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Re: cladistics question [the long, simple version for beginners]

        Chris Brochu has already responded quite effectively to most of
this, so I'll concentrate on going into a little more detail on the simple
concepts which may have gotten lost in the scuffle.

Joseph C. Daniel wrote:

>One question that I have had with cladistics for a long time was the
>time factor.  As an example, the ceratosaurs at least used to be
>considered "basal" or "primitive" theropods, right?
        Lemme try to restate Chris' response a little more simply: When you
look at a cladogram, you're generally looking from the "bottom up", trying
to find the sequence of taxa which are progressively closer to a certain
animal or group of animals. Why are you doing this? Who knows, probably
because you started by being interested in only one group represented in the
analysis. What's important is that your slanting your view towards a
particular branch on the tree. To use a dinosaurian example, you look at
theropods, and you say ceratosaurs are "basal neotheropods", because they
branch off at the bottom of the tree, and you're looking at birds or
tyrannosaurs or something farther up.
        However, you should be aware that if you're looking at ceratosaurs,
you might just as well call the Tetanurae "basal neotheropods", because
you've unconsciously changed the "axis" of the cladogram so that ceratosaurs
are the "endproduct". There is nothing wrong with doing this. There is no
one direction to a cladogram. Just because it seems like a lot of individual
taxa branch off in a neat little "comb" towards birds does not mean that
these are somehow "primitive" or "transitional" taxa.
        If you take the family tree back in time, you might see just such a
comb, with _Hadrosaurus_ and _Iguanodon_, _Apatosaurus_, _Ceratosaurus_,
then _Spinosaurus_, then _Allosaurus_, _Tyrannosaurus_ and _Ornithomimus_,
_Oviraptor_, _Velociraptor_, and birds. Does this mean that each one of
these taxa is "just a step on the way to birds"? No, each one of these has
turned out to represent an important radiation of animals. At the time, they
may not have looked like much, because they were connected to the "main
stem" of the cladogram by a very short line, and they didn't have any other
taxa associated with them.
        When looking at a cladogram, it is very important to remember two
        1) The lengths of the branches do not always mean anything.
        2) There are always taxa which have not been included in the study

        Missing taxa and branch lengths can imperceptably affect your
perception of the phylogeny. For example, you might be tempted to think that
_Ceratosaurus_ is somehow more primitive than coelophysoids, or more closely
related to birds, because it is shown branching off first on the ceratosaur
limb of the cladogram (e.g. in Holtz's tyrannosaurid paper 1994, I believe).
This is just a perception, however. You can "spin" the taxa at a node,
bascially exchanging the branches so the left side is now on the right,
without ever changing the meaning of the cladogram. Try it. Look at the
cladogram, figure out which animals share more recent common ancestors, then
flip a node, and see if anything is changed.
        Also, all of the ceratosaurs are equally closely related to birds.
Their distance along the branches means nothing. All that matters is whether
any of them share a more recent common ancestor with birds. They all share
the same most recent common ancestor with birds (represented by the node
connecting Ceratosauria and Tetanurae).
       So you might think (again, to use Holtz 1994 as an example), that
_Torvosaurus_ is pretty similar to the common ancestor of tetanurans because
it is so far down on the tree, and is only connected to the main stem by a
short line. You have been mislead. It probably does not share the supposedly
"advanced" characters of theropods closer to birds, but what makes those
characters "advanced"? They appear in later, more birdlike forms. Well duh!
Of course _Torvosaurus_ lacks them! :) _Torvosaurus_ is only "far down the
tree" because you're looking at birds. If you look at _Torvosaurus_, it's at
the top ( with a very "bushy" sister group)! And remember, that branch
length there means nothing (in this case). heck, just add as many
hypothetical members of the "torvosaurid" clade until the branch length is
long enough to convince you.
        You may say, "well, _Torvosaurus_ doesn't have many characters which
are different from the character states Holtz says existed at the Tetanuran
ancestral node, so isn't it primitive?". You must recall that not all
characters are included in the study. You wouldn't code characters which are
present only in _Torvosaurus_, because they aren't shared with any other
form, so they won't help you assess relationships. _Torvosaurus_ may have
many such characters (called autapomorphies), or it may have very few. Heck,
it may have a bunch, which later turn out to be shared with other taxa we
haven't found yet, in which case we would have to code them into the data,
since they are shared with other forms. Of course, _Torvosaurus_ might have
such characters, and we simply haven't recognized them at all because we
haven't found close relatives with the same features.
>Yet they didn't appear until tens of millions of years after the earlier more
>derived theropods, a huge expanse of time in which a great deal of evolution
>could and probably did occur.
        Remember, evolution doesn't have a direction it's "going" in.
Evolution is not required to change everything every so often. We all know
too well the stories of "primitive" animals surviving long long times with
very little morphological change.
        Also, since cladistics looks at recency of common ancestry, these
long periods of time are only important in that many new closely related
taxa can be spawned during them. The ammount of time, and the high degree of
change which may (but does not have to) accumulate is immaterial. Just like,
as you get older, you look less and less like the child your mother gave
birth to, and you look more and more like you uncle Bill. But this by no
means makes you more closely related to William than to mom.

>So how can they be considered primitive or basal.
        "Primitive" is a term best avoided. It carries connotations which
are counterproductive, and can force you to think in terms which impede
understanding. Still, it does get used. Just try to be aware that
"primitive" animals are under no obligation to show up early in the history
of their group. Further, the way the term has been used in the past,
"primitive" animals do not seem to be under any obligation to look like the
most recent common ancestor of the clade in which they are considered

        Hope this helps.

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