Re: Two new FAQs: Everything You Wanted To Know About Cladistics

["Jaime A. Headden" <qilongia@yahoo.com>]

I wrote [in double angles]:

<<I'd disagree with the inclusion of "reversals" of character polarity and 
expression as a
function or aspect of homoplasy: in a computer analysis, they tend to pull the 
taxon backwards, as
it were, and collapse nodes -- they do not make false synapomorphies.>>

Mike Taylor (mike@tecc.co.uk) wrote [in single angles]:

<I'm sorry, I'd like to modify the FAQ answer to take this into account, but I 
don't understandf
what you mean by "pull the taxon backwards" or "collapse nodes".  Could you 
possibly spell it it
out in words of one syllable?>

  Sure :) I'll try, anyway. I guess a good excercise for the haughty-taughty is 
to take
hyper-language and break it down into an English syntax -- now that takes guts 
and brains ... and
I'm being serious here. Let's see if I can pull it off [maybe, maybe not]:

  In a computer program that runs sets of numbers tagged to a name, like the 
matrix of a
phylogenetic program [say:

Xenopus ---- 00000
Canis ------ 00001
Lacerta ---- 00111
Crocodilus - 01111
Passer ----- 11111]

  This is a clear case of phylogenetic nesting, and would produce the following 
tree (kid thee
not):

--+--Xenopus [salamander]
  `--+--Canis [dog, duh :)]
     `--+--Lacerta [lizard, again duh :)]
        `--+--Crocodilus [my great aunt]
           `--Passer [someone stinks in here...]

however, with the following tree:

Xenopus ---- 00000
Canis ------ 00001
Lacerta ---- 00111
Ichthyosaurs 01010
Crocodilus - 01111
Passer ----- 11111
Pterosaurs - 11100

  I get a fuddled mess: not a single taxon is consisten with another save that 
*Xenopus* is always
at the base, by factor of it not having a derived feature in common with the 
other taxa [now mind,
this tree is completely false, I made up the series of numbers, so they are 
subjective to my
purposes]:

  (xeno (ichthyos (dogs (lizards (crocs (birds and pteros))))))
  (xeno (dogs (ichthyos (lizards (crocs (birds and pteros))))))
  (xeno (dogs (ichthyos ((lizards & crocs) (birds and pteros)))))
  (xeno (dogs (ichthyos (lizards (crocs (birds and pteros))))))
  (xeno (dogs (ichthyos (lizards, crocs (birds and pteros))))) -- in this case, 
lizards and crocs
        plus the bird + pterosaur clade form a trichotomy, or single branch 
with three equally
        diverging stems
  (xeno (dogs (ichthyos (pteros (birds (lizards and crocs))))))
  ....

  and it goes on ... I do not feel like writing out 11 of these, so pardon me 
:) Needless to say,
one already gets a sense of what homoplasy is: any primitive feature in common 
with a descendant
will, in the lack of overwhelming features to add the descendant to another 
group, "pull" the
taxon towards the base of the tree. This is called long-branch attraction in 
genetics, but that
occurs over a genomic sequence, whereas I only have five "chracters" here. 
Also, a reversal, as
seen in the Pterosaur sequence above (11100) tends to do two things: it 
attracts to birds based on
the first "character" as a synapomorphy, but the number of 0's at the end tend 
to pull the taxon
to others, as well, including ichthyos, and ends up pulling birds with it, so 
that pteros and
birds are almost always next to each other, or just one node removed. This, 
too, acts as an
homoplasy in a compuiter algorhithim. However, when dealing with a fossil on 
it's own terms, the
feature must first be interpreted as a new feature; i.e., that reversal is a 
character in and of
itself.

<                                          ^^^^
             Did you mean "keeping mammals _in_ Reptilia"?>

  Nope, I meant "from"...

<OK, I am a bit confused here.  The way I remember the tree (and I'm not sure 
where I got it from)
is:
 
                              Aves
                               /
                              /
                 Crocodilia  /
       Mammalia    \    Dinosauria
            \       \      /
             \       \    /
              \       \  /
          Synapsida  Diapsida
                \      /
                 \    /
                  \  /
                Reptilia
 
 Which is what I originally used in my examples. Then I checked the 
classification in the
dinosauricon, spead over the two pages:
 http://dinosauricon.com/taxa/tetrapoda.html
 http://dinosauricon.com/taxa/sauropsida.html
 which has Synapsida _outside_ Reptilia.  So I changed my example to how it is 
now, which is a
shame, because I was previously using "traditional reptiles" as an example of a 
doubly
paraphyletic group, {Reptilia-Aves,Mammalia} and I no longer have any such 
example.>

  Okay, the clarification: Reptilia has never included Mammalia; they are 
classically direct polar
opposites. However, in including Synapsida into the use of Reptilia (which HAS 
been done), and
applying the tree to a strict monophyletic paradigm, one does get a Mammalia 
within Reptilia.
However, no modern systematist favors this, that I'm aware of. The trick here 
is making the node
Reptilia to the same spot as Diapsida, which singly excludes Mammalia, and 
renaming that node, as
has been done for decades and decades, Amniota. Outside that are the 
salamanders and such (in my
example above, *Xenopus*).

<Now reading [Jaime's] comments, I am getting the impression that my first idea 
was right, and
Mammalia _is_ inside Reptilia after all. Am I right? What's the story with the 
dinosauricon?>

  Mike Keesey has the tree as most phylogenetic systematics agree on the 
subject, where the trees
agree, as it were. Mammals are not within Reptilia, and are explicitly excluded 
by use, classic
use, PT definition, etc..

  Hope this helps,


=====
Jaime A. Headden

  Aaaaaaaaaaaaaaaaaaaahhhhhhhhhhhhhhhhhhr-gen-ti-na
  Where the Wind Comes Sweeping Down the Pampas!!!!

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