Phylogeny Friday -- 25 April 2008

Duh! That's Obvious, Edition

Take a look at this mastodon skeleton:


Does it look like anything you recognize? Perhaps a large terrestrial mammal with big tusks. If you said "elephant" you win. The prize: nothing.

That is half of the conclusion from a recent paper in Science (doi:10.1126/science.1154284). Really. The other half: birds and dinosaurs are pretty closely related. Or, more specifically, birds and Tyrannosaurus rex -- THE COOLEST MOST AWESOMEST OF ALL DINOSAURS EVER!! -- are closely related. And, for this, they get a Science paper.

Now, the way they did this is pretty damn cool: they sequenced proteins from T. rex bones. But that was reported last year (doi:10.1126/science.1137614) in the paper where they screwed up the species name in the title (they got it right this time around). Anyway, some of the same people took those sequences and, along with some other sequences that they mined from various databases, constructed a phylogenetic tree of vertebrates.


That right there is the tree, with dinos and birds together, and mastodons and elephants together. It's totally unremarkable, but it got into Science (no, I'm not jealous). Now, this approach has the potential to resolve some long-standing conflicts in vertebrate systematics. This paper, however, does not resolve anything. It's a sexy method that will probably be difficult to implement elsewhere.

Asara JM, Schweitzer MH, Freimark LM, Phillips M, and Cantley LC. 2007. Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry. Science 316: 280-285 doi:10.1126/science.1137614

Organ CL, Schweitzer MH, Zheng W. Freimark LM, Cantley LC, and Asara JM. 2008. Molecular Phylogenetics of Mastodon and Tyrannosaurus rex. Science 320: 499 doi:10.1126/science.1154284

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The resolution on this tree is terrible, though. Tyrannosaurus is grouped in with birds rather than diverging between birds and the crocodylian like it should have, the the Anolis results are waaaaaay out of order. It's cool that T. rex proteins have been recovered from preserved collagen, but the general reaction of paleontologists to this paper seems to be "Tell us something we didn't already know."

The purpose of our paper was not to phylogenetically place these fossils - we already knew where they should go based on morphology. And yes, the clade Dinosauria in our tree can only be resolved to a polytomy given our dataset. Collagen sequence from a dinosaur is an extraordinary claim and the point of this work was to see if we could support or refute the original claims made by John Asara and Mary Schweitzer (and therefore, this is not a MPU - I wasn't involved with the first study at all). I think the results support the claim that there are original biomolecules preserved in these fossils and that they contain some degree of phylogenetic signal.

By Chris Organ (not verified) on 25 Apr 2008 #permalink

Chris, thanks for the comment. I agree that it is important to validate Asara and Schweitzer's sequencing with a phylogenetic analysis. It's amusing, however, to see the popular press cover this story as: "Study confirms birds and dinos are close relatives!" Also, I agree with your conclusions (that some interesting stuff can be done with sequences from fossils), but how often will people be able to get good sequences from fossils? And how many unresolved phylogenies will those sequences help solve?

Hey RPM,
Well, it is depressing how bad the press misquotes and takes things out of context (makes me feel extra bad, actually, given the current presidential primary race...). I think you raise a good point about how often this might be possible - the answer could be "rarely to never." I also agree concerning the possibility for this approach to resolve parts of the tree, but if there is a chance, it should be explored. Very few people have looked for preserved proteins in old fossils so it could be more common than we previously thought. Who knows what lies in the undiscovered country?
Good blog by the way, I read it at least once a week.
Best, Chris

By Chris Organ (not verified) on 25 Apr 2008 #permalink

This wasn't meant to be a definitive phylogenetic study. The conclusion of the brief paper is:

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. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas of the vertebrate evolutionary tree that have, so far, been intractable. The findings presented here also bolster the use of morphology in phylogenetics because our results are consistent with studies on the evolutionary relationships of fossil forms that rely on morphology.

That is, it is a study about whether a) the collagens recovered really were from dinosaur or mastodon, b) ancient molecular information agrees with morphology, c) phylogenies could in principle be investigated using ancient molecular data.

What the press has to say is another issue... :-)

Yeah, it's just a sexy method paper. So what? That's one of the niches of Science.

By Sven DiMilo (not verified) on 30 Apr 2008 #permalink

Well, it is depressing how bad the press misquotes and takes things out of context...

Chris, this is a delightful piece of work but I'd note that your own freaking press release is headlined "Molecular Analysis Confirms T. Rex's Evolutionary Link To Birds". I'm having trouble understanding how "Study confirms birds and dinos are close relatives!" is a further mischaracterization of that.

In general, as much as scientists bitch about the quality of science journalism, those academic Communications Departments are worse offenders by far.

Hi JSinger - agreed!

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