Ancient protein analysis solve a Darwinian mystery – University of Copenhagen

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18 March 2015

Ancient protein analysis solve a Darwinian mystery

STRANGEST ANIMALS  The evolutionary puzzle surrounding what Charles Darwin called the ‘strangest animals ever discovered’ has now been solved by an international team of researchers. Their remarkable technical feat in obtaining a molecular phylogeny based on Pleistocene protein sequences is a first, which could herald a new chapter in palaeontology. Scientists from the Centre for GeoGenetics and samples from the Natural History Museum of Denmark's South American Collection were part of the project.

The puzzle involved the long-standing question of the fossils of Toxodon and Macrauchenia, the South American native ungulates (SANUs) first found by Darwin 180 years ago in Uruguay and Argentina.

It has been unclear if Toxodon and Macrauchenia had a single origin or several, whether or not they arose before or after the Cretaceous period and whether they belonged to the order of mammals that includes elephants or to the one that includes cattle and horses.

Previously, attempts by scientists to pinpoint the origin of SANUs using morphology-based analysis and ancient DNA, had failed. The latter approach was compromised because scientists were unable to recover any identifiable mammalian DNA from fossil specimens. This is likely to be the case for large numbers of important fossils from tropical or temperate deposits, as DNA preservation is ultimately controlled by the thermal history of material.

Toxodon fragment of lower jawbone with teeth. Photo by Kristian Gregersen, NHMD

Toxodon fragment of lower jawbone with teeth. Photo by Kristian Gregersen, NHMD

Protein survives longer than DNA

But collagen, a structural protein abundant in bone, is likely to survive around 10 times longer than DNA so the scientists used proteomic analysis to screen 48 fossil bone samples of Toxodon and Macrauchenia discovered in the 19th century in the same area as those recovered by Darwin. This produced sequences covering more than 90 per cent of the collagen molecule, effectively providing a phylogenetic barcode for the two species.

The collagen sequences proved that Toxodon and Macrauchenia are closely related to horses, rhinos and tapirs. And thereby solved Darwin's mystery.

Enrico Cappellini, Assistant Professor at the Centre for GeoGenetics took part in the project. He says:

- With colleagues in the Quantitative Proteomics group at the Novo Nordisk Center for Protein Research, we are developing new proteomic techniques and applying them to the archaeological and palaeoanthropological record. Our contribution in the clarification of this so far unsolved ambiguity is a direct result of those efforts.

One of the Toxodon samples analysed in this study is part of the collection of the Natural History Museum of Denmark. It was found at Arroyo del Medio, which is an area of pampas near Buenos Aires (Argentina), by Santiago Roth and bought by Valdemar Lausen. It arrived to the museum as a gift from Lausen on the 25th November 1887 and was recorded in the general collection with the catalogue number CN 223. Later it was transferred to the Quaternary Collections and re-entered with the accession number Z.M.K. 16/1887.

Professor Eske Willerslev, Associate Professor Ludovic Orlando and Assistant Professor Enrico Cappellini from the Centre for GeoGenetics participated in the project together with scientists from the University of York, The Natural History Museum of London and The American Museum of Natural History.

The paper ‘Ancient Proteins Demonstrate South American Ungulates are Laurasiatheres, not Afrotheres’ is published in the latest issue of Nature.


Assistant Professor Enrico Cappellini, tel. no. 3532 1338,