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Re: BCF in perspective (LONG!)

G.O. writes:

>>The main objection I have to the BADD phylogeny is that it tells us nothing
>about the critters _on the branches_ (not at the terminal points) of the

        Of course any cladogram only shows real taxa on the terminal
points; all others are purely hypothetical. Just filling in the gaps.

        Formulating hypothetical phylogenies has a few basic steps AFAIK;
for example (probably the best way):
1) Collect data from specimens (preferrably hands-on, otherwise using
published data from others). The more characters used, the more accurate
the cladogram will be. Good character choice is absolutely imperative here;
you must use any relevant characters, not only include the characters that
seem to support a preconceived notion of the phylogeny.
2) Form a data matrix, analyze it to form a cladogram (the most
parsimonious is best), a hypothetical evolutionary history of the taxa
involved (including at least one outgroup, the closest related taxon not
included in the clade under consideration, e.g. crocodilians).
3) Compare the cladogram to the fossil record; see if your proposed
phylogeny matches the stratigraphic record of the taxa included.
4) If desired, formulate macroevolutionary hypotheses to explain trends -
i.e. the origin of flight in that clade. Not at all necessary, and maybe
not even good falsifiable science, but still fun.

        The problem that I have with BCF, besides the fact that I have not
seen the phylogeny, is that:
1) Archosaurs did not start out small, unless you're redefining the
definition of Archosauria to include some small diapsids as basal
2) The robin is not, not, not a good representative for the birds in
general. About 140 million years of evolution separate the modern robin and
the earliest conclusively known birds. Ratites and paleognaths are the best
guesses for the earliest non-Archaeopterygian birds; passerines such as the
robin came later.
3) The Archosaurs did not start out with large forelimbs; their hindlimbs
and forelimbs were of equivalent length (unless you're using pterosaurs as
your outgroup). The earliest conclusively known birds (i.e. Archaeopteryx)
had huge forelimbs compared to non-dinosaurian archosaurs.
4) Parsimony is used after cladograms are created, not in the formulation
of phylogenetic hypotheses without cladograms. Once the most parsimonious
cladogram is found, we have our _hypothetical_ phylogeny (which is more
than likely slightly wrong, but if we used good data and character choice,
is probably better than anything else we have).

If BCF is to overturn BADD, it must play by the same rules as Gauthier and
others did when they overturned SWDKWTHBATLLRTM (sorry, we don't know what
the heck birds are, they look like reptiles to me). It simply doesn't have
a snowball's chance otherwise. Unfair? No. Cladistics is not inherently
biased against any phylogenetic hypothesis that uses real data; it is an
objective method to resolve phylogenies, and according to the majority of
professional paleontologists, it is the best method that we have for
resolving the phylogenetic relationships of extinct organisms.

I'll add my mandatory disclaimer: This entire message is all IMHO. I'm no
expert in cladistics (or a BADD fanatic), I just am trying to think clearly
on this important and interesting topic. I probably made some errors in the
above statements, but someone will scold me if they notice and we'll all be
the better for it. All right, I'll be quiet now. Sorry about the length and
all. And of course, nothing personal G.O.  8-)

                        John R. Hutchinson
                  Evolving Evolutionary Biologist
                 Department of Integrative Biology
                  3060 Valley Life Sciences Bldg
                University of California - Berkeley
                        Berkeley, CA 94720
                          (510) 643-2109