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RE: Cladistics algorithm? <FIN?>
At 4:40 PM -0500 01/31/2001, Thomas R. Holtz, Jr. wrote:
> From: email@example.com [mailto:firstname.lastname@example.org]On Behalf Of
>However, the topic you are discussing is one of computer science and/or
>computational phylogenetics, and not dinosaur science per se. You should
>seek out the various systematic discussion groups or
>groups for those details.
Is this true? I know this list is volatile, and that
threads start up as soon as you look at them, but cladistics has had
such an impact of dinosaurian phylogenetics and, hopefully, will
continue to do so, that surely asking what the programs actually _do_
is fair game? Is it likely anyone is going to initiate an in-depth
discussion on ACCTRAN/DELTRAN optimisations, Dollo, Wagner or Fitch
parsimony or Farris' Parsimony Jacknife? Goloboff's Ratchet
implimentations? I hope not, because there are other lists better
suited (and less interesting). But surely someone asking what
fundamental cladistic algorithms actually _do_ is worthy of a reply
and some pointers?
It was my impression that the question was essentially one of code: as in
"what precisely is the computer code that runs the analysis?" If I was
wrong, please let me know.
However, in the short form:
You take a matrix of taxa and characters, filled with 0s, 1s, 2s, ?s etcs.;
You open that matrix in the software;
You choose one of various options (exact ones vary by program: in PAUP*
there is Heuristic, Branch-and-Bound, and Exhaustive Search; NONA has
Heuristic and Parsimony Rachet; etc.);
Using the particular batch of code, the software compares potential
alternative trees under some parameter (parsimony, maximum likelihood,
etc.), calculating (for example) tree length for each tree generated;
The software saves only the shortest trees (i.e., those with the lowest tree
length) (unless you ask it to save something else);
You then have a set of shortest trees, which then you can examine (i.e.: see
the topology of the trees; get certain tree statistics; etc.).
If the original poster wants more details on the exact nature of the various
options, I again recommend going to a particular software package and
seeing the particular algorithm used.
Hope this helps.
Now that everyone who is interested in this has no doubt read the
chapter on infinite series and matrices, and have all reviewed Thom's
description..... it gets even more fun! ;^)
Let's add to both Thom's and My earlier posts on this for those of
you who have never really had an opportunity to do a cladogram of
your own. You can build a matrix of characters - to infinity if you
choose. You get to choose the characteristics and number them from 0
to infinity, from the most primitive to the most derived functional
characteristic the organism has, ........ you get choose.......each
and every one of us building a cladogram gets to
choose.........therein lies the caveat that builds the passion so
many people rise to the debate with, when it comes to clades and
You (the person building the tree) select the characters - what is
the most primitive characteristic (in your opinion) and then what is
each the next most successively derived characteristic (in your
You then, the researcher, select the matrix you want to process, hit
return, and hope that you get the most parsimonious tree. You can and
will find however, that in some programs, like "MacClade" that you
can manually often create a tree that is more parsimonious than the
one the computer gave you, simply by moving the branches around.
Another person may heartily disagree with your cladogram and by
selecting characteristics differently, in a different order, and
create an entirely different clade.
I give this as a lab in Honors Historical Geology - and give groups
of 4 students each, the same set samples to work with (Trilobites,
Echinoderms, Brachiopods, etc.) You get a very good feel for how many
different parsimonious cladograms can be created by a group of
people, using single set of data.
You may perhaps then begin to see why cladistics raises the passions
of so many people........ and you can certainly discern what is the
potential for inherent bias within such a system as well as its
=00= =00= =00= =00=
Marilyn D. Wegweiser, Ph.D.
Adjunct Curator of Vertebrate Paleontology
Cincinnati Natural History Museum
Assistant Professor of Geology
Department of Geology
Ball State University
Office: 765-285-8268; 765-285-8270