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

RE: Reptilia, reversals, and polytomies
You were right. Traditional Reptilia is doubly paraphyletic, containing all amniotes except for two exgroups (Aves and Mammalia). I don't know of anyone who has ever advocated putting mammals in Reptilia (so we can dismiss that as a straw-man). Traditional synapsids (pelycosaurs and therapsids) were classified as reptiles until the cladistic prohibition against paraphyly began. Many people still refer to them as mammal-like "reptiles", and classify them as such. It would be similar to saying that theropods (traditional) are "bird-like reptiles" (but the reptile-mammal transition has a strong pair of synapomorphies that makes drawing the line very clear-cut; the reptile-bird transition is unfortunately not nearly this clear-cut).
For us traditionalists, synapsids are reptiles unless they have the mammalian jaw joint (and three ear ossicles that were part of the jaw in their reptile, i.e. pelycosaur and therapsid, ancestors). The traditional Reptilia may be based on plesiomorphies, but everyone knew what you meant when you said reptile (not so these days). The same is true of the word monophyletic, which means different things to different people. This is precisely why traditionalists don't like cladists redefining the old terminology instead of coming up with new names. Eureptilia instead of redefining Reptilia, and holophyletic instead of the now muddled "monophyletic", and so on.
Now on to other things. Reversals are particularly confusing (as pseudo-synapomorphies) for molecular cladistic analyses, but I think even for morphological analyses, reversals may be more problematic than Jaime might think (especially in invertebrates).
And finally, true polytomies are probably rare even at species level. They would be almost non-existent at higher taxonomic levels. Polytomies in a cladogram are just an expression of lack of knowledge (or great uncertainty) about the order in which three or more taxa split from one another. Once I have completed a classification, and am still completely undecided about the splitting order in a clade, I use the repetition of a letter to code for polytomies, for example:
3A X-idae
A Y-idae
A Z-idae

From: Mike Taylor <mike@tecc.co.uk>
Reply-To: mike@tecc.co.uk
To: qilongia@yahoo.com
CC: dinosaur@usc.edu, kinman@hotmail.com
Subject: Re: Two new FAQs: Everything You Wanted To Know About Cladistics
Date: Thu, 23 Aug 2001 14:16:52 +0100

> Date: Wed, 22 Aug 2001 21:43:41 -0700 (PDT)
> From: "Jaime A. Headden" <qilongia@yahoo.com>
> Ken Kinman (kinman@hotmail.com) wrote:
> <One thing I would like to see on the second one is some mention of
>  homoplasies (convergences and especially reversals), and how they
>  can sometimes trick both computers and people into believing they
>  are synapomorphies (and thus can negatively affect reliability).>
> 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.

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?

> <And on the first one, I would quibble a little with equating
>  "traditional Reptilia" with "Reptilia minus Aves". Many
>  traditionalists continue to removed both Aves and Mammalia from
>  Reptilia, and leave the traditional paraphyletic synapsids
>  (pelycosaurs and therapsids) in Reptilia. This is the way it was
>  traditionally done for much of the 20th Century, and it is still
>  often done this way outside of cladistic circles.>
> And these fellows are still in academics? *shakes head in wonder* I
> thought Romer and Cox got rid of all that nonsense decades ago? I'm
> glad to see people are keeping mammals from Reptilia [...]
           Did you mean "keeping mammals _in_ Reptilia"?

OK, I am a bit confused here.  The way I remember the tree (and I'm
not sure where I got it from) is:

                Crocodilia  /
      Mammalia    \    Dinosauria
           \       \      /
            \       \    /
             \       \  /
         Synapsida  Diapsida
               \      /
                \    /
                 \  /

Which is what I originally used in my examples.  Then I checked the
classification in the dinosauricon, spead over the two pages:
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.

Now reading Jamie'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?

Thanks again,

 _/|_  _______________________________________________________________
/o ) \/  Mike Taylor | <mike@miketaylor.org.uk> | www.miketaylor.org.uk
)_v__/\  "Hoddle had stepped beyond the bounds of Blair's new,
       carefully focus-grouped and concensus-adjusted definition of
       freedom of speech, which is the freedom to say only those
       things which no one else could possibly object to" -- Giles

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