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Re: Juravenator; or How not to perform a phylogenetic analysis

Today's description of Juravenator included a phylogenetic analysis, which moved me to write this post. I noted a couple problems which plague a large portion of published phylogenetic analyses I see.

Gohlich and Chiappe's analysis is the Theropod Working Group (TWG) analysis with 27 taxa excluded, 8 taxa added, 43 characters deleted and 10 characters added. WHY did they delete taxa and characters!? Studies show that including taxa and characters is VERY important to resolving "correct" trees. I mean, I know it takes time to code taxa, but they were already coded! It took more time to bother deleting them. Ughh. Maybe they weren't relevent taxa, you say. Gohlich and Chiappe were trying to determine basal coelurosaur phylogeny, not phylogeny of all non-pygostylian coelurosaurs after all. Alas, the deleted taxa include Alvarezsaurus and Pelecanimimus, which as basal representatives of their clades, are very important when placing taxa falling near Ornithomimosauria and Alvarezsauridae. And why bother deleting any at all? They're not going to harm the analysis if included.

They recovered a tree where the compsognathid/coelurid taxa formed a polytomy at the base of Maniraptora.

What to do when you have a large polytomy? Well, here's what not to do. Gohlich and Chiappe ran a second analysis "omitting seven taxa, either less relevant (i.e., Alxasaurus elesitaiensis, Erlikosaurus andrewsi) or largely incomplete (i.e., Mirischia asymmetrica, Scipionyx samniticus, Nqwebasaurus thwazi, Coelurus fragilis, Nedcolbertia justinhoffmanni)." I already explained that taxa should not be deleted, especially those close to your group of interest. How are therizinosaurs less relevant than, say... oviraptorosaurs? Or avialans? Also, something that almost every author needs to learn... *ahem* incomplete taxa don't necessarily lead to decreased resolution. In fact, they can actually help. It all depends on what codings are unknown. So don't delete incomplete taxa just because they're incomplete. They may influence topology regardless.

After deleting the seven taxa, Gohlich and Chiappe recovered new trees. Ornitholestes was still a basal maniraptoran, but Compsognathus, Sinosauropteryx, Huaxiagnathus and Juravenator ended up in a monophyletic clade sister to Maniraptoriformes. The fact this topology is incongruent with the original topology should have raised alarm bells.

So here's what you should do if you have a large polytomy you want resolved. Display a majority rule consensus in PAUP (contree "" majrule = yes) to find the poorly resolved taxa (they'll have the most seldomly occuring nodes around them). Then delete one taxon at a time BUT don't delete them from the analysis. Instead, just delete them from the saved trees. When you type "delete Juravenator" for instance, PAUP will ask whether you want to delete it from the saved trees or just prune it. Select prune. This will leave the trees the same, but without your deleted taxon and any polytomies caused by it falling out in different positions. Keep deleting taxa until your tree is as resolved as you want. If this is done to Gohlich and Chiappe's tree, the following tree results-


The excluded taxa help move 'compsognathids' into Maniraptora and make them paraphyletic to derived maniraptorans. Juravenator is no longer a compsognathid, but is instead more basal. And it's SO easy to do. So please, authors of future papers...
1. Don't exclude taxa from analyses because they are incomplete.
2. If you want to resolve a polytomy, just prune the poorly resolved taxa from the tree. Don't delete them and rerun the analysis.

Mickey Mortimer