Svante Pääbo wins Medicine Nobel for his work in analysing ancient DNA

His research led to discoveries that laid to rest many incorrect theories about human evolution.

Svante Pääbo  with a replica of a Neanderthal skeleton at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.  | Photo Credit: Hendrik Schmidt/AP

We are all interested in the question “where did we come from?” Different cultures and religions have different answers. Hinduism has multiple answers. A central one found in the Rig Veda is that the gods sacrificed the Cosmic Man, Purusha, to create man. The Jains, on the other hand, hold that the world, living souls, and time have always existed and will always exist. Science has a different answer. Charles Darwin proposed, with reasonable observational support, that humans arrived by gradual biological changes from ape-like ancestors. Thus, the belief that humans were “created” was dispensed with. Over the years, Darwin’s proposal gained strength, especially after scientists were able to analyse DNA.

Various branches of science—notably, anthropology, archaeology, chemistry, genetics, physics, and statistics—have contributed to the understanding of where humans come from. Genetics has made the most robust contributions to this understanding. The invention of methods to extract DNA from cells and to read its linear sequence, nucleotide by nucleotide (DNA alphabets are called “nucleotides”), has made this possible.

DNA is transmitted intact across generations virtually unchanged. When an individual is born, all cells of the body contain identical DNA. Parents contribute equally to their child’s DNA. Various internal biological errors and external forces, rays of the sun included, cause small changes to the DNA that are passed on to the next generations, possibly with the addition of other changes. It is because of these changes that the DNA sequences of two individuals are never identical. However, the DNA of any two individuals is over 99.9 per cent similar. Human DNA has about three billion nucleotides, so a difference of 0.1 per cent is a difference of about three million nucleotides. This small fraction of non-identical DNA sequence confers uniqueness to every human. Differences in this small fraction of the DNA can, for example, make one individual susceptible to a disease, while conferring protection to others from the same disease.

The same phenomenon of DNA continuity and change takes place in each species of an organism. When a large number of changes accumulate, a new species is born from the pre-existing species. By studying the DNA sequences of various species, it is possible to infer which species evolved from which. By observing how changes accumulate in DNA over time, it is possible to estimate when a species evolved from an ancestral species.

Split from chimpanzee

Extensive comparisons of the DNA differences between the great apes—gorilla, chimpanzee, bonobo—and humans resulted in the inference that the human line of descent split from the chimpanzee line about five million years ago. Chimpanzees are, therefore, our nearest non-human relative. DNA changes accumulate over time and create diversity in a group of individuals. Thus, it is logical to conclude that a group of humans with a highly diverse set of DNA sequences is older than a group whose sequences are less diverse. Looking at humans resident in different regions of the world, one finds that Africa has the highest DNA diversity. From this and other DNA evidence, it has been inferred that Africa is the cradle of humankind. We, modern humans, Homo sapiens, all evolved in Africa about 1,50,000 years ago. We stayed put in Africa for over 50,000 years, coming out about 1,00,000 years ago to start exploring other regions. The main evolutionary stem from which we evolved was that of H. erectus, who lived about one million years ago in Africa. From this stem arose many new branches (new species of Homo), most of which became extinct.

Chimpanzees are our nearest non-human relative. Here, a sculpture of a 17-year-old male chimpanzee named Jaska in London, in September. | Photo Credit: Vadim Ghirda/AP

When we came out of Africa and went into West Asia and then Europe, we met some cousins who were similar looking but different in many respects. We and these cousins, called H. neanderthalensis or, more commonly, Neanderthal man, evolved from a common ancestor, H. heidelbergensis. Neanderthal man also became extinct; the last one lived about 30,000 years ago. Modern humans coexisted with Neanderthal man for about 70,000 years. Why did the Neanderthals become extinct? They were efficient hunters; they made sharp wooden spears and killed large animals and ate their meat. They were certainly capable of defending themselves.

There were contradictory speculations regarding the causes of their extinction. Geneticists felt that if it was possible to find and sequence Neanderthal DNA then a definitive answer might be obtained. No one dared to explore this possibility. Even if a Neanderthal fossil was found, would the cells from which DNA can be extracted have survived for thousands of years? DNA is a biological molecule and degrades on exposure to the environment.

Feldhofer Cave

One scientist dared. Svante Pääbo, an evolutionary anthropologist, who won the Nobel Prize in Physiology or Medicine this year. A fossil of a Neanderthal was discovered in Feldhofer Cave in the Neander Valley in Germany. A small sample of bone was ground up to extract DNA.

This is when Pääbo’s group encountered some major scientific challenges. Bones that lie around for many thousands of years are exposed to the vagaries of nature. Microbes, notably fungi and bacteria, grow on such “debris”. These microbes also have DNA. How does a researcher know that the DNA extracted from such bones is not contaminated with DNA from other organisms? Also, the archaeologists who dug up the bones may have inadvertently contaminated the bones with their own DNA since people shed cells from their bodies all the time.

‘Contaminating’ DNA

One may argue that such “contaminating DNA” would be a tiny fraction of the total DNA extracted from the bones and, thus, does not matter. However, the quantity of DNA in a sample is usually too small for its sequence to be determined, and it has to be “amplified” by a process called polymerase chain reaction (PCR). Kary Mullis was awarded a Nobel Prize in Chemistry in 1993 for his role in the invention of PCR technology, without which most DNA research undertaken today would not have been possible.

Even if the bone DNA was contaminated by other DNA in trace amounts, because of many technical reasons, the contaminating DNA may be more efficiently amplified than the bone DNA. Thus, after the amplification process, one may be left with a soup of DNA in which the contaminant DNA is dominant. It must be noted that the sequence of an entire DNA molecule of three billion alphabets cannot be determined in one go: sequences of short fragments of DNA are determined and then the short sequences are assembled to form a longer sequence using mathematical and computing methods. The process of assembly is also a challenge.

When the pool of these DNA molecules extracted from the bone and amplified are analysed for sequence determination, most of the short sequences derived may actually be of fungi, bacteria, or of the archaeologists who dug up the bone, not the ancient DNA of the bone. This was one big challenge that Pääbo and his group had to overcome. Special suits had to be made for people to wear while handling the bones. Special artificial air pressure chambers had to be created in the laboratories in which DNA extraction and amplification were done.

There were also other challenges. Because the bones were exposed to the environment, degradation of DNA took place, including physical changes such as fragmentation and chemical changes known as cross-linking and deamination. This degradation reduces the quality of the ancient DNA to such levels that most extracted ancient DNA is unsuitable for analysis. Ancient DNA degradation is slower in a cool, dry environment than in a hot, humid one.

While the vast majority of scientists would have given up on trying to analyse ancient DNA, Pääbo and his team worked hard and doggedly for over two decades to overcome the challenges of analysing ancient DNA. Now all scientists engaged in such research use the techniques Pääbo and his team perfected and the protocols they devised.

Pääbo and his group produced the first Neanderthal DNA sequence in 2010, albeit with some gaps, determined from three individuals found in Vindija Cave, Croatia. In 2014, the group produced a high-quality complete DNA sequence of a Neanderthal woman who had lived in a cave in the Altai Mountains of Siberia about 50,000 years ago. The parents of this woman were closely related, perhaps half-siblings or uncle and niece. Therefore, one can say that Neanderthals, like some modern humans, practised inbreeding, or mating between close relatives. The practice is popular in many population groups of south India.

After the first Neanderthal DNA was sequenced, Pääbo and his group and other researchers sequenced and published DNA obtained from many other Neanderthals. Not unexpectedly, these sequences were not identical, just as DNA sequences of humans are not identical. However, the extent of genetic diversity among the Neanderthals was smaller than that of modern humans, perhaps a consequence of their smaller population size. These comparative data resulted in a catalogue of sites in the DNA where the nucleotide present in the human is either shared or unshared with a Neanderthal.

Neanderthal DNA in modern humans

How did modern humans obtain DNA variants from Neanderthals? Statistical analyses of the catalogues of DNA variants of Neanderthals and humans allowed Pääbo to conclude that Neanderthals and humans did interbreed. Comparison of the data on Neanderthal DNA variants with those of human population groups resident in different geographical regions provided estimates of the contribution of Neanderthals to the variable portion of human DNA. The estimates have been dissimilar, primarily depending on the estimation procedure.

Overall, Neanderthals contributed about 1-4 per cent to the DNA of non-Africans; one study claimed this contribution to be 20 per cent. Since Neanderthals were not present in Africa, human populations in Africa were not expected to have any genetic contribution from Neanderthals. However, some studies have estimated a small (<1 per cent) contribution of Neanderthals to the DNA of contemporary Africans. This may have arrived in Africa with ancient Europeans whose ancestors had left Africa, met and mated with Neanderthals, and then returned to Africa and mixed with local populations.

When modern humans came out of Africa, were Neanderthals the only hominin species they met? The answer is no. At least another species, which was named Denisovan, roamed in Eurasia. DNA analysis of small bones found in the Denisova cave in Siberia revealed that the individuals (Denisovans) from whom these bones came were a different species.

Collecting sediment samples at the Denisova Cave in the Altai Mountains, Siberia, a June 2021 picture. Pääbo and his team carried out DNA analysis of small bones discovered in this cave and found that they belonged to a different species, later called Denisovan. | Photo Credit: Dr RICHARD G. ROBERTS/AFP

Two separate teams, Pääbo’s team being one of them, carried out DNA analysis and generated DNA sequences of the Denisovans; both teams published their findings in 2010. Comparisons of the DNA sequences of contemporary humans, Neanderthals, and the two Denisovans showed that Neanderthals and Denisovans had also interbred and that Denisovans contributed 4-6 per cent to non-African DNA.

Interestingly, in 2018, Pääbo’s team sequenced the DNA extracted from another bone found in the Denisova cave and identified that bone as belonging to a child of a Neanderthal father and a Denisovan mother.

It was of considerable interest to us to estimate the contributions of Neanderthals and Denisovans to the people of India. We carried out DNA analysis of individuals belonging to 42 population groups spread across India and belonging to different cultures and languages and published the results in 2019. We estimated that Neanderthals contributed 1.89-2.49 per cent to various Indian populations and Denisovans contributed 0.08-0.40 per cent. Interestingly, the extent of Denisovan admixture in India is lower than that of the Neanderthal. And, the mean level of Denisovan admixture is higher among tribal populations of India than among caste populations.

At the Karolinska Institute in Stockholm, a member of the Nobel Committee for Physiology or Medicine explains Pääbo’s research work during a press conference on October 3.  | Photo Credit: JONATHAN NACKSTRAND/AFP

If modern humans interbred with Neanderthals and Denisovans and produced children, why did these species become extinct? The likely reason is that the children of the unions between humans and Neanderthals or Denisovans remained with the humans. Over thousands of years, the population sizes of the hominin species started to shrink, and they became extinct.

Ancient DNA analysis has also taught scientists many lessons about biological evolution in relation to human exposure to pathogens and other factors. Research has shown that Neanderthal DNA contributed to genes of the immune system. When humans came out of Africa into Europe, they encountered new pathogens. Neanderthals had lived with these pathogens for generations, and their immune system genes were adapted to fight them off. When humans and Neanderthals interbred, children who received from Neanderthals the immune genes with the variants that conferred resistance had a better chance of survival than those who did not. Such resistance variants obtained from Neanderthals have been found among Europeans but not among Africans.

Pääbo was awarded the Nobel Prize this year “for his discoveries concerning the genomes of extinct hominins and human evolution”. Indeed, his discoveries were startling, laid to rest many incorrect theories about human evolution, and provided many deep biological insights into what made us human. His ability to overcome challenges to answer path-breaking scientific questions is his hallmark.

The Crux

• The science of genetics and the invention of methods to extract DNA from cells and to read its linear sequence has made it possible for scientists to understand where humans came from.
• However, there are challenges to getting genetic information from ancient DNA because samples would have degraded and/or become contaminated.
• Svante Pääbo, an evolutionary anthropologist, and his team worked for two decades and devised and perfected techniques and protocols overcome these challenges.
• In 2010, they produced the first Neanderthal DNA sequence, albeit with some gaps, from remains of three individuals found in a cave in Croatia.
• Through DNA analysis of bones found in the Denisova cave in Siberia, the team identified a new species of hominin, which are now called Denisovan. They published their results in 2010.
• In 2014, they produced a complete DNA sequence of a Neanderthal woman who lived about 50,000 years ago.
• Pääbo and his team were able to conclude that Neanderthals and humans interbred. They were also able to show that Neanderthals and Denisovans interbred.
• Pääbo won this year’s Nobel Prize in Physiology or Medicine “for his discoveries concerning the genomes of extinct hominins and human evolution”. 

Partha P. Majumder is National Science Chair (Scientific Excellence), Government of India; distinguished professor and founder, National Institute of Biomedical Genomics, Kalyani, West Bengal; emeritus professor, Indian Statistical Institute, Kolkata; honorary professor, Indian Institute of Science Education & Research, Mohali and Kolkata.