Early Denisovans

Denisovans are elusive in many ways. When did they first appear and where, how spread where they geographically and how the different Denisovan populations interacted with each other and with other archaic and modern human populations.

A small step towards understanding the early Denisovans, their toolkit and subsistence strategies was the discovery of Denisovan remains using ZooMS and subsequent genetic analyses from the lowermost, securely dated layers of the East Gallery of Denisova Cave. At 200,000 years before present, these new Denisovans are the oldest so far identified.

This work is published in Nature Ecology and Evolution and can be accessed here https://rdcu.be/cB2U4. It has also made the cover of the January 2022 issue of the journal! We are very excited to see these  beauties attracting the spotlight they deserve!

For a first-person account of how ZooMS works and how it was applied to the bone assemblage from Denisova Cave you can see the post by ex FINDER student Dr Samantha Brown here .

The genetic analyses were led by post-doc Dr Diyendo Massilani from the MPI EVA in Leipzig. Needless to say that no scientific analyses could have been accomplished in the Denisova bone assemblage without our Siberian colleagues from the IAET RAS SB (Profs. Shunkov and Derevianko, Dr Maxim Kozlikin) painstakingly excavating the site for almost 6 months each year and offering their valuable support and expertise.

Democratisation of ZooMS: Jena lab protocols published

One of the biggest challenges we faced at the onset of the project in 2016-17 was the lack of transparency in terms of the nitty gritty of ZooMS, the actual analytical protocols, from the wet chemistry laboratory procedures, to equipment settings, data analyses and full data deposition (both reference data as well as analysed unknown samples). I used to jokingly call the method “the best kept secret in archaeological science”.

In FINDER, to ensure that our workflow and results were not only as transparent as possible, but also reproducible and fully accessible by any interested party, we committed early on to work towards the “democratisation” of ZooMS.

The first step towards this was to test and publicise in a free and accessible format our analytical protocols. In a series of publications, the 3 main wet chemistry protocols we use at the ZooMS/Palaeoproteomics laboratories of the MPI-SHH were described and deposited in protocols.io. In more detail:

  • The AmBic protocol can be used on samples where destructive analysis cannot be undertaken or where collagen preservation is particularly good hence matrix demineralisation is not necessary. 

Zooarchaeology by Mass Spectrometry (ZooMS) for bone material – AmBiC protocol dx.doi.org/10.17504/protocols.io.bffdjji6

  • Two acid based protocols are slight variations of a more destructive approach in which the samples are pretreated with hydrocholric acid to demineralize the bone matrix and release inter- and intra-crystalline collagen.

Zooarchaeology by Mass Spectrometry (ZooMS) for bone material – Acid insoluble protocol dx.doi.org/10.17504/protocols.io.bf43jqyn

Zooarchaeology by Mass Spectrometry (ZooMS) for bone material – Acid soluble protocol dx.doi.org/10.17504/protocols.io.bf5bjq2n

In a different publication in the Journal of Proteomics we test the aforementioned protocols on 400 archaeological bones from different parts of the world. This allowed us to compare how each protocol works depending on collagen preservation.

ZooMS methods comparison


The full reference and publication can be found here:

Wang, N., Brown, S., Ditchfield, P., Hebestreit, S., Kozilikin, M., Luu, S., Oshan, W., Grimaldi, S., Chazan, M., Horwitz Kolska, L., Spriggs, M. Summerhayes, Gl, Shunkov, M., Korzow Richter, K., Douka, K., Testing the efficacy and comparability of ZooMS protocols on archaeological bone. Journal of Proteomicshttps://doi.org/10.1016/j.jprot.2020.104078 


Proteins are getting older!

One of the most exciting aspects of this work, at least for someone who was previously limited by the radiocarbon limit, is the wider applicability of ZooMS to material covering not only the last 50,000 years but as many as a few million years. Recent publications have pushed the survival of animal proteins in tooth enamel to 1.77 Ma and 1.9 Ma– an exciting pushback in time! A nice write-up with comments from various researchers, including one of us, can be found here.

As for FINDER, we have been hard at work in 2019 both at the lab and travelling to places across Europe, Asia and Australia to access “new” old collections. We’ve hit 10,000 bones from Denisova Cave and analysed material from another 6 sites from northern Asia.

The oldest, protein- and DNA-containing human fossils from Denisova Cave can now be placed, comfortably, to ~200 ka  and possibly beyond this, and we will be reporting more on this as new data come out. For now, here are two pics of the student team (Samantha Brown and Naihui Wang) working at the labs in Jena.