gorilla genomes differ more than thought. In this example, we can see the extreme case of a duplication that has expanded (has increased its number of copies) in the chimpanzee and gorilla genomes, while remaining stable in the human genome, where it is represented by a single copy. The green arrows and the circle mark the position of the ancestral copy. The red arrows show where the new copies created in the chimpanzee and gorilla genomes are located.


Reference work:

Toms Marqus-Bonet; Jeffrey M. Kidd; Mario Ventura; Tina A. Graves; Ze Cheng; LaDeana W. Hillier; Zhaoshi Jiang; Carl Baker; Ray Malfavon-Borja; Lucinda A. Fulton; Can Alkan; Gozde Aksay; Santhosh Girirajan; Priscillia Siswara; Lin Chen; Maria Francesca Cardone; Arcadi Navarro; Elaine R.Mardis; Richard K. Wilson; Evan E. Eichler. "A burst of segmental duplications in the genome of the African great ape ancestor", Nature (12 th February 2009).