The Sues et al. 2011 matrix has flaws, but there is good news, too…

Earlier posts on Daemonosaurus reported that Sues et al. 2011  nested sauropods outside of theropods and ornithischians outside of those two. That tree topology is often repeated. It has become the paradigm. The Sues et al. analysis was built upon the the Nesbitt (2011) analysis, which was looked at earlier here and here.

Over the past four days
I rebuilt the Sues et al (2011) supplementary material matrix into a computer-friendly .nex file (MacClade) and recovered the same tree as Sues et al.

Then I dived in
and examined every pertinent character score. Unfortunately I found over 200 errors. Some were not scored correctly. Others should have been scored but were left blank. Just a few others should not have been scored because, to my understanding, those parts were not preserved.

I also deleted
the pterosaur and Lagerpeton clades because, according to the large reptile tree, they both nest outside of the clade that includes Euparkeria, the listed dinosaurs and all the intervening taxa.

When the Sues et al. matrix was corrected,
a single tree was recovered that almost matched the large reptile tree in topology (Fig. 1). A single exception at the base of the Dinosauria: Marasuchus shifted to a proximal outgroup node. This is likely due to the exclusion by Sues et al. of several bipedal basal crocodylomorph ancestors of dinosaurs, as recovered by the large reptile tree. Only one bipedal crocodylomorph was included, Dromicosuchus, but it is the most derived of the bunch. Fiurthermore, the theropod sisters of Marasuhcus (Procompsognathus and Segisaurus) were also excluded from the Sues et al. dataset.

Sues et al. 2011 tree topology modified to the re-scoring. Click to enlarge.

Sues et al. 2011 tree topology modified to the re-scoring. Note that sauropodomorpha and ornithischia now nest as sisters to Tawa and the Theropoda, all derived from herrerasaurids with crocs as the proximal outgroup to the Dinosauria. WhileAetosaurus and Arizonasaurus do not look alike, they nest together here, even without the presence of Ticinosuchus, a stem aetosaur, and other clade taxa excluded by Sues et al.

This is good news
With the matching tree topologies now we have two large datasets that produced very similar tree topologies for the Dinosauria using two different character lists, one with 228 traits and the other employing 319. Very few traits are common to both. That’s boosts confidence that the tree topologies mirror actual evolutionary events.

How was it then, that so many erroneous scores were made in Sues et al.?
As a human being myself, I understand that bias is part of every decision. If a particular score started to veer from the accepted paradigm, then perhaps the scored should be questioned. That’s why we need each other. That’s why writers need editors. That’s why artists need art critics. A different perspective might not be correct. Then again, it might be. Every matrix that is published is done for two reasons: to demonstrate validity and to invite criticism so the next matrix can be improved. This is Science at its best, working under the paradigm that humans are behind every datapoint.

Anyone interested in having both .nex files (the Sues dataset and the revised Sues et al dataset) can have them both sent via email on request. Please let me know if I should ZIP your files to a PC or Mac format. If you find any bad scores, please report them.

Sues, Nesbitt and Mortimer
have all been sent the rescored file and I look forward to their comments.

References
Nesbitt SJ 2011. The early evolution of archosaurs: relationships and the origin of major clades. Bulletin of the American Museum of Natural History 352: 292 pp.
Sues H-D, Nesbitt SJ, Berman DS and Henrici AC 2011. A late-surviving basal theropod dinosaur from the latest Triassic of North America. Proceedings of the Royal Society Bpublished online

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2 thoughts on “The Sues et al. 2011 matrix has flaws, but there is good news, too…

    • Good idea, Rob. If I had created a diary while working, I would have done exactly that. Alas, I did not. I slogged through the files over four very long days. So anyone interested is going to have to open the MacClade file and look for autapomorphies (candidate mistakes) on both files. Sorry. Loads of data do not invite a fine tooth comb (BORING!), that’s why matrices are so rarely tested. A few tidbits were offered earlier when I reviewed the Nesbitt 2011 tree (links above). You might recall he scored pterosaurs as lacking an interclavicle and clavicle, but pterosaur workers know those are incorporated into a sternal complex. That sort of thing. Sorry I can’t recall any other anecdotal instances, but many made me scratch my chin.

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