Scientists have at last uncovered the closest living relative of the mighty Tyrannosaurus rex, the most feared and famous of all the dinosaurs. For the first time, researchers have managed to sequence proteins from the long-extinct creature, leading them to the discovery that many of the molecules show a remarkable similarity to those of the humble chicken.

The research provides the first molecular evidence for the notion that birds are the modern-day descendants of dinosaurs, as well as overturning the long-held palaeontological assumption that delicate organic molecules such as DNA and proteins are completely destroyed during the process of fossilisation over hundreds of thousands of years. It also hints at the tantalising prospect that scientists may one day be able to emulate Jurassic Park by cloning a dinosaur.

Mary Schweitzer, a palaeontologist at North Carolina State University and the North Carolina Museum of Natural Sciences, led a team of researchers in analysing the 68m-year-old leg bone of a T-rex, recovered in 2003 in Montana. To her surprise, she found that it still contained a matrix of collagen fibres, a protein that gives bone its structure and flexibility. Working with colleagues at Harvard University Medical Centre and with the help of equipment normally used to identify and sequence tiny amounts of protein in human cancers, Prof Schweitzer managed to extract and sequence seven different T-rex proteins.

The results are published today in a series of papers in the journal Science.

"The analysis shows that T-rex collagen makeup is almost identical to that of a modern chicken - this corroborates a huge body of evidence from the fossil record that demonstrates birds are descended from meat-eating dinosaurs," said Angela Milner, the associate keeper of palaeontology at the Natural History Museum in London. "So, it is very satisfying that the molecules have provided a positive test for the morphology."

Prof Schweitzer had already sequenced protein from a woolly mammoth in 2002, but that material was from fossils that were merely 300,000 years old.

When the 68m-year-old T-rex's proteins had been isolated from the surrounding dust and rock, Prof Schweitzer's team compared them with the known proteins in living animals.

"Out of seven sequences, we had three that matched chicken uniquely and we had another that matched frogs uniquely and another that also matched newt uniquely and a couple of others that matched multiple organisms that include chickens and newts," said John Asara of the Beth Israel Deaconess Medical Centre in Boston, one of the authors of the study.

Dr Asara said the results supported the view that birds evolved from dinosaurs, but added: "If we had more species in the database to compare it to, such as alligator or crocodile, which have not been sequenced yet, we may also find matches to those species. Based on this study, it looks like chickens might be the closest amongst all species that are present in today's genome databases."

Molecular information like this can help to build better evolutionary family trees between extinct and living organisms. "The fact that identifiable proteins and amino acids can be recovered from at least some fossil vertebrates has opened up an exciting new field of investigation that may tell us more about the patterns and rates of evolution from the past to the present. And we can now do it from molecules as well as bones," said Dr Milner.

But Jack Horner of Montana State University said that sequencing the T-rex protein would also lead to a new era in palaeontology, which has so far relied on looking at the shapes and sizes of fossil bones to infer the relationships between extinct animals. The important thing was to find well-preserved material that had been protected from water and air. "To get specimens like that requires enormous amounts of material, getting specimens that are covered in tens of feet of rock."

Lewis Cantley, a biologist at Harvard University who took part in the analysis of the T-rex's proteins, said the techniques used had pushed medical technology to its limits. "The exciting thing is that this technology is still in its infancy, we're going to see it get a lot better. The machines are improving, the software is improving and there will be a lot of excitement in the palaeontology community of applying this technology to other bones that are preserved."

However, Dr Milner counselled against indulging in Jurassic Park fantasies just yet. "The fact that protein sequences from collagen of a T-rex have been recovered does not mean that we will be able to clone dinosaurs, despite what the makers of Jurassic Park suggest. Cloning any organism needs its DNA which carries the instructions to make a copy. DNA is not a protein, it is not a very stable molecule and it has never been recovered from any organism more than 30,000 years old."