Evolution influences our physiology today. Here’s how

The vulnerability of present-day humans to different diseases is hidden in the history of genetic composition and sequences. In 2003, almost the full genome sequence of present day human (Homo sapiens) was done. 

Humans diverged from chimpanzees from 5-6 million years ago. But it was not enough to establish the evolutionary tree of modern humans. Svante Paabo and his team were already on the path of searching for the ancestor of modern humans through paleogenomic study, by analysing the ancient DNA from archaeological samples. 

In the early 80’s at Uppsala University, Sweden, Svante Paabo was able to get a skin sample from an Egyptian mummy and under the microscope, he found some cell nuclei in the basal layers of that skin sample. 

During the experiment, he found that these cell nuclei were getting stained with the stain for DNA. Then he was able to clone these DNA in bacteria and in other microorganisms in nature. So, it had been proved that these DNAs were not coming from the mummy itself. 

He concluded that DNAs in the mummified humans or in stuffed or mounted animals should be degraded by chemical modification or by the bacterial contamination for a long time and may be extracted in the form of short and ultra-short fragments. These are called ancient DNAs (aDNAs).

Long chains of DNAs extracted from archaic substances of hard and soft tissues are treated as contamination. Modern polymerase chain reaction (PCR) was sufficient to analyse the long chain of DNAs, but it was not suitable to sequence the ancient DNAs (aDNA) from the archaic substances. 

During this period, archaeologists were already able to find the skull of Neanderthals, the extinct hominin from Vindija Cave in Croatia of Western Eurasia. So there was a definite source of ancient DNAs from the extinct hominins. 

But the limiting factor was a proper sequencing method for ancient aDNA analysis. But in 2006, Nick Mc Cooke from Solexa, a UK-based genomics research company, came up with his high throughput Next Generation Sequencing (NGS) to sequence short and ultra-short DNA / RNA fragments (<100 base pairs). 

With this high throughput sequencing technology in 2010, SvantePaabo and his team were able to extract and sequence 55 per cent of the Neanderthal nuclear genome from its archaic skull. 

During this period, archaeologists found fingertip bone of another extinct hominin from the Denisova cave in Russia. Svante Paabo and his team were able to sequence and publish high coverage Denisova genome in 2012. 

Extraction & sequencing of ancient DNA from archaic bone of extinct hominin

Source: cell.com

Based on their study, they have explained that about 200,000-300,000 years ago modern humans originated in sub-Saharan Africa and then about 100,000 years ago, they started migrating out of Africa towards Western Eurasia. 

In Western Eurasia they mixed several times with the Neanderthal form or group of early humans and lived together. Then, modern humans reached further east to Eastern Eurasia and encountered another distinct form or group of early humans, the Denisovans. 

They then mixed several times with Denisovans and lived together and reached the Pacific. Thus, in different areas, the interbreeding between Neanderthals and Denisovans with modern humans took place several times. 

The other insight was that both Neanderthals and Denisovans have contributed DNA to present day people, the Homo sapiens.

Both Neanderthals & Denisovans contributed DNA to present day people

Source: Browning et al / Cell

After matching the sequenced DNA they found that at present, we carry 1-2 per cent of Neanderthal DNA and varying amounts of Denisovan DNA, mainly in the Chromosome 9 and Chromosome 3 loci. 

At present the 50 per cent human population of South Asian countries like India, Pakistan, Sri Lanka, Nepal, Bhutan, Bangladesh, Afghanistan and 16 per cent human population from Europe carry the Neanderthal variant in their DNA. 

As per the study of Paabo, the Neanderthal variant controls the function of progesterone receptor, a specific protein which is responsible for binding progesterone hormone at pregnancy. This Neanderthal variant is associated with preterm birth, but also protects against miscarriage of carrier pregnant women and thus results in more live births. 

So, the Neanderthal variant in Homo sapiens is responsible for more live births, with a risk of premature delivery. The women who are not carrying Neanderthal variants in their DNA are associated with the risk of miscarriage at pregnancy. 

After DNA sequencing from the samples of UK Biobank, Paabo and his team found that out of 362,944 individuals, 1,337 (0.4 per cent) carry the Neanderthal variant or allele. People carrying the Neanderthal variant report more pain in life than their non-Neanderthal counterparts and it is estimated to be about 8.5 years of additional pain. 

Functionally, the Neanderthal variant or allele facilitates a sense of pain modulated through the spinal cord and thus, Neanderthal carriers experience more pain in their lives. Neanderthal variant associated with Type-2 diabetes are also among us. 

Recently, Paabo and his team proved that Neanderthal carriers are associated with a high risk of COVID-19 deaths. During the recent pandemic, the Neanderthal variant contributed to around 1.1 million extra deaths due to COVID-19. 

But interestingly, people carrying the Neanderthal variant that is vulnerable to COVID-19 are less exposed to HIV / AIDS. Functionally, carriers of the Neanderthal variant in Chromosome-3 locus express less C-C chemokine receptor type 5 proteins on the surface of the immune cell. Thus, the HIV virus was unable to attack the immune system and the risk of HIV infection decreased. 

But this same variant increases the risk for severe COVID-19 infection in humans. 

So it can be concluded that, the genetic influences of extinct hominin both the Neanderthal and Non-Neanderthal factor equipped us with a balanced protective and risk factor in our physiology or life, with a double-edged sword or necessary evil through the passage of human evolution.

The author is a science communicator and health writer. He is the deputy conservator of forests, personnel at Aranya Bhawan, office of the principal chief conservator of forests (head of forest force) under the directorate of forests, the government of West Bengal.

Views expressed are the author’s own and don’t necessarily reflect those of Down To Earth.

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