The archaeological site of Harappa, of the Indus Valley civilisation. Photo: Wikimedia Commons
- Swedish geneticist Svante Pääbo received the 2022 Nobel Prize for medicine “for his discoveries concerning the genomes of extinct hominins and human evolution”.
- Two of Pääbo’s findings stand out in his career as a geneticist: the sequencing of Neandertal DNA in 2009 and the discovery of the Denisovan hominin in 2010.
- Evidence of the usefulness of the work of Svante and others is the quantity of funds, time and interest that have been devoted to piecing together the ancient history of humans.
- Today, palaeogenomic insights are important to question the identity politics dominant in India, where the government has openly defied awkward scientific findings.
Bengaluru: The anachronistic structure of the Nobel Prizes was thrust into the spotlight when the prize-giving committee awarded the medicine prize for 2022 to Svante Pääbo for his contributions to palaeogenomics: the study of ancient humans using their DNA. Pääbo is a Swedish geneticist who helped found the field of palaeogenetics (contrary to an official press release‘s suggestion that he founded it all by himself).
The timing of the prize is also slightly amusing because of the inescapable comparisons it draws to India – whose government has vehemently disputed palaeogenomic as well as archaeological evidence that the Vedic people migrated to India, and which recently abolished a panoply for national scientific prizes and indicated its favour for a homegrown version of the Nobels.
Two of Pääbo’s findings stand out in his career as a geneticist: the sequencing of Neandertal DNA in 2009 and the discovery of the Denisovan hominin in 2010.
For many years until the advent of palaeogenomics, the study of human ancestors was dominated by palaeontology – the study of these ancestors’ bones and other fossil remains – and archaeology. In 2008, a team of researchers from Austria, Germany, Russia and the US, led by Pääbo, excavated a finger bone from the Denisova cave in the Altai mountains of Siberia. They were able isolate mitochondria in the cells of the bone and sequence the DNA in the mitochondria.
By then, Pääbo as well as others had been able to sequence Neandertal DNA from other specimens. When they compared the sequences from the two sources, they found that the mitochondrial DNA (mtDNA) from the finger bone was sufficiently different to indicate that it was a separate subspecies.
The human cell contains DNA in two places: in its nucleus and in its mitochondria. Nuclear DNA is the DNA with which most of us are familiar; mtDNA on the other hand is distinguished among other things by the fact that it is much shorter, by about a million times and that the body has many more copies of it. Finding mtDNA is thus easier than finding well-preserved nuclear DNA. Pääbo et al. called the individual to whom the finger bone belonged the Denisova hominin, after the name of the cave where the bone had been found.
There are too few fossils of the Denisovan hominins known even today, which means scientists studying them don’t have enough information to say whether they’re a separate species or a subspecies. In any case, their scientific name is Homo denisova.
The team’s analysis further indicated that the common ancestor of Neandertals, Homo sapiens and Homo denisova lived at least 0.78-1.3 million years ago. The team also reported that the Denisovan mtDNA had twice as many differences from modern human mtDNA as the Neandertal DNA did, meaning that the Denisovan hominins were genetically more separated from modern humans than the Neandertals.
Finally, using information gleaned from archaeological artefacts in the area, Pääbo et al. hypothesised that Denisovans, Neandertal and modern humans lived around each in the region where the cave is around 40,000 years ago. The Denisovan hominin paper was published in March 2020.
Only two months later, another paper was published reporting the finish of another effort that Pääbo and his peers had undertaken much earlier. The paper reported that Pääbo et al. had successfully prepared a draft sequence of the Neandertal genome.
We know today that the Neandertals emerged around at least 315,000 years ago (although other estimates place their emergence 500,000 years earlier) and went extinct around 30,000 years ago. Thirty millennia is too long a time for DNA to survive without any contamination or degradation. At the time Pääbo et al. commenced their effort to put together and sequence Neandertal DNA, both him and others had developed numerous insights and techniques to help obtain, purify and store ancient DNA.
For example, since the 1990s, scientists had been able to obtain some Neandertal genes thanks in part to the PCR technique (also used for the RT-PCR test for COVID-19). When other scientists found genetic material, they could compare parts of it to the previously known genes and determine if the material could have come from Neandertals. For another, researchers also compared DNA to that of humans and chimpanzees, using the differences to understand when the DNA might have formed and then determining which subspecies it could have originated from.
Yet another important development was the invention of high-throughput DNA-sequencing in the 1990s. The advent of high-throughput sequencing led to the production of the famous “next-gen” DNA sequencing machines. Unlike their predecessors, these machines were capable of sequencing multiple parts of the genome at the same time, and used computers to rapidly piece together the final picture. All of these advancements together charged the tools and the theories of genetics with a greater ability to extract information from DNA, RNA, etc. – but fundamentally, what they did was allow geneticists to answer deceptively simple questions with greater confidence. These questions were of the form “Does this sample really contain modern human DNA or is it contaminated?”, etc.
So by the time the project to sequence Neandertal DNA got underway, in 2006, Pääbo et al. were concerned chiefly with whether Neandertals and Homo sapiens had interbred. Their findings thus far hadn’t provided an unequivocal answer.
First, the researchers obtained 21 Neandertal bones from a cave in Croatia, ascertained the presence of Neandertal DNA therein and extracted mtDNA for sequences. Next, they determined the quantity of Neandertal DNA in the genetic material and tagged them in preparation for sequencing. Third, they enriched the Neandertal DNA so that the sequencers could detect their presence more faithfully than the presence of DNA from contaminants (modern humans and bacteria, e.g.). Finally, they sequenced the DNA, taking special care to ensure they were able to identify all potential errors and correct for them in the final results.
With these results, the team was able to report a wealth of discoveries. One, for example, was the following (quoting from the paper):
“The data suggest that between 1 and 4% of the genomes of people in Eurasia are derived from Neandertals. Thus, while the Neandertal genome presents a challenge to the simplest version of an ‘out-of-Africa’ model for modern human origins, it continues to support the view that the vast majority of genetic variants that exist at appreciable frequencies outside Africa came from Africa with the spread of anatomically modern humans.”
The team also reported that Neandertal DNA “contributed only 1-4%” of modern (non-African) human DNA, meaning that the two groups did interbreed but not much.
For all these findings, both the study paper and the Nobel Prize say that the principal achievement here was that scientists could retrieve and study DNA from many millennia ago. Evidence of the usefulness of the work of Pääbo & co. is the quantity of funds, time and interest that have been devoted to piecing together the ancient history of humans.
Both archaeogenomics and palaeogenomics have opened wide windows into the way humans have travelled, cultivated crops, organised themselves and survived natural disasters through several centuries. Today, in 2022, archaeogenomic and palaeogenomic insights are also part of the identity politics dominant in many countries, including India.
While the Indian government as well as independent scientists have undertaken archaeological and palaeontological studies around the country for many decades, their discoveries assumed greater significance the moment the government began to openly dispute the provenance of ancient Indians.
It is important for the Hindutva nationalist project that the originators of the Vedas, simply called the Vedic people, first emerged in modern-day India and emigrated to other parts of the world. But recent genomic studies – especially two that were published in 2019 – have found evidence for the opposite: that these individuals migrated to India from Eastern Europe during the late Harappan period.
Another study published in 2020, based on studying chemical residues in artefacts, reported that the Harappan diet included pig and buffalo meat – further defying attempts by nationalists in government to assimilate the Harappan civilisation into their revisionist narratives.
The migration of the Eastern European population is believed to have begun around 10,000 years ago, with one population breaking off around 1900 BC into Bactria and around 1500 BC into the Punjab region. The Harappan civilisation lasted from around 3,000 BC to around 1,200 BC. By the time the Eastern Europeans arrived, most Harappan settlements had already disbanded, with their residents migrating to central and south India.
The work of Svante Pääbo and his peers from around the world have been instrumental to understand how the human story first began and how the various subsequent chapters can be put together. Today, scientists in countries like India are instrumental to plugging important nationally relevant gaps in this book, deciding how the book itself will end and – crucially – whether it will survive their governments.