Re: Defining clades like a REAL man (Was: New PaleoBios pa

[Tim Williams <twilliams_alpha@hotmail.com>]

Mike Taylor wrote:

> > The monophyly of Diplodocoidea looks set in stone, but I wouldn't  hold 
> my breath when it > comes to resolving the relationships of many Chinese 
> taxa (_Euhelopus_, _Mamenchisaurus_, > _Omeisaurus_, _Shunosaurus_, etc).

> ... which is precisely why it would be premature to erect a clade for those 
> guys.

Yes, but the family-level names Euhelopodidae, Mamenchisauridae and 
Shunosauridae do exist.  AFAIK, none have phylogenetic definitions.  Should 
they be defined, it would be helpful if the definitions did allow for future 
changes in topology.

> Given sufficiently weird topologies, it might consist of _Diplodocus_ 
> alone, or of all
> sauropods except _Saltasaurus_, but it would still be monophyletic.

Yes, so wouldn't it be handy to have a definition that catered for such an 
eventuality?  I'm not saying it would happen with Diplodocoidea, but it 
could happen with other clades.

Here's one  example.  The Dinosauria is defined as the most recent common 
ancestor of _Passer_ (sparrow) and _Triceratops_, plus all its descendants 
(Padian and May, 1993).  However, in the event that saurischians and 
ornithischians are found to have separate origins from basal archosaurs, 
then the Dinosauria might also include crocodilians.  Thus, an emended 
definition that read "All descendents of the most recent common ancestor of 
_Passer_ (sparrow) and _Triceratops_, but not _Crocodylus_" would mean that 
Dinosauria would ceast to exist if either _Passer_ or _Triceratops_ was 
closer to _Crocodylus_.  This ballooning Dinosauria would be popped.

> You know this, of course; so what do you mean when you talk about the 
> monophyly of Diplodocoidea looking secure?  I think (stop me if I'm wrong) 
> that what you really mean is that the _content_ of that clade is stable -- 
> the Diplodocoidea as "traditionally" conceived (i.e. in
> the last ten years) has not had too much happening in the way of taxa 
> dropping out or others coming in.

Yep, exactly.

> And _Haplocanthosaurus_ is a diplodocoid only in months with an "R" in 
> them.

And _Haplocanthosaurus_ is only a problematic taxon on days of the week 
ending in "y".

;-)

> Definitions should be anchored on the deeply nested and well resolved taxa.

But "well resolved" can change from one analysis to the next.  The discovery 
and or inclusion of one new specimen or one new taxon can shift taxa around 
and play havoc with topology.  I seem to remember that _Mononykus_ once 
looked quite secure as a basal avialan more derived than _Archaeopteryx_, 
and there were plenty of papers arguing this point.  Perle et al. (1993) 
erected the clade Metornithes under the assumption that _Mononykus_ 
(=_Mononychus_) was a bird more derived than _Archaeopteryx_.  Subsequently, 
_Mononykus_ (and other alvarezsaurs) fell out of the Avialae.  Now, with its 
current definition, Metornithes is bigger (more inclusive) than Avialae!  If 
Metornithes had been defined as "all descendents of the most recent common 
ancestor of _Mononykus_ and _Passer_, but not _Archaeopteryx_", then 
Metornithes would disappear in the event that _Mononykus_ was found to be 
more basal than _Archaeopteryx_.  In other words, once the avialan 
hypothesis for _Mononykus_ was no longer supported, the clade Metornithes 
(which was erected in the context of _Mononykus_ being a bird) would also 
expire.

Perle A., M.A. Norell, L.M. Chiappe and J.M. Clark. (1993).  Flightless bird 
from the Cretaceous of Mongolia, Nature 362: 623-626.

> Pet peeve: the "evidence" that Brachiosauridae is paraphyletic is a 
> sequence of unsubstantiated assertions in Salgado and Calvo 1997, backed up 
> by the phylogenetic analysis in the companion paper Salgado et al. 1997, 
> which claims to have recovered a paraphyletic Brachiosauridae based on the 
> inclusion of two (2) potentially brachiosaurid OTUs -- _Brachiosaurus 
> brancai_ and _Chubutisaurus_.

I meant Brachiosauridae in the traditional sense, which included a LOT of 
sauropods.  Not just _Brachiosaurus_ and _Chubutisaurus_, but 
_Volkheimeria_, _Lapparentosaurus_, _Pleurocoelus_ and many others as well.  
See McIntosh (1990) for an example.  I don't disagree that there is a valid 
clade Brachiosauridae that includes _Brachiosaurus_ and some (several?) 
other genera; but Brachiosauridae has in the past been used as a wastebasket 
for basal titanosauriforms.

> Wilson and Sereno's solution in the case of Brachiosauridae was to define a 
> stem-based clade (_Brachiosaurus_ not _Saltasaurus_) rather than a node; 
> which seems eminently sensible.

Yes, it is sensible.  Eminently so.  But this a stem-based clade; a 
node-based clade would not be so easy for Brachiosauridae.

Cheers

Tim