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Re: Stratigraphy, biogeography & cladograms

I was thinking of letting this one go with what I said earlier, but in
hindsight there's more I can say, so here goes.

John V Jackson wrote:

> >>I liked Tom's critique of stratigraphic evidence, but would add another
> >criticism - stratigraphy and biogeography are not heritable.  Parsimony
> >analyses, whether based on morphology, molecules, or behavior,
> >explicitly assume that the characters under study are heritable.  (And
> >yes, there are potential problems with this, such as phenotypic
> >plasticity.  With living groups, we can test heritability; with fossils,
> >our confidence that we're not seeing something pathological increases
> >with histological examination or the collection of a population.)  This
> >is why we can never, ever, combine stratigraphic and character
> >information in a single matrix, and why stratocladistics has serious
> >problems.
> ...and by using this argument you hope to get away with saying the fact that
> all the identifiable maniraptorans and arctos appear after Archy and none
> before can be totally ignored. 

No, it can't.  But here's the crux - unless you have a specific
hypothesis to compare with those presented by Tom and others, it means
absolutely nothing.  The central point in the work I did with Norell on
the temporal paradox was the importance of making such statements in a
comparative context.  Saying that stratigraphy is a problem for current
phylogenetic hypotheses, but not proposing an explicit competitor, is
like saying a sauropod is big.  By itself, that means nothing - but "a
sauropod is bigger than a hummingbird or an elephant" means something. 
The "temporal paradox" means nothing unless you have a tree that (a)
explains the character evidence at least as well and (b) is less
temporally paradoxical.  

 If it wasn't unintentional it would be
> sophistry. Incidentally the claim that stratigraphic and character
> information cannot be combined, if that is what you're saying, is
> contentional even within cladistic circles.  Some claim that any currencies
> that can be converted to likelihoods may be realistically combined.

There are many meanings of "cladistics," but none of them involve
likelihood.  Max like is another kettle of fish - some of us (including
yours truly) regard it as a tool no more nor less useful as parsimony;
some prefer it; others regard it as philosophically bankrupt.  But if
you read any of the current phylogenetic literature, you'll find that
the most fundamental division in the profession is between "pattern
cladists" and "statistical phylogeneticists."  The likelihood models
that Huelsenbeck, Rannala, and Wagner are working on are absolutely not
cladistic.  (This is not a condemnation - merely a statement of fact. 
That Pete Wagner is not a mongoose a statement of fact as well.  If
y'all don't believe me, stop by - his office is next to mine.)  

In the interest of having you hit the library, I won't expand further on

> >
> >On the other hand, I do agree that stratigraphy and biogeography should,
> >at some level, preserve a phylogenetic signal, and that they can be used
> >as external comparative criteria.  But for stratigraphy to be used, we
> >must try one of two things:  either calculate error margins on the
> >ranges of our taxa (and for dinosaurs, a great many species are known
> >from a single occurrence and will have infinite error margins - hence,
> >we will be unable to reject any hypothesis on stratigraphic grounds)
> OK so not every fossil can be used

Not what I said at all.  What I said is that for some groups, error
margins placed on fossil taxa will be meaningless.  Dinosaurs are such a
group.  Now it's you who appear to advocate ignoring information ;-)

> >or calculate tree-wide comparative metrics, such as SCI, SMIG, or MSM.
> >Mark Norell and I did this at SVP, and as it turns out, moving birds
> >outside of Theropoda usually makes these stats worse.
> Which of Martin and Feduccia are you mistaking me for Chris?

Neither, and both.  The similarity relates to what you implied earlier -
that stratigraphy presents a problem to current dinosaurian relationship
hypotheses.  Got an explicit hypothesis to bring to the table?  Than you
can say that.  Don't have one?  Than you can't.  Martin and Feduccia
have both listed the temporal paradox as a problem, but will not present
a tree that fits the stratigraphic signal (and I mean the treewide
signal) better.  I am not implying that you don't think birds are
dinosaurs, if that's what your question meant.

> >
> >What it all boils down to - what you're not allowed to do is simply say,
> >"I don't like your tree," and leave it at that.
> I don't like it because it flies in the face of every category of evidence
> except cladistics.

Once again - show me the numbers on an explicit hypothesis (cladistic or
otherwise), and we have a discussion.  Otherwise, we don't.


> >
> >
> >Not in modern phylogenetics.  Really.  Have a look at the literature on
> >internal global support to see how carefully most systematists qualify
> >their trees and go out of their way to consider alternatives.
> So when you go shopping do you have to have a clear margin of strawberry
> icecream over rapsberry before you choose it?

Not sure what this means, so I'll assume it's your way of saying "I
don't know what you mean."  I will therefore say it more carefully.

In most phylogenetic analyses, the researcher does not simply present
the consensus of most parsimonious trees and leave it at that.  If
someone else has published a different tree, the two will be explicitly
compared.  Many (including myself) will look at trees one, two, or more
steps longer.  If another external signal (e.g. stratigraphy,
biogeography) suggests a different pattern, the reasons for that
difference will be explored.  But don't take my word for it - here's
your formal invitation to read some of the literature out there and see
how modern phylogenetics actually works.


> >
> >Which leads us to the concept of testing the hypothesis that characters
> >are dependent.
> This is a foundation you *really do* have to prove for certain before
> building a tower of Babel on.

Then may I expect you to read some of the literature out there on
testing for character correlation?  Here's something to start with:

Maddison, W.P.  1990.  A method for testing the correlated evolution of
two binary characters:  are gains or losses concentrated on certain
branches of a phylogenetic tree?  Evolution, 44:539-557.

Harvey, P.H., and M.D. Pagel.  1991.  The comparative method in
evolutionary biology.  Oxford Univ. Press, New York.

There's been much more published since then, esp. for discrete
characters, but I don't have them handy at the moment.  If anyone's
interested, drop me a line and I'll try to exhume them later.

> > We can test character correlations on a tree very
> >simply, both for continuous and discrete data.  Lots of papers out there
> >on this - again, the most recent Syst Biol. has an article on it.
> You've done nothing remotely resembling proving all the input characters are
> independent!!

I was unaware that a particular data set was being tested here.  Is
there a specific set of characters you would like me to test?  

In the meantime - why not have a look at the literature I cited.  Or
what are you afraid of?

> >
> >About Peter Wagner's points - although I agree, in principle, that
> >parsimony can underestimate real change,
> So you grant that, in principle, it may have been possible for an early bird
> to have gone flightless, and if it did, its arms might have shortened, and
> that this might have happened more than once.  But you'll argue till the
> cows come home that it didn't happen.

In principle, it's possible that all tetrapod forelimbs are
independently evolved, and that the ancestral tetrapod was limbless.  I
think that highly unlikely on the basis of what the available evidence
tells me.  So far, no one has presented an explicit hypothesis to
suggest the model you propose.  

> Perhaps you would like to answer this question now:  Why did Archaeopteryx
> give rise to no flightless forms in the Cretaceous except Mononykus and its
> relatives?

On what basis do you argue that Archaeopteryx was the direct ancestor of
the alvarezsaurids?  Moreover, one could argue that hesperornithiforms
were flightless.

Also, given that most flightless lineages today are restricted to
islands, and given that our sample of small island faunas in the
Mesozoic is very restricted, I'm not sure we can confidently say that
flightlessness arose only twice in noncrown birds.