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(The following are some thoughts inspired by comments by Tom Holtz and

Uh-oh, I have a sense that it's deja vu all over again. 

You see, many moons ago, I had some outrageous notions. Why, I used to say
that small dinosaurs were probably feathered (but that definitive evidence
either way was not yet available), that one cannot use feathers to define
Aves, and that one cannot assume that isolated Mesozoic feathers belong to
birds rather than dinosaurs. Most researchers vigorously disagreed, although
exactly why was never really clear. Seemed to have something to do with the
notion that feathers are only found in birds, so parsimony demanded that
feathers must be assumed to be avian unless proven otherwise. I countered that
considering the absence of any scales or other skin for small dinosaurs, the
matter was entirely open, parsimony was not present in either direction, and
restoring small theropods with either feathers or scales was equally valid. In
other words, I used a scientific methodolgy called "we don't know the heck
what is going on yet, so let's wait for new evidence to tell us what is
correct, and until then relax and accept all viewpoints as equally valid". You
want to illustrate your little dinosaurs without feathers fine, with scales go
right ahead. Now the issue is essentially settled:)

Many moons ago I suggested that most small Cretaceous, advanced, bird-like
theropods were secondarily flightless, and closer to birds than Archaeopteryx.
Here is where the deja vu is creeping in. A few researchers agree to at least
a certain extent. If alvarezsaurs are closer to birds than the urvogel as the
AMNH group argues, then they should be secondarily flightless (the dino-bird,
not the paleontologists). Andre Elzanowski argues that oviraptors and other
theropods with folding arms are closer to birds than Archaeopteryx, and that
they are secondarily flightless. (Of course George has taken the hypothesis to
an extreme, but this is a distinctive issue I'm not going to discuss here.)
However, most researchers seem to be reacting with the same kind of mode that
the feather problem was addressed. Something along the line of 'Archaeopteryx
is a bird, it flew, the most bird-like dinosaurs did not fly, they are
dinosaurs, and current cladograms place them as sister taxa to Archaeopteryx
and Aves, so the dinosaurs have only preflight characters, and it should be
assumed to be so unless shown otherwise". 

Now, just as it was possible that small dinosaurs were not feathered, it is
quite possible that there were no secondarily flightless dinosaurs above the
level of the urvogel. The problem here is that the evidence is NOT definitive
in either way. We are yet again in the stage of we simply do not know what
happened. It is clear that birds descended from dinosaurs, probably in the
Jurassic. We also have a fairly good idea of what theropod groups are closest
to birds. Beyond that just about everything is up for grabs. 

This is because it is obvious that massive parallalism and reversals - intense
mosaic evolution - was going on as birds first developed. It is a fact that
all of the Cretaceous small theropod groups possess nonflight avian characters
not seen in Archaeopteryx (too many to list here). It is equally true that
Archaeopteryx has nonflight avian characters not seen in the various
theropods. We know that loss of flight is fairly common in birds, and one
might expect it to be especially prone to occur in early, poor fliers that
still had long, clawed fingers to grab things with. It is a fact that many
Cretaceous theropods have flight related characters (folding arms, large
furcula), sometimes the flight related characters are better developed than
those of Archaeopteryx (large sternal plates, ossified sternal ribs, ossified
uncinate processes, shorter tail, tail with pterosaur-like ossified rods). 

What are we to make of this? I argue that since the Cretaceous theropods have
both avian nonflight and flight related features not seen in Archaeopteryx,
that it is therefore very possible that they descended from fliers more
advanced, and closer to birds, than the urvogel. Certainly it is a valid and
strong hypothesis, at least as good as the conventional view. 

Tom suggested that I favor scenario over phylogentic based hypothesis. Nyet!
Moi strongly disfavors those who prefer scenario over phylogenetic arguments.
That is the methodology of Feduccia and Martin. I would never argue that some
dinosaurs were secondarily flightless unless they had a number of avian
characters not seen in Archaeopteryx. Both aspects of the problem are crucial.

As for cladograms and parsimony. I suspect one reason cladograms tend to plot
Archaeopteryx closer to birds is because they do not include all the relevant
characters. Also, avian flight characters that are lost along with flight can
bias the results. For example, flying Confuciusornis had a long, strut-like,
retroverted coracoid like that of modern flying birds. A flightless ostrich
has a shorter, broader, procumbent coracoid that looks like that of a
dinosaur. Yet the ostrich is phylogentically much closer to modern flying
birds. In losing flight, the ratite coracoid has reverted to the dinosaur
condition. Likewise, it is possible that the seemingly less avian - compared
to Archaeopteryx - coracoids of say dromaeosaurs are actually secondarily
reversed to the dinosaur condition. Scored on a cladogram, it would plot below
the urvogel. But maybe its just secondarily flightless. 

So far those doing cladistic studies have completely ignored the potential
bias introduced by the possibility of early loss of flight. Taking steps to
negate the bias (by running the character analysis while including and
excluding flight related characters and seeing if there is a difference)
should be the norm.  

As for cladistic parsimony, it is a useful but dangerous thing. If one ran a
cladistic analysis on the skeletons of gorillas, chimps and people, the apes
would clump together way from the human. But of course DNA analysis shows that
chimps and humans form a clade above the level of other apes. The problem is
not really with cladistics. A much better set of tranistional fossils,
analyzed cladistically, would also show the correct pattern. 

The chart that appears in Natl Geogrpahic illustrates the problem. It places
Caudipteryx closer to Archaeopteryx than dromaeosaurs. Yet there is little
doubt that  the closest relatives of Archaeopteryx are dromaeosaurs, they
share so many detailed features absent in other theropods. At the same time,
each of the three types has avian features not seen in the other.
Archaeopteryx is an obvious winged flier, but the two dinosaurs have the
larger sternal plates and ossified sternal ribs, like those of flightless
birds. The two dinosaurs also have more flight developed tails (very short in
Caudipteryx, rod stiffened in both). It is possible that the dinosaurs never
evolved flight and their flight characters are really pre-flight. It is
possible that they are secondarily flightless and are above Archaeopteryx. It
is possible that one of more of the dinosaurs is secondarily flightless and
the other is not. Just one of the dinosaurs may be closer to birds than
Archaeopteryx. Perhaps one or more of the dinosaurs had evolved and then lost
flight independently from birds. And on and on. There is no current
methodology that can sort this jumbled mosaic out. The gaps are too big. 

At this time, there is not enough fossil information to decide how the
advanced bird-like dinosaurs and early birds are related to one another, or
whether any of the dinosaurs did or did not lose flight. Parsimony and
cladograms are useful and necessary, but they are unlikely to settle the
issue. What will decide things someday are more fossils. We'll just have to

For now, the notion that some dinosaurs were secondarily flightless is as good
as the hypothesis that they were feathered was a few years ago. I hope those
of us who work on the origin of birds from dinosaurs can avoid falling into
the trap of dogmatically opposed procedural camps coming to premature firm
conclusions. (Not that we should not all pursue our own methodologies,
multiple approaches are more robust than a single party line.) Secondarily
flightless theropods should not be considered the inferior hypothesis, at the
same time it should be considered a working hypothesis that has neither been
falsified or verified, it should always be considered when executing cladistic

On a related matter, it was asked by a list member what the taxonomic
implications of placing some dinosaurs closer to birds than Archaeopteryx may
be? Would secondarily flightless theropods be birds? Or would this mean that
Feduccia and Martin are right that Caudipteryx and Protarchaeopteryx are just
secondarily flightless birds? Here we are getting into a danger zone where
semantics drives phylogenetic conclusions. All we can do is sort out the
phylogenetic relationships between the most bird-like dinosaurs and early
birds. If some dinosaurs prove to be closer to modern birds than
Archaeopteryx, this only supports rather than refutes the link between the two
groups. As for whether to call such dinosaurs birds, it is an interesting
question but not really important, and will eventually be settled albeit not