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Re: TETRAPODS, PHYLOGENETIC TAXONOMY, AND CLEAR DEFINITIONS



        Once again, let's take this off line, shall we? I think we've all
said our piece.

At 11:33 PM 7/21/98 -0400, Jonathon Woolf wrote:
>> be involved.  How tetrapodish do you have to be to be a tetrapod?
>Good question.  Do you have a good answer?  I don't.  That's my main
objection >to what some people have done with phylogenetics
        Pete's question was rhetorical. The PT answer is "if you're a
descendant of the MRCA of Lissamphibia and Amniota, you're a tetropod." It
solves the issue right there. No more listing characters that "make" you a
tetrapod. You are a tetrapod by birth.

>Now, what do you do if you get an organism that has every feature on your list,
>but for some reason you can't tell if it's actually within the defined clade?
        Say, it's in a polytomy (multiple branches from the same node). You
label the taxon incerta sedis, just as you would in Linnean taxonomy. No
harm done.

>I'm a computer programmer by trade.  That's how I work; that's how I think.
        Having done a bit of this, you have my sympathies. Howevere, in
science, we do thinga a little differently. We have different needs and
different requirements. May I suggest that, rather than trying to change the
entire scientific community, you just try it our way for a while?


>You have to know what animals are and aren't descendants of that LCA before
you >know what the group includes.
        a) the advantages to phylogenetic taxon definitions are enormous,
and outweigh the disadvantages (percieved or real). See the extensive
discussion s by DeQuiroz and Gauthier.
        b) Someone will already have done this for you anyway. If you have
something new, code it into someone's data matrix, or take the time to make
your own.
        c) When folks like Romer put together their Linnean classifications,
they probably went to at least as much work as cladists did. 
        d) You still get diagnoses from cladistic analyses, and these can
and are still used when people for some reason (time, energy, in the middle
of the desert, I dunno) can't do the cladistics.

>Does the crown-group Tetrapoda include _Seymouria_? Anthracosaurs?  Microsaurs?
>_Diadectes_?  _Edaphosaurus_?  All of those have four legs, a
differentiated >head and neck, and a number of other traits that mark them
as land-capable.  Is >that enough to call them a tetrapod?  Should it be
enough?  What traits >separate members of this crown group from nonmembers?
Is there any way to tell >that _Hylonomus_ is a descendant of that LCA, but
_Seymouria_ isn't?  I don't >know.  Do you?
        I know. The answer is called cladistics. It is a very popular,
advanced, and accepted means of answering these questions with testable
reproducable hypotheses. The sister discipline of phylogenetic taxonomy
helps by allowing explicit formulation of the questions. How else do you
know what "tetrapods" are? Both Pete and I have pointed out that there are
intermediates for all things (such as "four-leggedness"). PT provides a
straight up yes/no approach to determining taxon membership. It is truly a
heady time to be asking such questions.

>If it's the first _diagnosable_ dinosaur, how do you tell that, say,
>_Plateosaurus_ is not a descendant of _Eoraptor_?
        You are being confused by two competeing theories. One says that
_Eoraptor_ is a theropod, the other says it is outside of Saurichia and
Ornithiscia (and there fore not a dinosaur sensu stricto).

>Do you see what I'm getting at?  In at least some circumstances, saying
that "X >is not a member of group Y" requires you to prove a negative.
        No, it simply require that you demonstrate (note: never prove) that
it is closer to some other group, or the members of group Y are more closely
related to each other than any of them is to Y.

>What are the diagnostic features of a tetrapod, and how does _Seymouria_
not >meet them?
        We're going in circles. If _S._ is hypothesized not to be a
descendant of the common ancestor of Lissamphibia and Amniota, it isn't a
Tetrapod, diagnostic features be darned.

>Most are pretty unequivocal in calling _Morganucodon_ a mammal, even though
it >clearly dates from before the probable LCA of monotremes and therians.
So, how >can you possibly tell that it _isn't_ a descendant of that LCA and
therefore a >member of Mammalia?
        A) They call it a mammal because they use a different definition of
mammal.
        B) The dating of the MRCA of mammals will never be "clear", only
more or less certain. I have yet to hear evidence from you that it is more
certain than not.
        C) PLEASE try to divorce the relative time aspect of cladograms from
abosulte time as determined by, say, molecular clocks. Morphological
cladistics makes NO statements concerning time. I believe Chris Brochu would
say something like "absolute time can be an independant check on phylogeny."
We do not use data suggesting when a most recent common ancestor lived to
determine membership. If independant data suggest a conflict between
morphological and molecular data fine, if they don't so much the better. But
the two methods are different.
        D) The way you tell whether it's a descendant of the MRCA of mammals
is called cladistics.

>First, what makes you think cladistic analyses are any more objective than
the >old Linnaean methods?
        The character selection may or may not be more objective, but it is
explicitly testable. Phylogenetic Taxonomy *IS* more objective because the
arrangement of taxa within other taxa is not reliant on individuals special
knowledge or opinion. Any taxonomic assignment above the generic level may
be tested.

>The Linnaeans must have gotten most things right, because cladistic analyses
>haven't really modified the whole Tree of Life all that much.
        Yeah, yeah, yeah. They didn't do such a bad job, did they? Everybody
knows this story. If the "old timers" did a good job, well fine. I expect
nothing less. I'd hate to think my idols were all a bunch of idiots.
However, just because people got it "right" in the past doesn't mean they
did it the right way. Cladistics and PT are methodological improvements,
allowing reproducable phylogenetic reconstruction and explicitly falsifiable
taxonomic decisions. The "old timers" couldn't do that.
        Besides, I can't figure out hide nor hair of the phylogeny from
those old taxonomies. You have to have a darned Romergram, and even then
it's pretty confusing.

>What I object to is the elevation of PS from a tool to an end-in-itself.  I
get >the distinct feeling that too many people are
>building too many cladograms and classifications based on a desire to get
>everything into a slot, not a desire to better understand the evolution and
>relationships of these animals.
        As opposed to the old days when they just left taxa lying around all
the time? For crying out loud, that's how taxonomy works! You just notice it
more, because you hate the methodology. For crying out loud, this is
sounding like a whole bunch of sour grapes.

>Does it actually mean anything significant that
>_T. rex_ is closer to _Ornithomimus_ than either is to _Velociraptor_?
        If you're a mammal worker, probably not. If you're a theropod
worker, Darned skippy it's significant. And you were just complaining that
no one want's to understand the relationships of animals anymore? Make up
your mind!

>This is a noble goal, but from where I sit, it ignores reality.
Paraphyletic >taxa are _inevitable_ in any system that tries to separate
organisms into >species and genera -- because every species originates from
a previous species,
        And you don't think people have figured this out? There have been
proposals to require species to be paraphyletic, but it just doesn't work. I
don't recall hearing of anyone recently who doesn't accept paraphyletic
species. However, this is ok, because a biological species is still a
natural group (even though it isn't a clade). As for genera, well, you're
required to have them for each species, and keeping them paraphyletic is
better than naming a new genus for every species. Personally, I hate the
darned things, and I prefer splitting them if you can demonstrate paraphyly.
The gig is, though, that supergeneric taxa never have to be paraphyletic.

>and every genus originates from some species in an older genus.  All horses
>evolved from _Hyracotherium_
        I did not know this. Please demonstrate it, using scientific evidence.

>so do we classify all the various horses of the past sixty-odd million
years >as different species of _Hyracotherium_?
        It has been suggested.

        Wagner
----------------------------------------------------------------------------
    Jonathan R. Wagner, Dept. of Geosciences, TTU, Lubbock, TX 79409-1053
                    "...To fight legends." - Kosh Naranek