Will Protein Analysis Unravel Human Evolution?

Protein analysis of this Denisovan jawbone gives new insights into human evolution.

Move over DNA. Ancient protein analysis is the newest fave. Researchers hope it will unravel the mysteries of human evolution? Or, will it? Will Palaeoproteomics fit the bill where DNA Sequencing faltered?

What is Palaeoproteomics?

Well, palaeoproteomics is a new field of scientific study. In this branch of science, researchers use the technique of mass spectrometry (MS) to analyse proteins found in fossils to answer questions about human evolution. Using this tool alone, recently they have identified a specimen of Denisovan from the Tibetan region of China. In this technique, scientists break down proteins into their constituent to deduce their chemical make-up. Well, peptides are essentially short chains of amino acids. Let’s note, however, that Proteomics is much more than just MS which paints a picture only in broad brushstrokes. Proteomics aims to identify all the protein sequences in a sample — its proteome — just as genomics studies the complete genome of an organism. To add a point, proteomics is essentially an outgrowth of the later. Proteomics is a new branch of discipline, the term got coined only in 1994. Palaeoproteomics is newer still.

Why the emphasis on proteins?

This is because proteins stick around in fossils much longer than DNA. The genetic codes don’t last beyond a couple of hundred thousand years. Moreover, DNA degrades faster in warm environments. So, fossils are there, DNA is lost. In comparison, tooth enamel successfully preserves amino acids for a couple of million years. Now, tooth enamel is the hardest material in the vertebrate body and therefore is invariably found in the fossilized ensemble. 

Due to the limitations cited above, DNA-sequencing has so far been possible for just three groups of hominins: Neanderthals, Denisovans and of course, Homo sapiens. The specimens are not earlier than 1,00,000 years ago. Well, one Spanish Neanderthal specimen does date back to about 4,30,000 ya. But, that is an exception not to be expected all too often. DNA sequencing fails miserably to go older as the genetic material is just non-extant. As it is, the sequence of human evolution of that period is more important because of hectic evolutionary activities. Denisovans and Neanderthals branched off at that time from their parental branch which in due course gave rise to the humans.

By the way, the recently discovered Tibetan Denisova is the first individual of the clan found outside Denisova Cave in Siberia. We indeed have records of all the earlier specimens only from and around that cave. Well, they got their name from there! This time, Anthropologists could happily confirm their discovery on the basis of a single amino-acid variant that isn’t present in the collagen of modern humans or Neanderthals but identified in the hominin group called Denisovans. Palaeoproteomics, holding a position of advantage vis-a-vis DNA, promises to get past the earlier mentioned age barrier and get around geographical blind spots, too.

Who were our direct ancestors?

That is the billion dollar question in Anthropology. History written in the fossils is hazy history. To take one case, despite DNA sequencing, we don’t know for sure, whether Homo heidelbergensis were ancestors to both Homo sapiens and Neanderthals. Or, they were part of only the Neanderthal branch. Notably, Heidelbergensis lived around 7,00,000 – 2,00,000 years ago.

Will Protein Analysis unravel Human Evolution?

Palaeoproteomics may one day settle the above yaksh-prashna once for all. Right now, the fledgling science has recovered proteins from 1.8-million-year-old animal teeth and a 3.8-million-year-old eggshell. On top of this, the ostrich eggshell is not from a better-preservable cold polar region. It is from Tanzania with average annual air temperature around 18 °C. Looks promising! Protein analysis may indeed solve the riddle of human evolution. It may some day help us reach out to 3.2 mya Ethiopian Lucy i.e. Australopithecus aferensis.

Nonetheless, to extract proteins from fossils of hominins from Homo erectus to Homo floresiensis is a challenging job. To prepare an actionable map of the proteins is still more — even with the modern technologies. We may note that Homo erectus lived from 1.9 mya to 1,40,000 years ago while the later diminutive ‘hobbit’ species lived in Indonesia as recently as 60,000 years ago. Its fossil was discovered in 2003. Incidently, Homo floresiensis appears to be the first species scientists hope to study by sequencing ancient proteins. Floresiensis is a discovery from the Indonesian island of Flores in 2003. It might be a dwarf descendant of H. erectus.

Is Palaeoproteomics a brand new thing?

You know, the idea is not new: as early as the 1950s, researchers had found amino acids in fossils. But, the technology enabling scientists to sequence ancient proteins just didn’t exist. The technique used, as told earlier, is that of mass spectrometry. This same MS technique is used to study modern proteins, too.

Issues & Challenges

  • Right now, palaeoproteomicists are working in an envious situation. They have before them an evolutionary road-map. They have the knowledge provided already by DNA sequencing and other traditional methods. Researchers have just to confirm what they know already. Sooner, when they start working with fossils more than half a million years old, they will have to work from scratch without a map.
  • Secondly, ancient teeth and bone contain limited number of proteins.
  • Moreover, if time takes away DNA from our ancestors, it also degrades proteins in the fossils. To our rescue, the proteins however are still identifiable.
  • Furthermore, for similar functions, the amino acids are the same whether in extinct or extant hominins. So, the task becomes statistically difficult compared to genetic material. The amino-acid sequences might provide too scanty information to say anything definitive and declarative on their own. The peptide variation is truly small.
  • In general, the information obtainable from proteins is limited compared with the information that we can get out of DNA sequences. There are only few thousands of amino-acid sequences against a few millions of genome variants. A pale comparison, to say the least.
  • Additionally, there needs to be more basic research into how proteins survive and degrade over long timescales. We understand that that is a different matter and need not bother the palaeoproteomics practitioners.
  • Last but not the least, over hype may result in methodical error or false findings. It has happened earlier with the DNA sequencing. Strict adherence to methodological standards is, therefore, called for.


Ancient DNA mapping has provided unrivalled information regarding evolutionary history of mankind. But there is a catch. Too old or adverse climatic fossil specimens do not preserve DNA too well for scientific investigation. Here, ‘too old’ means just half a million year which is rather not ‘too old’ in evolutionary history. Similarly, a little warmer climate like 25º Celsius becomes ‘adverse’.

By contrast, proteins resist age or climate factored degradation. Evolutionary scientists have mapped the proteome in some millions of years old non-human fossils. Proteins dating back more than one million years have been extracted from some fossils, and could help to answer some difficult questions about archaic humans. As such, we should hope for new insights apart from re-confirmation in evolutionary history. It will definitely take decades more. Meanwhile, researchers should follow investigative discipline rigorously. More importantly, we shouldn’t downplay DNA sequencing even slightly. Remember that the credit of discovery of Denisovans itself goes to the genetic material. In conclusion, Palaeoproteomics and DNA sequencing may work in unison complimenting each-other. In any case, protein analysis is the only hope regarding species like Homo erectus because we just can’t hope of any DNA evidence around 1.9 million years ago.

P.S. – A point aside:

Denisovans chose to live at the Tibetan Plateau — more than 3,000 metres above sea level — in very cold, low-oxygen environments although there was no scarcity of more habitable areas in those ‘days’. Did they migrate from Denisova cave in Siberia to the Tibetan Plateau in China? It is more that the two evolved on their own. To their credit, both the sites were equally inhabitable.

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