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RE: tiny-armed theropods

The reason we include OTUs in phylogenetic analyses is to determine their 
relationships.  Sometimes the resulting cladogram isn't fully resolved, giving 
us polytomies.  This is what would happen in the best case scenario for an 
actual nomen dubium, and it happens often with valid taxa as well.  It doesn't 
make including OTUs that cause polytomies pointless, nomina dubia included.  We 
still find out to the best of our ability what the holotype organism is related 
to.  Just because I can't refer any other organisms to ANSP 9259's species, and 
it may belong to the same species as Stenonychosaurus inequalis, doesn't mean I 
suddenly stop caring where it goes in the tree of life (or how it ate, or where 
it lived, or any other question that applies to organisms).

In any case, as is usual for email debates, this whole discussion has gotten 
removed from my original point.
- You said abandoning Troodontidae (if we keep the tooth as the holotype of 
Troodon) is preferrable, because we would supposedly have to include Troodon in 
our analyses to determine the extent of clades using it for definitions, like 
- I pointed out we use plenty of clades based on taxa not included in the 
analysis (e.g. Passer).
- You replied that somehow the situation is different.  "_Passer_ exists. It's 
a real animal - and a real taxon. However, if _Troodon_ becomes a nomen dubium, 
it is no longer a valid taxon. It therefore no longer represents a once living, 
breathing animal. It is *just* a name."

I still see a disconnect in your line of argument.  You admit we can include 
nomina dubia in analyses, just like we can include Passer if we wanted.  And 
you know that we often include inviduals as OTUs in analyses (oviraptorid IGM 
100/42, IGM 100/1015 that was later made the Tsaagan holotype, probable 
Ichthyornis individual YPM 1732, etc.), so an OTU doesn't have to be an actual 
taxon, population, species, genus, whatever.  Thus since Troodon could be 
hypothetically included in an analysis, we can still know which node to apply 
Troodontidae to even if Troodon itself is not included, just as we can know 
which node to apply Avialae to without the inclusion of Passer.

You can *prefer* that nomina dubia not be used in phylogenetic definitions, but 
unless they're indeterminate at a more inclusive level than their clade 
definition requires (e.g. if Troodon could be a dromaeosaurid), they don't 
actually cause any problems.  Similarly, your closing paragraph exemplifies why 
we end up talking past each other.  I argue about what the current rules are, 
while you argue about how you would like things to be, as if that has any force 
in the decisions we make about nomenclature and taxonomy.  I wonder if other 
areas of zoology are as populated by individuals following their own whims.  Do 
entomologists follow the ICZN or do they make up their own rules when it suits 
them, like 'no wing-based taxon can be used for a family level name'?  It'd be 
interesting to find out.

Mickey Mortimer

> Date: Sun, 16 Oct 2011 12:13:00 +1100
> From: tijawi@gmail.com
> To: dinosaur@usc.edu
> Subject: Re: tiny-armed theropods
> Mickey Mortimer <mickey_mortimer111@msn.com> wrote:
> > I don't know where you got the idea that nomina dubia aren't taxa or 
> > organisms.  Troodon formosus is a real animal, diagnostic
> > holotype or not.  There was a living organism which the type tooth of 
> > Troodon belonged to, and this individual can be included in a
> > phlogenetic analysis, regardless of whether additional individuals could be 
> > assigned to its species.
> Of course the tooth of _Troodon formosus_ came from a real animal.
> I'm not suggesting it was carved out of stone by Cretaceous trolls.
> But if a genus is declared a nomen dubium, then it no longer denotes a
> real taxon. For example, the teeth named _Deinodon horridus_ (a nomen
> dubium) could belong to any number of tyrannosaurid species. So
> although the teeth came from a real individual, that individual does
> not represent a distinct taxon. Thus, it would serve no purpose to
> code the teeth and put them into a phylogenetic analysis. Yes, you
> *could* put _Deinodon_ into a phylogenetic analysis. But it's like a
> dog chasing a car: it can be done - but what's the point?
> > There's no rule that says only taxa or only valid taxa can be included in 
> > such analyses.
> Yes, I know. But since a nomen dubium no longer represents a real or
> distinct taxon, it's removed from taxonomic consideration. Sticking a
> nomen dubium into an analysis is just going through the motions. It's
> not advancing the scientific process in any way. The only reason you
> would include a nomen dubium in an analysis is if it happens to be a
> name-nearing taxon of a clade, which strikes me as circular reasoning.
> I'd prefer that nomina dubia be excluded from clade definitions.
> > The microraptorian NGMC 91 is included by Senter (2007) for instance, 
> > despite being only a single individual that has not been
> > conclusively differentiated from Sinornithosaurus.  Indeed, it has only 
> > been described as Dromaeosauridae gen. et sp. indet. and
> > Sinornithosaurus sp. indet..
> IMHO this is irrelevant. If NGMC 91 is recovered as a distinct taxon
> in the analysis, then it is no longer indeterminate. On the other
> hand, if it cannot be conclusively differentiated from
> _Sinornithosaurus_, and can be conclusively differentiated from other
> dromaeosaurids - then NGMC 91 belongs in _Sinornithosaurus_.
> > What's the point of having a rulebook for a community if they only follow 
> > the rules they want to anyway?  It's like enforcing laws only
> > when they don't inconvenience you.  We might as well just get rid of the 
> > ICZN if we're going to call it wrong when we don't like what it
> > says.
> Well, now that you mention it... :-) I have repeatedly opined that
> the ICZN Code should *not* apply to family-level taxa (family,
> subfamily, tribe, superfamily), only to genera and species. So while
> I don't advocate completely getting rid of the ICZN, it's focus should
> be removed from family-level taxa. It just causes too many problems
> when phrasing sensible phylogenetic definitions.
> Cheers
> Tim