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Re: Stratigraphy, biogeography & cladograms

John V Jackson wrote:
> --Original Message-- From: chris brochu <cbrochu@fmppr.fmnh.org>: Monday,
> January 18, 1999 11:17 PM

> >
> >
> >You seem to be saying that living birds are diverged enough to avoid
> >what is implicitly a long-branch problem that might arise in nonavian
> >theropods.  This is actually very unlikely, as a long-branch problem is
> >much, much likelier when lineages are long separate.
> I'm not saying it's easier to *make a tree* when for example everything
> diverged a long time ago but very quickly, I'm saying it's easier to see
> differences - between flightless parrots and flightless rails for example.

So what you're saying is that flightlessness will transform a lineage,
but at a certain threshold its modifications will be insufficient to
overturn a primary phylogenetic signal.  Again, a good way to test this
is to downweight the flightless-linked characters. 

But you implicitly assume that flightless rails and geese are more
different from each other than a putative flightless oviraptorosaur and
dromaeosaurid, assuming these are secondarily flightless.  Do you have
quantitative evidence for this assertion?  (Amount of time since
divergence is, by itself, only a crude measure of this - see below.)

> >Aside from that there are ways of quantitatively testing your
> >assertion.  Compare your preferred nonavian phylogeny with those
> >recovered by someone else - Tom, Chiappe, Sereno, Forster, anyone.
> >Since you're dealing with discrete character data in a parsimony
> >environment, apply the Wilcoxon signed-rank test first used in this
> >context by Templeton, and now lovingly referred by systematists
> >everywhere as the "Templeton test," to your comparisons.  This would
> >tell you whether your tree is *significantly* longer or not.
> One way to know whether a tree is longer or not is to count the years: 

No, that won't work. In phylogenetics, "length" refers to the number of
character transformations along a lineage.  This may be correlated with
time, but won't be linked with it, as rates of evolution will vary from
one lineage to another.

Meanings of "branch length" are muddled in the literature -
paleontologists tend to use it with respect to time, while neontologists
use it to mean character divergence.  In nearly all of the current
phylogenetic literature, it's the latter definition that is meant.  And
by "longer tree," I refer to the total number of transformations, not
the amount of time. 

> tree linking "now" with the last common ancestor of parrots and rails is
> longer than the tree separating the last non-flying ancestors of Archy with
> its earliest flightless descendants.  And before you say this is entirely
> theoretical, let me remind you that I was providing an explanation for a
> phenomenon, not proof nor evidence.

But it's still an assertion that can be tested, and (as explained above)
applies "length" very differently from me and other systematists.

The rest of what you wrote basically boils down to "I really really
don't like cladistics."  That's your option.  But I would hope you'd
learn something about it before discounting it.  Best of luck.