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Re: Stratigraphy, biogeography & cladograms

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

>John V Jackson wrote:
>> Modern insects and birds are not a good analogy for this reason:  early
>> flightless dino/birds went from one form to another and then back to the
>> earlier one:
>>     flightless -> flying -> flightless
>> modern flightless birds and insects effectively just do this:
>>     flying -> flightless
>> The confusion in early birds/dinos is between the first and the second
>> flightless stages, and since the time difference might be
>> 10mys..5mys...0.1mys, little divergence need have arisen.  In modern
>> birds/insects, the comparisons would have to be between flightless forms
>> to the right of the arrow.  We seldom confuse such groups since, in the
>> of birds at least, they split say 60-80 mys ago.
>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.

>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: the
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.

You've taken great care to address the issue here Chris, but since many of
your arguments are based on reliance on parsimony, unjustified independence
and goodness knows how many other erroneus usages all conflated together so
that even if there were only one fault in the system everything would be
corrupted, I simply have to discount it.

Have you ever written a system with a theoretical justification this complex
(though the process itself may be fairly straightforward) that someone's
life or livelihood depended on?  If there were some easy way of testing it,
for example seeing if it flew or supported a thousand tons in a strong wind,
how many bugs would be found in it?  I don't believe many of the bricks it's
made out of, I don't believe the structure is sound, and I don't believe
it's ever been tested, particularly for the task I have in mind.

But even if it worked 90% of the time - even if it worked 99% of the time it
*still* doesn't matter, because I'm not really, at the end of the day,
interested in cladistics, I'm interested in just one cladogram.  What
profiteth an early bird worker if he gets a zillion easy mollusk trees
right, yet mucks up the maniraptorans?

Regretful though I slightly am to snip most of the rest, I know the
justifications are all based on clad-think, which I have commented on above
and elsewhere.

>> However, if we did - how would we know?  (Especially if we are placing
>> of our trust in one method.)
>Well, we're not, at least not those of us who consider multiple data
>sets. But that's another matter.

More data to be input into a clad program isn't the kind of multiple data
set I was thinking of.  Why do you never consider any use of stratigraphic
information for the maniraptoran problem?

> When a cladistics result is obviously wrong,
>> people usually aren't keen to publish it - especially if the problem can
>> solved
>> by adjusting the input data.
>I seriously disagree with this.  Try reading some of the molecular
>journals some time.  Are you familiar with the "guinea pig" problem?

The answer to the guinea pig problem is not "obvious".

>And what do you mean by "adjusting the input data?"

Selecting a different set of characters for input.

>>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

...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.  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.

>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

>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?

>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.

>You have to specify and
>*quantify* the source of not liking it, and as listed above, the current
>literature provides you with a fairly diverse toolbox to use against us.

...but you don't allow stratigraphy of course, you've said that above.  And
I'm sure you wouldn't allow any evidence such as the observation that
feathers progressively drift away from their aerodynamic format in
flightless forms.  It may well be possible to prove statistically that
certain types of circumstantial evidence are, individually, useful markers
for judging theories, yet you would say, because you don't know how to
combine them, they are invalid.

>> However, neither BAMM nor 2F has yet been disproved.
>Birds, pterosaurs, and bats springing from dragonflies hasn't been
>disproved, either.
>I wouldn't be surprised if some gene out there
>supports it when aligned just right.

If you didn't run a cladistic analysis on it you must have been using
alternative methods.

>But I consider it highly unlikely,
>based on the common signal extracted from all available information.

..."all available information"?  But you use only a small fraction of the

> With regard to levels
>> of "proof" for circumstantially supported theories, the evidence need
>> differ by the estimation of a hair in a person's mind for them to support
>> one side or the other.
>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?

>[shortened - here's another post]
>> > I hope we can take it that the points dealing with the unacceptability
>> > dependent characters, the value of circumstantial evidence, and Peter
>> > view that "parsimony often underestimates actual evolution" are valid,
>> > that 2F can now be accepted.
>Uh --- no.
>First - I think you're confusing character correlation and character
>dependence.  Two characters can be correlated (and even causally linked
>in a functional sense), and yet still be treated as phylogenetically

No I'm not.  You know perfectly well what I mean.  I even gave an example.

>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.

> 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

>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.

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

>one has to understand that Pete
>is approaching the issue as an expert on Paleozoic gastropods - taxa
>with very few characters and lots of time with which to evolve and
>reevolve them.  He and I have discussed several times the differences
>between those who work with simple organisms and those who work on the
>complex - and I'm not convinced that the "character saturation"
>phenomenon he's recovering is not a sampling issue driven by observer
>bias and the nonrandom selection of hard-part-based matrices.  Moreover,
>several studies have shown that simple levels of homoplasy are tightly
>linked with data set size, and the amount of homoplasy by itself is a
>very poor indicator of reliability between data sets.

Well I prefer his opinion.

I'm sorry but in the end I wasn't pleased with the email of yours I've had
to spend such a long time picking the bones out of.  I'm sure you're a very
nice chap, but the fact that you express your faulty arguments so
superficially plausibly makes them more dangerous than most.