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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.