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Re: Convergence and Coding Characters



        Hmmm... this is straying a little... maybe we should consider
running this off-list soon.

Jerry D. Harris wrote:
>        As I did in my _Acrocanthosaurus_ paper, I held out a special code
>("9" in my paper, although certainly any number can be used if 9 or more
>differing states come up in a multi-state character) which I labeled as
>"not applicable." I'm not quite sure how this affected the analysis --
        That's a problem, there. IMHO: you should have some idea how the
computer treats this before you run the data. Personally, I can't say
anything because I don't really know how the computer handles "?". I like
the idea of an NA code, though. 

>        Based on specimens of _Velociraptor_ we have, _Velociraptor_ does
>not have a pygostyle.
        But, can you prove that none of its ancestors ever did? If not, what
right do you have to attribute a pygostyle shorter than 5 vertebrae to it?

>we don't know if, historically, the
>immediate _ancestors_ of _Velociraptor_ had a pygostyle or a long
>tail...but then again, by including a large number of other taxa, both
>with and without pygostyles, we can try to get a handle on the
>probability that pygostyles evolved lower down in the lineage leading to
>_Velociraptor_,
        Ok, you're missing the point. I don't care to speculate on whether
or not _Velociraptor_ actually descends from pygostyled ancestors or not.
Indeed, that is not something I want to determine a priori of cladistic
analysis. My point is that I don't want to weight against that possibility
by biasing by character coding towards assuming the "primitive" character
state for characters which I have *no idea* about. Whether or not we
consider it likely, we must code the data in such a way that there is the
possibility that _Velocirpator_ descends from animals with a long, robust
pygostyle.

>        Exactly; I agree wholeheartedly.  The additional benefit to this
>system is that, when you look at an individual character in the data
>matrix, you can easily eyeball some "trends" in the evolution of a
>character
        I think the yuppie term is something like "data management". As long
as your choice and coding of multistate characters is thoroughly thought
through (say that ten times fast), the advantages are real, IMHO.

>        Again, I agree...but hopefully the coding cladist would be astute
>enough to realize that characters 1 and 2 are really rather redundant...
        Unfortunately, there are idiots like me running around thinking they
know enough about cladistics to do it. And, like I said, I have seen
examples, granted they were from a fairly disreputable team.

>(Of course, imitation being the sincerest
>form of flattery, I'm sure Pete'll take it as a compliment anyway!  ;-D
        What is this "Pete" thing? I really must wonder. Yeah, Buchholz and
I talk occaisionally, but we're not married or anything! Yeah, I know,
there's some kind of Peter Wagner out there somewhere... :)

>        I think it may be useful if, in instances such as this where
>multi-state characters are present, both unordered and ordered analyses
>be performed, just to compare the results.
        I'd like to see Dr. Holtz run ordered/unordered analyses for every
combination in his 300+ character theropod data set. Only because, in the
five+ years it takes him to do it, there will be a vaccuum ready to be
filled by other aspiring theropod systematicists (no, I don't have anyone in
mind... :).

>        Well, I don't know that trying to account for all the
>possibilities would overweight anything
        Ah, but see the examples I proposed last posting. There are ways to
overwieght towards your preferred phylogeny through the back door without
ever realizing it.

>I think that the best one could hope for in a scheme of coding
>and designating useful characters would be to attain a matrix and
>resultant cladogram that is accurate down to the level of differences
>between species,
        This would be useful. IMHO, useing species- or genus-level OTUs is
far superior to higher OTUs, and is a useful test of your proposed
phylogenies for more inclusive groups. I'd suppose that, in general, any
time you're using a suprageneric OTU with polymorphic characters, it would
be appropriate to subdevide it to the level at which it no longer has any
"p"s in the matrix (even down to the individual specimen level). Maybe not
for publication, but just to assure yourself that the group stands up to
rigorous examination. For example, I should be very unimpressed with a study
that codes _Pelecanomimus_ in with the other "ornithomimisaurs".

>I'm not an expert in
>statistics, so I can't speak to the statistical functions utilized by
>cladistic analysis programs, but I suspect that even if minute
>differences were coded for, ultimately we'd only see species-level
>differences.
        Hmm... not sure what you're getting at.

>        Well, let's take another (!) hypothetical example: [...]
>If we just code for the presence or absence of streptostyly, the analysis
>might conclude that A and B were close sister taxa, indicating that
>streptostyly arose only once, in the common ancestor of A and B. [..]
>between A and B); we'd have to conclude that streptostyly arose twice,
>once in the lineage leading to A and once to B.
        But that analysis might conclude this way anyway. As far as I can
see, the extra "nature of streptostyly" characters are just like any other
characters, in that they can be used to establish a closer relationship with
other taxa. In the case of birds and lepidosaurs, I'm not all that sure
they'd help, though, since none of the intervening taxa (that I know of)
exhibit streptostyly.
        Of course, this is a character classification issue now, and
essentially semantic. Birds probably share many aspects of the suspensorum
with non-kinetic skulled relatives closer to them than to squamates. We
would say that these characters were related to kinesis (in birds) because
they are part of the kinetic assembly. However, they are not really
necessarily elements of the kinetic assembly per se, but have exapted from
the akinetic ancestral skull pattern.
        Characters which actually contribute to streptostylic kinesis in
birds should *not* be found in an akinetic skull (obviously), and thus will
only be useful as autapomorphies of Aves or a more inclusive taxon. So these
characters, true streptostylic characters, will not be useful in determining
the phylogenetic relationships, nor will they bear on the issue of whether
streptostyly itself is homologous in birds and lizards.

>        To address your specific point, concerning the likelihood of
>streptostyly arising at the Squamata+Aves (Avialae) node
        Your nomenclature is dangerous here, as it sounds like you're saying
Squamata and Avialae are sister taxa. Of course, you're not. How about "at
the node representing the MRCA of S and A?" Being anal retentive is it's own
reward.
        :)

>, if you're just
>looking at those two groups, then yes, it has an equivocal chance of
>arising at that particular node.
        I think you misunderstood. All I was saying was that the addition of
autapomorphic character states will not alter the possibility (ceteris
paribus) that the character transforms at that node. Obviously, adding
character states which are potentially synapomorphic for Aves and other
ingroup taxa but not Squamata will certainly make this less likely. However
many of these characters have to do with the suspensorum, I doubt any such
character states will have to do directly with the manner of streptostyly.
They may, however, be exapted from the akinetic state. In that case, the
plesiomorphic state has guided the development of streptostyly in new
directions... but I'm getting off track.

>>Again, what concerns me is only that you might actually eliminate
>the possibility that it is homologous.<
>        I'm still not positive that this is possible, particularly if lots
>of intermediate taxa are included in the analysis.
        Well, some people might just code the nature of it. An extreme
example (not from any published source), comes from an hypothetical
coelurosaur dataset:
        1)      Second Toe: 0) normal morphology, 1) sickle claw with a
prominant flexor tubercle on the ungual, 2) sickle claw without a prominant
flexor tubercle on the ungual  UNORDERED
        This coding eliminates the possibility of homology between the two
forms of sickle claw, unless one evolved directly from the other. The
problem being, of course, that if you separate it as two characters, sickle
claw present/absent and flexor tubercle present/absent/NA, you potentially
overwieght the character. Gives me a headache.
        (Note, there is a possible exception in a broader concept of
homology, not apparently always shared by everyone, which considered all
character states of the same character to be homologous).
        So, using this idea, we could have:
        1)      Quadrate: 0) immobile, free from quadratojugal, 1) quadrate
mobile and hinged to squamosal, 2) quadrate mobile and fuzed to
quadratojugal and jointed at paroccipital process  UNORDERED
        Apart from the possibility that one state evolved directly from the
other, the two types of streptostyly cannot be homolgous. The character
legistlates their potential homology away.
--------------------------------------------------------------------------------
     Jonathan R. Wagner, Dept. of Geosciences, TTU, Lubbock, TX 79409-1053
 "Only those whose life is short can truly believe that love is forever"-Lorien