New Insights into Human Origins - Part 1

Kia ora, 

What a surreal last few weeks this has been! I hope everyone reading this is safe and well. Here in New Zealand we are in the second week of a national lockdown to try and eliminate the Covid-19 virus. I thought I'd use some of the extra time I now have up my sleeve to start writing for this blog again! This past week has presented a great opportunity to reflect on and write about a real interest subject of mine - human origins - with the publication of a number of relevant scientific papers reporting the discoveries of important new fossils and the application of new (and refined) analytical approaches to glean new information from older fossils. 

Quick side note here: I'm not a trained palaeoanthropologist and I welcome feedback from those that know the field better if factual errors are spotted, as I would like this blog to be regarded as an accurate source of information. Hopefully I somehow manage to do justice to such a complex and fluid field while also keeping things accessible!!!     

An example of a rapidly developing analytical approach that has led to some remarkable insights into human origins is the retrieval of DNA from hominin fossils. These insights include the revelation in 2010 that members of our own species, Homo sapiens, interbred with what had on the basis of the fossil evidence alone been considered a distinct species of hominin, Homo neanderthalensis (commonly known as Neanderthals), as well as the identification of the Denisovans, a genetically distinct 'sister' group of the Neanderthals presently known only from a few fragmentary fossils in Siberia and Chinese Tibet, that also interbred with members of our species, as well as Neanderthals. But unfortunately, because of the degradation of DNA over time, the oldest hominin DNA that has been successfully retrieved is around 400,000 years old. Within the context of the millions of years of hominin evolution, this is quite a limitation! 

In a new study published in the scientific journal Nature on the 1st of April, scientists successfully retrieved and analysed ancient protein sequences from an around 800,000 year old hominin molar tooth recovered from the Gran Dolina site in Spain in 2004. Proteins are biomolecules consisting of chains of organic compounds called amino acids that are assembled using information encoded in DNA, so the more similar two species' DNA is, the more similar we would expect the composition of their proteins to be. Proteins slower rate of degradation compared to DNA presents the opportunity to study hominin phylogeny (the evolutionary relationship between different species) further back in the past than is possible using DNA.  

Excavations in progress at the Gran Dolina site in Spain in 2012. Image sourced from Wikimedia Commons.

    

The tooth from the Gran Dolina site had previously been assigned to a species of hominin known as Homo antecessor, a controversial species designation. Since they began in 1994, excavations at Gran Dolina have produced a large number of hominin fossils exhibiting a unique combination of features that led the discoverers to announce they had found a new species. However, many researchers consider the remains from Gran Dolina to be from an early and variable group of another species - Homo heidelbergensis (of course, in a not uncommon theme in palaeoanthropology, the species designation H. heidelbergensis is not without its detractors itself!). 

Reconstructed skull of a juvenile Homo antecessor from the Gran Dolina site in Spain. Image sourced from Wikimedia Commons.

The classic view among palaeoanthropologists is that H. heidelbergensis - dated to between about 700,000 and 200,000 years ago - was the most recent common ancestor (MRCA) of H. sapiens and Neanderthals, whose lines were initially estimated by DNA studies to have diverged somewhere around 400,000 years ago. This is Scenario A in the figure below. Neanderthals more closely resembled H. heidelbergensis, with recognizably 'anatomically modern' H. sapiens emerging in Africa sometime around 200,000 years ago.  Of course, nowadays we have the genetically distinct Denisovans to consider as well - although this is considered to be the result of a later split off from the Neanderthal line, as illustrated in Scenario A. It's also worth pointing out that for the purposes of the present discussion I have deliberately chosen to use relatively simple tree diagrams to represent these scenarios, despite recognizing that there are better representations of human origins in light of DNA evidence. 

Simplified representation of phylogenetic Scenario A discussed in text. Figure created by author. (MYA = million years ago; KYA  = thousand years ago).

One interesting feature of H. antecessor's face that its discoverers point to is a lower face that is 'flatter' (i.e. more orthognathic) than fossils that have been assigned to H. heidelbergensis or Neanderthals. In this respect, the face of H. antecessor is more similar to that of H. sapiens. The face of H. antecessor does however have other H. heidelbergensis and Neanderthal-like features such as a very pronounced brow-ridge.

Skull of modern human (Homo sapiens; left) and Neanderthal (Homo neanderthalensis; right). Note the more pronounced brow-ridge & projecting (i.e. prognathic) lower face of the Neanderthal skull. Image sourced from Wikimedia Commons.

Given the presence of a unique combination of H. sapiens and Neanderthal-like features in H. antecessor, and that known occurrences of H. antecessor in the fossil record have been dated earlier (between about 1.2 million and 800,000 years ago) than known occurrences of H. heidelbergensis, it was suggested by the discoverers of H. antecessor that this species may be a better candidate for the MRCA of H. sapiens and Neanderthals. In this case, later European Middle Pleistocene fossils attributed to H. heidelbergensis would be on the line leading to Neanderthals only and not ancestral to H. sapiens. This is Scenario B in the figure below. The suggestion of a MRCA that lived closer to the time that H. antecessor did has since gotten a bit of additional support from the analysis of that 400,000 year old hominin DNA I referred to earlier (a link to a New Scientist story about this analysis is here). Another finding from the DNA analysis was that the Neanderthal and Denisovan lines split much earlier than previously thought - also reflected in Scenario B. 

Simplified representation of phylogenetic Scenario B discussed in text. Figure created by author. (MYA = million years ago; KYA  = thousand years ago).

In the new study, the researchers concluded from their analysis of ancient protein sequences that H. antecessor was probably not a direct ancestor of our species after all, but is probably instead a close sister group to the MRCA of H. sapiens and Neanderthals. This is Scenario C in the figure below. As the authors of the paper note, the H. sapiens-like lower face of H. antecessor could have been a feature shared by the true MRCA. Just like in Scenario B, the lower face morphology of Neanderthals would have evolved sometime after the split from the line that lead to H. sapiens - the upshot of this being that our faces are actually 'more primitive' than that of Neanderthals! A longer antiquity of our facial structure compared to other distinctive anatomical attributes of our species has previously been hinted at by the discovery of around 300,000 year old fossils in Morocco that combined a distinctively flattened H. sapiens-like faces with an 'archaic' elongated skull, similar in shape to the Neanderthal skull in the photo above. 

Simplified representation of phylogenetic Scenario C discussed in text. Figure created by author. (MYA = million years ago; KYA  = thousand years ago).

More exciting than these conclusions, however, is the potential for the analysis of ancient proteins (or 'palaeoproteomics') to provide insights into hominin phylogeny further back in the past than is possible with DNA. The Middle Pleistocene (about 780,000-130,000 years ago) is the period during which our own species, Homo sapiens, originates, but which has been referred to as the 'muddle in the middle' with regards to hominin phylogeny.  

Thanks for reading! (more soon ... hopefully!)

Nick

Footnote (added October 2021): Although the potential of palaeoproteomics to contribute to our understanding of hominin phylogeny is exciting, it is important to add that proteins are far from a perfect substitute for DNA itself. Less than 2% of our DNA contains information for creating proteins (a stretch of DNA that encodes for a protein is called a gene). The remaining >98% of our DNA (and the DNA of other hominins as well) is therefore invisible when proteins are all that are available.