Hwang et al. dataset runs

["Nick Gardner" <ratites637@hotmail.com>]

I'm not sure what's up, I ran Hwang et al.'s original dataset in PAUP* 
4.0b10 and I could not recover anything more than a large polytomy of any 
taxon more derived than the Tyrannosauridae.

Just to see what would happen, I deleted all taxa that were not discussed in 
Paul 1988, and actually got something... I particularly am not saying this 
supports anything, just that's its interesting.  To say this right off, no 
other basal birds were included, which is possible that's why that 
_Archaeopteryx lithographica_ is so basal within Maniraptora.

--+--Allosaurus fragilis
     `--+--+--Tyrannosaurus rex
         |   `--Albertosaurus libratus
         `--+--+--Harpymimus okladnoviki
             |   `--+--Garudimimus brevipes
             |       `--+--Gallimimus bullatus
             |           `--Struthiomimus altus
             `--+--Archaeopteryx lithographica
                 |--Ornitholestes hermanni
                 |--+--Segnosaurus galbinensis
                 |   `--Erlikosaurus andrewsi
                 |--+--Troodon formosus
                 |  `--+--Saurornithoides junior
                 |      `--Saurornithoides mongoliensis
                 |--+--Dromaeosaurus albertensis
                 |   |--Deinonychus antirrhopus
                 |   |--Velociraptor mongoliensis
                 |   |--Adasaurus mongoliensis
                 |   `--Saurornitholestes langstoni
                 `--+--Ingenia yanshini
                     |--Oviraptor philoceratops
                     |--Conchoraptor gracilis
                     |--GI 100/42
                     |--Chirostenotes pergracilis
                     |--Microvenator celer
                     `--Avimimus portentosus

I think the overall point that can be made by this, is that basal members 
are very important in phylogeny.  Enigmosaur monophyly seems to be highly 
dependent on basal members of both the Oviraptorosauria (_Caudipteryx_) and 
the Segnosauria (_Alxasaurus_).  The same goes for the monophyly of Paraves 
and Eumaniraptora.  I originally expected a monophyletic Deinonychosauria to 
be recovered, but even that was not found.  So again, basal members are very 
important! :-D

The next run includes _Confuciusornis sanctus_, I'm not including anything 
outside of the Maniraptora because there was no change there.

--+--Ornitholestes
     |--+--Segnosaurus
     |   `--Erlikosaurus
     |--+--Troodon
     |   `--Saurornithoides
     |--+--Ingenia
     |  |--Oviraptor
     |  |--Conchoraptor
     |  |--GI 100/42
     |  |--Chirostenotes
     |  |--Microvenator
     |  `--Avimimus
     |--+--Dromaeosaurus
     |   `--+--Deinonychus
     |       |--Velociraptor
     |       |--Adasaurus
     |       `--Saurornitholestes
     `--+--Archaeopteryx
         `--Confuciusornis

I would like to offer the suggestion that by including _Confuciusornis_, 
_Archaeopteryx_ is no longer a basal maniraptor, so whatever similarities it 
has with certain dromaeosaurids are intrepreted as convergent, which is why 
_Dromaeosaurus_ is more basal to the other dromaeosaurids.  Again, there is 
no monophyletic Enigmosauria.  Of course, there's also no Paraves or 
Eumaniraptora. ;-)

Now, this run does not include _Archaeopteryx_, but does include 
_Confuciusornis_.  I originally thought that _Confuciusornis_ would be found 
to be close to the oviraptorosaurs...

--+--Ornitholestes
     `--+--+--Segnosaurus
         |   `--Erlikosaurus
         |--+--Troodon
         |  `--Saurornithoides
         |--+--Ingenia
         |   |--Oviraptor
         |   |--Conchoraptor
         |   |--Chirostenotes
         |   |--GI 100/42
         |   |--Microvenator
         |   `--Avimimus
         `--+--Confuciusornis
             `--+--Dromaeosaurus
                 `--+--Deinonychus
                     |--Adasaurus
                     |--Velociraptor
                     `--Saurornitholestes

...the change in the tree is surprising, I was clearly wrong about 
_Confuciusornis_.  Instead, what do we find?  We get Eumaniraptora back!  
Sort of!  And _Ornitholestes_ is more basal to the other maniraptors.

Now, let's try something different.  I've excluded the segnosaurs but 
included _Confuciusornis_.  This is the result, I'm posting the amount of 
the tree that was affected in an obvious way.

--+--+--Harpymimus
     |  |--Garudimimus
     |  `--+--Gallimimus
     |      `--Struthiomimus
     `--+--Ornitholestes
         `--+--+--Troodon
             |   `--Saurornithoides
             |--+--Archaeopteryx
             |  `--Confuciusornis
             |--+--Dromaeosaurus
             |   `--+--Velociraptor
             |       |--Deinonychus
             |       |--Adasaurus
             |       `--Saurornitholestes
             `--+--Avimimus
                 `--+--Ingenia
                     |--Oviraptor
                     |--GI 100/42
                     |--Chirostenotes
                     |--Microvenator
                     `--Conchoraptor

The results are fairly standard.  As usual, no maniraptoran group tries to 
even closer to the other.  We've got a polytomy of Oviraptorosauria, 
Dromaeosauridae, Troodontidae, and Avialae.  The only difference between 
this tree and the previous ones is that _Avimimus_ is more basal to the 
other oviraptorosaurs.

I ran the analysis again and excluded _Confuciusornis_.  It produces the 
same result as the above tree, just without _Confuciusornis_.

Take as one will take it.


Nick Gardner

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