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

Keep in mind that some reviewers (and journal editors) are now strongly
pressuring authors to at least do lip service to phylogenetics when a new
taxon is described.  Pressure is even put on paleontologists who do not
"specialize" in the subject.  The result is, for the sake of expediency
in getting the new animal to press, a less than complete cladogram.

The solution to this problem?  Stop pressuring those who's specialty is
something other than cladistics to include cladistic phylogenies in their
papers.  They will be happier, and phylogenetic specialists like you, who
know what you are doing, will be happier too.

Not every paleo paper needs to have an accompanying cladogram.


On Thu, 16 Mar 2006 09:48:01 +0000 Michael Mortimer
<mickey_mortimer111@msn.com> writes:
> 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-
> |--non-maniraptoriformes
> `--+--Ornithomimosauria
>    `--+--Juravenator
>       |--Scipionyx
>       `--+--Compsognathus
>          `--+--Huaxiagnathus
>             |--Sinosauropteryx
>             `--+--Ornitholestes
>                `--"oviraptoriformes"+paravians
> 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