Chimpanzees and Us: How Genetic Evidence Reveals Shared Ancestry

We share common ancestry with chimpanzees. And the shared ancestry becomes not only obvious in the anatomy but also in the DNA level. Today, let’s set out on a journey to explore the connection with our closest relatives. In our search for proof of an ancestral link with our fellow cousins, the chimpanzees, let’s methodically examine the most minute details at the intracellular level. 

In this article, we will dive into unraveling the secrets hidden within our bodies in a journey that tells millions of years of history. Our investigation will go deep into our DNA’s enormous informational storehouse, giving us a window into our distant history. We’ll explore the genetic archives to learn about early viral infections’ history and carefully examine the viruses’ fossilized remains. In our discussion today, we will search for evidence of our kinship with chimpanzees at the genetic level, which includes:

  • Conservation of the Nanog protein gene
  • Fused chromosome-2
  • Conservation of beta-globin gene mutations
  • Human endogenous retroviruses (HERV), a witness to ancient infections.

Conservation of the Nanog Protein Gene

Let’s start our journey through Celtic mythology.

Once upon a time, somewhere in the earth, there existed a remarkable waterfall, unparalleled in its grandeur, surpassing even the mightiest seas and vast oceans, dwarfing the most extensive forests and jungles – and that majestic cascade was known as “Nanog” (na nÓg). Legend had it that the waters of this extraordinary waterfall possessed a unique property: the gift of immortality. Its touch was believed to bestow everlasting life upon those fortunate enough to experience it.

Indeed, humankind has pursued the existence of such a mystical waterfall, even though its elusive nature defied discovery. While the legendary Nanog of Celtic mythology remained beyond reach, however, there exists a realm of intrigue within a mysterious domain, which is akin to eternal youth unfolding – the world of stem cells.

Where does this extraordinary world reside?

Within the very core of your being – inside your cells, lies a minuscule universe waiting to be explored. Allow yourself to dive deep into the nucleus, the heart of the cell, and venture forth to discover the intricate web of chromatin fibers. These fibers play a vital role in distributing essential information during cell division. And now, focus your quest on chromosome 12, for it is here that the captivating journey of the “Nanog” gene commences. This particular gene, like a legendary artifact hidden within the cell’s blueprint, possesses the wondrous power to preserve and regulate the youthful potential of stem cells. Here begins the journey of the “Nanog” gene!

Structure of Nanog. Source: Wikipediea

The Nanog protein serves as a significant historical clue, offering a type of evidence that connects us to our closest ancestors from the bygone era.

The Nanog gene exists on chromosome 12. It preserves the youthfulness of stem cells. In our vast genome with millions of codes, a thorough investigation revealed that besides the Nanog gene on chromosome 12, 11 fragmented pseudo-Nanog processed pseudogenes are scattered. These processed pseudogenes earned their name due to mutations that rendered them incapable of producing functional proteins. Instead, they are mere remnants of their once-active counterparts, now silently scattered across various chromosomes – chromosomes 6, 7, 9, 10, 12, 14, 15, and X.

What intrigues researchers is the seemingly haphazard dispersion of these 11 genes on the chromosomes. Their distribution appears entirely random, lacking any discernible pattern or order. Now, a compelling question arises: how did these broken Nanog pseudogenes exist?

Let’s explain it in simple terms.

The Nanog gene on chromosome 12 underwent mutations during DNA replication and created another inactivated gene nearby. This newly processed pseudogene stays right beside the active Nanog gene on the same (chromosome 12). Then, it scatters in the rest of the chromosomes in a complicated process. In this way, numerous processed pseudogenes of Nanog are present in different places across chromosomes, including the eight other chromosomes mentioned above. [1]

Now, surprisingly, when the chimpanzee’s genome was searched, it was found that these pseudogenes are scattered in the same locations as in humans! They are found in Chromosome-6, 7, 9, 10, 12, 14, 15, and Chromosome X. The locations of these chromosomes are the same as in humans! In both cases, there is a 100% match!

Only when humans and chimpanzees have shared ancestors is this perfect match feasible. This has an unavoidable cause. Only when humans and chimps descend from the same ancestor can this specific incidence of these pseudogenes occur. 

The explanation for this is that these processed pseudogenes could only have appeared randomly in the body of one organism. These pseudogenes can only be discovered in the same places on the chromosomes of humans and chimpanzees when their ancestors originated from the same lineage. Furthermore, there was no alternative way for it to have occurred. [2][3]

Fused Chromosome-2

Do you know how many chromosomal pairs there are in humans? 23 pairs. Other Great apes, including chimpanzees, however, have 24 pairs.

So, are we unique?

No, we are not unique. We, too, should have had 24 pairs of chromosomes. But, our chromosome-2 is actually the fusion or combination of two chromosomes head to head. So, what happens when two chromosomes fuse?

  1. The presence of two centromeres (two centers). Our chromosome-2 does have two centromeres, one of which is functional.
  2. The fusion of two telomeres together. Chromosome-2 in humans also has two telomeres fused. This is the fusion site of the two chromosomes, precisely identified as 11,236,928 base pairs from the end.

It appears we should have had 24 pairs of chromosomes. However, due to a complex rearrangement through a Robertsonian translocation after the divergence of chimpanzees and our common ancestor, the fusion of two chromosomes occurred, resulting in today’s Chromosome-2. The genetic sequence of Chromosome-2 in the human body is the same as the combined chromosomes in chimpanzees. [4]

The fusion of these two chromosomes in our ancestors after their split from chimpanzees is beyond dispute, as it has been extensively researched and widely accepted in the scientific community.[5][6] This discovery is a significant testament to the evolutionary connection between humans and chimpanzees, providing compelling evidence of our shared history.

In the peer-reviewed journal, Proceedings of the National Academy of Sciences (PNAS), in the research paper titled “Origin of Human Chromosome-2: An Ancestral Telomere-Telomere Fusion,” Jaco W. Ijdo states,

“We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2.” [7]

Beta Globin Gene Mutation Preservation

Now let’s delve deeper into this molecular realm. Explore and discover how much history is written. Within the human genome, a fascinating cluster known as the beta-globin cluster comprises five genes arranged sequentially. These genes play a crucial role as the secondary chain of hemoglobin, commencing from the fetal stage and continuing through various developmental phases. Interestingly, nestled within this genomic region lies a segment similar to the beta chain gene called a “pseudo-gene.” As previously mentioned, this particular gene earns the prefix “pseudo” due to its inability to generate any functional protein due to mutations. Intriguingly, the chimpanzee genome harbors an identical pseudo-gene within the same segment.

Structure of Beta Globin gene. Source Wikipedia

Moreover, the human and chimpanzee pseudo-genes bear a striking resemblance, and the human pseudo-gene exhibits two nucleotide substitutions and one nucleotide deletion, precisely mirrored in the corresponding chimpanzee pseudo-gene.

This genetic parallelism extends beyond the beta-globin gene. For instance, in the production of Vitamin C, a pivotal nutrient for many organisms, a mutation in the GLO (or GULO) gene plays a significant role. However, primates in the Strepsirrhini suborder, including lemurs, can reportedly produce this vitamin. Unfortunately, humans and chimpanzees have lost the ability to synthesize Vitamin C due to such mutations.

The presence of identical mutations in the genomes of humans and chimpanzees, who share a common ancestor, shows how conserved these signs of mutations are! [8]

Human Endogenous Retroviruses (HERVs), a Witness of Past Infections

Now let’s examine evidence related to Endogenous Retrovirus DNA, which inevitably clarifies why humans and chimpanzees have emerged from a common ancestor!

What are Retroviruses?

Retroviruses are a special type of virus that promotes heredity by injecting their genes into the DNA of other cells. This is called horizontal gene transfer. Once the virus enters the host cell, it becomes a permanent part of its DNA. When the host cell divides, the viral DNA is also divided. Retroviruses typically infect the germ cells of mammals, which produce the sperm and the egg. When these germ cells are fertilized, the virus is transferred to the offspring and in every cell of the offspring as well. In subsequent generations, this virus is passed on. Every individual of that species becomes dependent on that particular virus for its reproduction. Without it, reproduction becomes impossible. The DNA of almost all primates, including humans, carries this permanent part of the virus. Scientists named it Endogenous Retrovirus (ERV) because it is present in our cells from birth. [9]

Shared ERVs among different lineages. Source The Scientist

The human genome carries thousands of ERV segments. About 8% of our DNA is made up of retroviral DNA. Today, these viruses are present in our cells because they infected our ancestors. It can be considered a kind of historical record.

Researchers have petrified and incubated human cells, and a very small amount of the cell’s Endogenous Retrovirus DNA has been mutated. This was the subject of exploration – could these DNA sequences revive the ancient virus? Astonishingly, these long-lost ancient viruses have indeed been revived! [10]

Now, let’s see how these endogenous retroviruses connect us with chimpanzees.

If it is true that humans and chimpanzees share a common ancestor, and if retroviruses infected that ancestor, then the genomes of present-day humans and chimpanzees should contain these viruses in the same locations of their genomes. Otherwise, it would be impossible for these viruses to be in the same places in their genomes if they didn’t come from a common ancestor.

Why is it impossible?

The first reason is that when retroviruses infect a host, their DNA can end up in many places in the host’s genome. Studies have shown that the human genome contains around 10 million insertion spots of retroviruses. [11][12][13]

As a result, if the same virus independently infected a human and a chimpanzee, the chance of the virus ending up in the same spot in both of their genomes would be approximately 1 in 100,000,000. Now imagine that independently these two species had 12 viruses that entered their genomes. Then the chance of these viruses ending up in the same spot in both of their genomes would be 1 in the observable universe. [14]

When the genomes of humans and chimpanzees were scanned, 211 retrovirus insertions were found in humans, and 208 were found in chimpanzees. [15]

So, whether it’s one, two, or even twelve – 205 retrovirus insertions are in the same locations in the genomes of humans and chimpanzees! [16]

This seemingly perfect match is only possible if humans and chimpanzees are infected by the same retrovirus from a common ancestor. The chances of these vast numbers of virus genes being in the same location in their genomes independently are virtually zero.

Researchers have found 205 retrovirus genes entered the body of our common ancestor with chimpanzees. Later, after diverging from that ancestor, humans gained six more retrovirus genes, and chimpanzees gained 3.

Our DNA carries the written history of hundreds of millions of years. The most secure evidence of evolution can be found right there in that segment. At the molecular level, these tweets of evolution have no contradiction, provided one has a genuine understanding.

Discussing the common ancestor requires an entire book. There are countless studies to show. Evolution is firmly established and goes far beyond our understanding. Science has made tremendous progress. Evolutionary biology has come a long way.

The opponents of evolution may tell you, “But chimpanzees and humans share only 4% of the same genes!” However, they won’t tell you about the FoxP2 gene. This gene exists in nearly all mammals. The gene contains over 2 thousand letters or codes. How many differences between humans and chimpanzees are there in this gene?

Only nine letters!

Now let’s look at the genes of a distant creature, like rats, and find 139 differences. [17]

How can we deny the historical connection with our ancient relatives? When a new species is discovered in the depths of the ocean, the process of naming and classifying it inevitably draws upon the theory of evolution. Without an evolutionary perspective, unraveling any species’ history becomes virtually impossible. Venturing into the molecular realm, we encounter a myriad of evolutionary traces, even at the cellular level. The evidence of change stretches back hundreds of millions of years.

Former Director of the National Human Genome Research Institute Francis S. Collins once said,

“If there was any lingering doubt about the evidence from the fossil record, the study of DNA provides the strongest possible proof of our relatedness to all other living things.”

Our DNA, a repository of genetic information, holds more than meets the eye. Among its constituents, we find non-coding genes called exons originating from various viruses. This presents a fascinating tale of change woven within the very fabric of our genetic makeup.

Today’s discussion merely scratched the surface, showing the extensive evidence supporting evolution. The existence of a common ancestor has been established through various avenues, such as shared protein-coding genes, long terminal repeat divergence, shared chromosomal inversions, and broken gene comparisons.

Despite the overwhelming evidence for evolution in the 21st century, anti-science propaganda continues to propagate. The transmission of sufficient information regarding this well-established scientific theory may not always be seamless from one generation to another. Exploiting this gap in knowledge, numerous colorful books flood the market, attempting to spread pseudoscience and mislead the curious minds seeking answers.

As proponents of scientific literacy, we must remain vigilant against disseminating false information. Educating ourselves and others about the robust evidence supporting evolution is essential in countering the spread of pseudoscience and upholding the integrity of scientific inquiry. By embracing the wealth of knowledge available, we can celebrate our shared evolutionary journey and connect with the extraordinary tapestry of life’s unfolding story.


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[2] H.Anne F. Booth, Peter W.H. Holland,Eleven daughters of NANOG, Genomics, Volume 84, Issue 2, 2004,Pages 229-238,ISSN 0888-7543,

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[3] Fairbanks, D.J., Maughan, P.J. Evolution of the NANOG pseudogene family in the human and chimpanzee genomes. BMC Evol Biol 6, 12 (2006). ( )

[4] Yunis JJ, Prakash O. The origin of man: a chromosomal pictorial legacy. Science. 1982 Mar 19;215(4539):1525-30. doi: 10.1126/science.7063861. PMID: 7063861. 

[5] Prüfer, K., Munch, K., Hellmann, I. et al. The bonobo genome compared with the chimpanzee and human genomes. Nature 486, 527–531 (2012). 

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[6] Suntsova, M.V., Buzdin, A.A. Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species. BMC Genomics 21 (Suppl 7), 535 (2020).

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[7] Ijdo, Jacob W.; et al. (1991). “Origin of human chromosome 2: an ancestral telomere-telomere fusion”. Proc. Natl. Acad. Sci. U.S.A. 88 (20): 9051–5. Bibcode:1991PNAS…88.9051I. doi:10.1073/pnas.88.20.9051. PMC 52649. PMID 1924367 

[8] De Tullio, M. C. (2010) The Mystery of Vitamin C. Nature Education 3(9):48

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[9] Chuong EB (2018) The placenta goes viral: Retroviruses control gene expression in pregnancy. PLoS Biol 16(10): e3000028. 

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[10] Dewannieux M, Harper F, Richaud A, Letzelter C, Ribet D, Pierron G, Heidmann T. Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. Genome Res. 2006 Dec;16(12):1548-56. doi:10.1101/gr.5565706. Epub 2006 Oct 31. PMID: 17077319; PMCID: PMC1665638.

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[11] Wang GP, Ciuffi A, Leipzig J, Berry CC, Bushman FD. HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res. 2007 Aug;17(8):1186-94. doi: 10.1101/gr.6286907. Epub 2007 Jun 1. PMID: 17545577; PMCID: PMC1933515. ( )

[12] Withers-Ward ES, Kitamura Y, Barnes JP, Coffin JM. Distribution of targets for avian retrovirus DNA integration in vivo. Genes Dev. 1994 Jun 15;8(12):1473-87. doi: 10.1101/gad.8.12.1473. PMID: 7926746. ( )

[13] Mitchell, Richard S. et al. “Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences.” PLoS Biology 2 (2004): n. Pag. 

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[14] The calculation:

[15] Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005 Sep 1;437(7055):69-87. doi: 10.1038/nature04072. PMID: 16136131. 


[16] Grandi, Nicole & Cadeddu, Marta & Blomberg, Jonas & Mayer, Jens & Tramontano, Enzo. (2018). HERV-W group evolutionary history in non-human primates: Characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini. BMC Evolutionary Biology. 18. 10.1186/s12862-018-1125-1. 


[17] Richard Dawkins, The Magic of Reality