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Protein the clue to solving a Darwinian mystery

Posted on 18 March 2015

Scientists at the University of York provided the key to solving the evolutionary puzzle surrounding what Charles Darwin called the ‘strangest animals ever discovered’.

Toxodon platensis. Illustration by Peter Schouten from the forthcoming
book "Biggest, Fiercest, Strangest"  W. Norton Publishers (in production).Scientists at the University of York provided the key to solving the evolutionary puzzle surrounding what Charles Darwin called the ‘strangest animals ever discovered’.

Published today in Nature, 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.

Researchers in the University’s BioArCh research facility and Centre of Excellence in Mass Spectrometry were called in by the Natural History Museum and the American Museum of Natural History to resolve the long-standing question of the fossils of Toxodon and Macrauchenia, the South American native ungulates or hooved mammals—the last of which disappeared only 10,000 years ago.

The research shows that South American ungulates, similar to those whose fossils were found by Darwin 180 years ago in Uruguay and Argentina, are actually related to mammals like horses rather than elephants and other species with ancient evolutionary ties to Africa as some taxonomists have maintained

Previously, attempts by scientists to pinpoint the origin of animals 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 the material.

But the structural protein, collagen, is likely to survive around ten times longer than DNA so the York scientists used proteomic analysis to screen 48 fossil bone samples of Toxodon platensis and Macrauchenia patachonica, 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 York research team was headed by Professor Matthew Collins, of BioArCh, and Professor Jane Thomas-Oates, director of York’s Centre of Excellence in Mass Spectrometry, and included PhD student Frido Welker and Dr Jessica Thomas from the University’s Department of Biology.

Dr Thomas, who conducted the phylogenetic analysis, said “By producing the most comprehensive example of sequencing of its type, we have been able to resolve the taxonomic placement of these mammals, and solve a question that has baffled paleaontologists for more than a century.”

Professor Collins said: “We now have the potential to address many more of these challenges and to explore the evolutionary process much further back in prehistory.”

Frido Welker, a Ph.D. student at the Max Planck Institute for Evolutionary Anthropology and in BioArCh at York, said:  “We are developing new proteomic techniques and applying them to the archaeological and palaeoanthropological record. To get 90 per cent sequence coverage for both species is a direct result of those efforts, and truly fantastic given the burial time and location.”  

Professor Thomas-Oates, of the University’s Department of Chemistry, added: “Our long-standing collaboration with scientists at Bruker Daltonics made it possible to analyse these samples using the most up to date mass spectrometric instrumentation.  The outstanding quality of the data was crucial in enabling us to determine the collagen sequences.”

Professor Ian Barnes, a curator at the Natural History Museum said: “Although the bones of these animals had been studied for over 180 years, no clear picture of their origins had been reached. Our analyses began by investigating ancient DNA to try to resolve the problem.”

Ross MacPhee, a curator in the American Museum of Natural History’s Department of Mammalogy said: “Fitting South American ungulates to the mammalian family tree has always been a major challenge for paleontologists, because anatomically they were these weird mosaics, exhibiting features found in a huge variety of quite unrelated species living all over the place.

“This is what puzzled Darwin and his collaborator Richard Owen so much in the early 19th century. With all of these conflicting signals, they couldn’t say whether these ungulates were related to giant rodents, or elephants, or camels—or what have you.”

With modern techniques of phylogenetic interpretation, the researchers were able to conclusively show that the closest living relatives of these species were the perissodactyls, the group that includes horses, rhinos, and tapirs. This makes them part of Laurasiatheria, one of the major groups of placental mammals. The molecular evidence corroborates a view held by some leading paleontologists that the ancestors of these South American ungulates came from North America more than 60 million years ago, probably just after the mass extinction that killed off non-avian dinosaurs and many other vertebrates. Because the South American ungulates were such a large and varied group, it is not clear whether other lineages not studied by the researchers all had the same origin.

This research was funded through the Systematics and Taxonomy research scheme (SynTax) supported by the Systematics Association, Linnean Society and the Biotechnology and Biological Sciences Research Council and the Natural Environment Research Council.

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