Science Literature

When Jurassic Park was written, I don't think any scientist seriously thought that genetic material from dinosaurs would ever be recovered. However, that is exactly what was reported in Science a few days ago. The genetic sequences are derived from collagen protein recovered from the fossilised leg bone of a T. rex. The main authors have been publishing for some time about their find of dinosaur soft tissue, and this new paper is the latest step of a remarkable journey of exploration. If amino acid sequences are preserved in other fossilised bones, many new avenues for research will open up.

The bone yielding the collagen used in the research (Source: here)

The paper would have been memorable if that were the only point made by the authors. However, the authors wanted to show that their data could be useful to molecular phylogenetics. They used 21 extant organisms and protein sequence data from an Ice Age mastodon. They used four methods to reconstruct an evolutionary tree. According to the New Scientist report:

"To build the family tree, Asara and colleague Chris Organ compared the T. rex sequence with collagen from other animals. Those with similar collagen sequences were grouped closely together on the tree, while differences in the sequences suggested the animals had long diverged. For the most part, the collagen tree captured relationships palaeontologists and evolutionary biologists had little reason to doubt, including T. rex's kinship to birds and the mastodon's ancestry to elephants."

The relationship between the dinosaur and birds caught the interest of the media. "T. rex confirmed as great granddaddy of all birds" said New Scientist. The Daily Mail had the headline: "Terrifying Tyrannosaurus rex had close links to the humble chicken". One of the more ingenious was the Washington Post: "T. Rex Closer to Gizzards Than Lizards". However, the New Scientist, particularly, over-reached itself with its portrayal of the find. The word "confirmed" is a gross overstatement (see below) and the word "granddaddy" is simply wrong, as birds were contemporaneous with T.rex.

What few have realised is that the T. rex sequence is mainly missing. In their supplementary information, the authors document their data for the dinosaur collagen. It looks like this (where the dashes represent missing data - visible in IE but there is a problem with Firefox. If you are using the latter, copy and paste into a text file to see the data):

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATGAPGIAGAPGFPGARGAPGPQGPSGAPGPK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GVQGPPGPQGPR------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSAGPPGATGFPGAAGR----------------------------------------------------------------------------GVVGLPGQR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLPGESGAVGPAGPPGSR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Since molecular phylogenies are somewhat controversial even with full data, it seems completely wild to claim "confirmed" results at this stage of research. Furthermore, surprising outcome was obtained for the green anole (Anolis carolinensis, a lizard). This was expected to be grouped with alligators as a sister taxon. However, the phylogeny reported puts it at the base of the amniotes. This puts it as close to mammals as to alligators. "Such errors are common when working with limited sequences, Asara says." But if the data re T. rex and birds is accepted, why not the Anolis-mammal data? There are indications here that the researchers are letting "generally-agreed relationships" guide their analysis. Even more worrying, they suggest that the phylogeny emerging from their study validates the genuineness of the collagen extracted from the fossil bones. This is dangerously close to a circular argument.

"These results support the endogenous origin of the preserved collagen molecules and confirm the prediction based on morphology that, if biomolecules could be retrieved from a nonavian dinosaur, they would share a higher degree of similarity with birds than with other extant vertebrates."

Some have looked at this analysis and find it too speculative. For example, the Washington Post report has this:

"Pavel Pevzner, director of the Center for Algorithmic and Systems Biology at the University of California at San Diego, said his own research, soon to be published, refutes Asara's work. He said he cannot describe details until they are published, but he was blunt in his response to the new study, which appears in today's issue of the journal Science. The findings are "a joke," Pevzner wrote in an e-mail. "Serious evolutionary biologists will laugh reading this piece.""

Molecular Phylogenetics of Mastodon and Tyrannosaurus rex
Chris L. Organ, Mary H. Schweitzer, Wenxia Zheng, Lisa M. Freimark, Lewis C. Cantley, and John M. Asara
Science 320, 25 April 2008: 499.

Abstract: We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen [alpha]1(I) and [alpha]2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.

See also:

Callaway, E. T. rex confirmed as great granddaddy of all birds, NewScientist.com, 24 April 2008

Weiss, R. T. rex closer to Gizzards Than Lizards, The Washington Post, April 25, 2008; A02