Some Palaeontologists Think They have Found Fossilised Dinosaur DNA. Others Aren’t So Sure

Some Palaeontologists Think They have Found Fossilised Dinosaur DNA. Others Aren’t So Sure
The fossilized skeleton of a dinosaur outside a Brazilian research centre. (Photo: CARL DE SOUZA/AFP, Getty Images)

Dinosaur researchers working on extremely well-preserved remains from the Jehol Biota in northeastern China recently reported that they had detected fossilised biomolecules in a duck-billed dinosaur from the Early Cretaceous.

The intriguing microscopic material was found in the femur of a Caudipteryx, a feathered, turkey-looking dino that lived between about 125 million and 113 million years ago. The team put cartilage from the femur under a microscope and stained it with chemicals called hematoxylin and eosin, which are used to highlight cell nuclei and cytoplasm in modern cells.

They also stained the cartilage of a chicken and found that the dinosaur and chicken cartilage lit up in the same way. The researchers say that nuclei and chromatin, the material our chromosomes are made of, were visible. The team’s research was published last week in the Nature journal Communications Biology.

“Geological data has accumulated over the years and shown that fossil preservation in the Jehol Biota was exceptional due to fine volcanic ashes that entombed the carcasses and preserved them down to the cellular level,” said study co-author Li Zhiheng, a vertebrate palaeontologist at the Institute of Vertebrate Palaeontology and Paleoanthropology of the Chinese Academy of Sciences, in an academy press release.

Members of this research team also described finding genetic material in another specimen last year; as Gizmodo reported at the time, some scientists were similarly sceptical of their claims that traces of genetic material were preserved in the fossilised Hypacrosaurus skull. The Caudipteryx fossil in the new work is about 50 million years older that the Hypacrosaurus.

“They were identified using completely different methods than in the Hypacrosaurus,” wrote Alida Bailleul, lead author of the new paper, in an email to Gizmodo. “But what was striking was the hematoxylin staining of the cell nucleus in Caudipteryx — it was comparable to the staining seen in a chicken cell nucleus,” said Bailleul, a palaeobiologist at the Institute of Vertebrate Palaeontology and Paleoanthropology in Beijing.

If this fossil did reveal the same structures that were highlighted in the modern chicken, it’d be a remarkable demonstration of how well biological material can preserve and how mercifully the cartilage was treated by Earth’s often-destructive processes. But not everyone is so convinced about what exactly was showing up in the stains.

“I don’t really see how much has changed here,” said Evan Saitta, a researcher from the Integrative Research Centre at the Field Museum of Natural History in Chicago. “The change in time we’re interested in here is not between the hypacrosaur and this new specimen; the difference is the amount of time between well-supported DNA preservation and any of these fossils.”

The oldest-yet sequenced DNA was described in a paper this February and came out of the teeth of a roughly 1-million-year-old woolly mammoth. All dinosaurs (besides birds) went extinct some 65 million years ago. That makes the dinosaur materials “absurdly older” than the “spectacular” results from the woolly mammoth remains, Saitta said.

So what exactly was reacting to the dyes and stains the recent team applied to the dinosaur cartilage? According to Saitta, it could be microbes that set up shop in the dinosaur remains or mineral infill of the space vacated by deteriorated genetic material. The latter is the opinion of Nic Rawlence, the director of the palaeogenetics laboratory at the University of Otago in New Zealand.

“The current limit of ancient DNA is 1.2 million years ago, and we don’t expect to be able to go much further back in time, certainly not to the Age of Dinosaurs,” Rawlence said in an email to Gizmodo. “While these fossilised cells and DNA in this new dinosaur may look like those from a modern chicken, they are a stone copy, where the cells and DNA have been replaced by minerals, in the same way a dinosaur bone is a mineralised version of modern bone.”

When bones fossilise, they do so from the obvious macroscopic features to the smallest elements of their structure. That allows paleontologists to do things like learn about the growth rates of T. rex, for example, as holes appear in the bone where blood vessels used to be. But genetic material is quick to deteriorate — one team estimated that DNA would cease to be readable after 1.5 million years, making the mammoth tooth find trepidatiously close to the material’s upper limit. And the mammoth remains were only so well-preserved thanks to their encasement in permafrost.

“Chemically speaking, you deal with a completely different set-up of compounds here, compared to when you look at permafrost material that’s pretty much comparable to frozen turkey in your freezer, to some extent,” said Jasmina Wiemann, a molecular palaeobiologist at Yale University, in a video call.

That makes the situation of that million-year-old mammoth fundamentally different from that of the 125-million-year-old Caudipteryx. Though the mammoth teeth did undergo diagenesis — the process by which organic compounds are gradually replaced by inorganic things like minerals — they were cooled by the Siberian climate, preserving the biomolecules to the modern day. (This is also the reason you occasionally read about Ice Age researchers being able to eat what they studied, like steppe bison.)

A woolly mammoth skeleton. The oldest sequenced DNA is from the teeth of a 1.2-million-year-old mammoth. (Photo: PHILIP FONG/AFP, Getty Images) A woolly mammoth skeleton. The oldest sequenced DNA is from the teeth of a 1.2-million-year-old mammoth. (Photo: PHILIP FONG/AFP, Getty Images)

“When it comes to actual DNA molecules, I think it is pretty much impossible that such molecules remain in dinosaur material,” wrote Love Dalén, a palaeogeneticist at the Centre for Palaeogenetics who was on the mammoth tooth team, in an email to Gizmodo. “We know from both massive empirical studies and theoretical models that even under completely frozen conditions, DNA molecules will not survive more than ca 3 million years.”

“Just because different dyes or stains react with parts of a fossilised remain does not mean that any actual DNA molecules remain in the fossil,” Dalén added.

What’s more, just because a bone fossilises doesn’t mean that every component of the once-living creature is exchanged, tit-for-tat, for any specific mineral or metal compound. Every dead dinosaur in every deposit around the world means a unique set of conditions are brought together, so no two fossils are really the same chemically. That means that a Hypacrosaur bone from Montana will have undergone a different sort of fossilisation than a Caudipteryx in China, making the work of molecular biologists, geochemists, and palaeontologists that much more complicated.

“It goes through, like, a grinder, but what comes out ends up looking very similar,” Wiemann said. “We’re missing a foundational understanding of how fossilisation works. I think that’s the whole challenge here.”

The mammoth DNA could be sequenced because it was more deep-frozen than it was fossilised. That is, the DNA wasn’t given an opportunity to interact with the molecular environment around it, and particularly with water, which causes the DNA to break down, as one co-author of the mammoth paper told Gizmodo.

So besides the question of what exactly was preserved in the Caudipteryx, it’s important to recognise that dinosaur DNA can’t be sequenced, at least not yet. The molecules have simply undergone so much change that they do not resemble the animals they were a part of. But ancient biomolecules can persist: dinosaur proteins were seemingly found on 200-million-year-old bone, though as a research team including Saitta pointed out in one paper, decaying dinosaur bones are a happy home for microbes, which can cosplay as dinosaur genetic material.

Part of the problem with the recent paper, several scientists said, was the staining method used to compare the Caudipteryx and chicken nuclei. Hematoxylin and eosin can bind to all sorts of things, not just genetic material, the researchers said, making the results pretty general. “I think it is tricky to apply a staining protocol that is not very specific at all to something like fossil materials that we don’t even understand what they actually represent,” Wiemann said.

A helpful step to address such ambiguity would be to cross-reference the staining results with additional, independent methods of looking at the cartilage. Such “triangulation” would help put the tissue issue to rest, Saitta said. Wiemann suggested using mass spectroscopy to look at the entire bone, and seeing if the material that was stained could be mapped to any nucleobases or DNA’s sugar-phosphate backbone. It’s an “incredibly exciting avenue of research,” Wiemann added, saying these additional methods would help home in on exactly what’s preserved in the fossil.

“I am a firm believer that if you dabble in deep time molecular bio, you MUST incorporate as many methods as you possibly can, AND you must consider and rule out, with data, any alternatives, such as invasion by microbes, either ancient or modern,” Mary Schweitzer, a molecular paleontologists at North Carolina State University and the Museum of the Rockies in Montana, told Gizmodo in an email. Schweitzer co-authored the hypacrosaur paper alongside Bailleul, who worked in Schweitzer’s lab. “For me, the ultimate goal is to obtain sequence information, so anything we can learn about diagenetic alterations to these recovered molecules becomes critical.”

Two fossils, 50 million years apart, turn up a biomolecular quandary in the span of two years. If that timeline is anything to go on, more data could come soon, hopefully bringing more clarity to this exciting new area of palaeontology.