The differences between traditional and phylogenetic taxonomic thought, and other semi-coherent ramblings [was Re: New alligatoroid paper as

["Jonathan R. Wagner" <znc14@TTACS.TTU.EDU>]

Chris Brochu wrote:
>First, many thanks to Jonathan Wagner for his kind thoughts.  Seriously
>- if anyone finds a mistake or error in what I did, let me know.
        Now, about that $50... ;)

>Regarding phylogenetic definitions of genera - though I've done it in
>two separate publications, part of me has misgivings.  Clearly, if
>species can be paraphyletic and if all species have a generic name, than
>generic names can also be paraphyletic.
        Yeah. It is a neat idea though. I'm afraid that requiring a
phylogenetic analysis to confirm that a specimen belongs in an established
genus may be a bit burdensome, and may be difficult in the case of
"metataxa" (taxa lacking autapomorphies). Also, it might require a great
deal of re-organization at the alpha-taxonomic level if established
phylogenies are disproven (admittedly, this isn't likely, but I doubt anyone
wants to call, say, _Caiman crocodylus_ _Alligator crocodylus_).

>I am beginning to regard the "genus" as like a family surname - not
>really a "taxon," but something carrying taxonomic information.
        I have heard this suggestion before. Perhaps the easiest approach
would be to code species whenever possible and just leave the old,
typological genus system as it is. For cases like Dinosauria, where it seems
likely most of the established genera are monophyletic (due to presumed
limited sampling), this may be less important than for folks such as
yourself who deal with modern representatives (and therefore the more
complete later Tertiary record).

Chris Brochu wrote, in response to Philidor11@aol.com:
>I'm not sure which specific cases y'all are talking about, but there are
>two reasons throughout the paper for a name to be "defined" and
>subsequently "discovered:"
>
>1.  The name is in the literature, and the analysis supports its
>monophyly.  Diplocynodon, Alligator, and Alligatoridae are examples.
        Ah, I forsee potential confusion. Again, as before, I believe Dr.
Brochu refers here to the monophyly of the *originally named group* (as used
in the literature) having been supported. 

>2.  The name is new to the analysis, but since I had a discussion of
>phylogenetic taxonomy at the beginning, it made sense (at least to me)
>to introduce all new names up-front, in one place.  I felt justified in
>doing this because two earlier papers presented more-or-less the same
>tree, so the "results" weren't really "new."
        In this case, Dr. Brochu refers to the discovery that a group of
taxa form a monophyletic group. As he notes, since he had defined this group
earlier, he goes ahead and uses the name for them. In a sense, he has
"discovered" the content of the group he named, or "discovered" a clade,
which he had already named. This is potentially confusing, but I believe
that as phylogenetic taxonomy becomes better established, this will become
less of an issue.

George Olshevsky wrote:
>There is indeed a contrast. On the one hand, the author says he has 
>>discovered< that a group is monophyletic, whereas on the other hand the 
>author has >defined< that group so that it is monophyletic. This is more than 
>mere semantics; it is philosophy.
        Or more precisely, logic, I suppose. George is right, in that there
is a philosophical difference in what was said. However, because this is a
difficult stage in the transition from traditional methodologies to
phylogenetic taxonomy, it is understandable that such confusions arise. It
seems clear (to me, anyway) that the point was that a monophyletic group was
discovered in the analysis, and this group corresponds to a particular taxon
name.
        Headache, anyone?

Philidor11@aol.com wrote:
>So, I think I was correct in observing:
><<My best guess at the moment is that you mean different classification 
>approaches lead to the same result, but I would like to be sure.>>
        Well, the previous classification conforms to Dr. Brochu's
phylogenetic reconstruction. In a way, we suffer here from the problematic
relationship between taxonomy and phylogeny. In the original Linnean type
taxonomy, animals were classified, and this heirachrichal ordering was a
book-keeping exercise. Apparently there were those who felt that this
classification reflected, either directly or indirectly, some inherent
feature of nature. My understanding is that it was usually attributed to
God's own Scala Natura. So, stage 1 is "taxonomy is an artificial
classification", and stage 2 is "taxonomic classification represents a
devine plan."
        With the coming of evolutionary theory, this heirarchical
relationship (remember, it is an organization imposed by man, a
classification) was re-interpreted to represent, as Darwin so eloquently put
it, propinquity of descent. So, just as in the early days of
chronostratigraphy, rocks were taken to "be" time, the classification was
used as a model of the phylogenetic relationships. Indeed, this was taken to
extremes, and even affected worker's views on the patterns of evolution to
the extent that classificatory units were treated as evolutionary entities
(e.g. "families" were thought able to give rise to other "families"). Stage
3 is "taxonomic classification represents phylogeny."
        Phylogenetic sysytematics (cladistics) came about in response to the
percieved subjectivity of traditional taxonomy, and offered instead the
notion that phylogeny should give taxonomy, and not vice-versa. Monophyletic
taxa were demanded, with the result that taxa were finally real evolutionary
units (clades). Taxa were still errected in a traditional manner, however,
with the result that they were not necessarily clades by definition. Stage 4
is "phylogenetic hypothesis gives the taxonomic classification."
        Phylogenetic taxonomy is simply a refinement of cladistic
principles. The element of classification (the division of individuals into
arbitrarily determined subsets) is abandoned in favor of a recognition of
natural clades. Taxon names are assigned to clades identified by their
ancestor-descendant relationships, eliminating the last vestiges of
typological character- or content-based taxonomy. One no longer has a
classification, one has an hypothesis. In this system, all taxa are
monophyletic, all are real evolutionary units. Stage 5 is "phylogeny is
directly represented by taxonomy."
        The problem is, you have people (authors, editors, and readers)
thinking in any or all of stages 3-5. Dr. Brochu was using Stage 5
methodology, but writing in terms of Stage 3 to relate to that audience.
        However, barring the philosophical flaw (in that Stage 5 is no
longer a classification), your statement holds. Dr. Brochu was showing that
the old, typological groups held up under modern analytical techniques.
        

>There is a problem in what you were saying ,though: [...]
>and it appears to be bothering Mr. Brochu as well: [...]
        Actually, Dr. Brochu was responding to an entirely different point,
a point upon which we agree. You may have to reformulate this part of your
posting, because I'm not sure I understand. I may have confused you,
however, by failing to make clear what I meant. PHYLOGENETIC Taxa are
defined to be monophyletic. Species (and for some workers, genera) are real
evolutionary units, but they are not phylogenetic taxa (because they are not
clades). Dr. Brochu was pontificating the ramifications of making genera
phylogenetic taxa, an idea which has some ramifications (see above) for how
natural historians do their business. I was pointing out the logical
contradiction invovled in testing the monophyly of a phylogenetic taxon (all
phylogenetic taxa are by definition monophyletic).

>If species can be paraphyletic then defining the possibility away by calling 
>them monophyletic does not work.  If I've misunderstood Mr. Brochu's 
>statement I'm sorry.
        You should not be sorry for misunderstanding, we all do it on a
regular basis. Heck, I'm probably doing it now! :)
        Anyway, hopefully my statements above clear this up. However, as a
thought exercise, you can try to demonstrate to yourself why it isn't a good
idea to insist on monophyletic species. Start with all life evolving from a
single ancestral species...

[quoting George]
><<On the one hand, the author says he has >discovered< that a group is 
>monophyletic, whereas on the other hand the author has >defined< that group 
>so that it is monophyletic. This is more than mere semantics; it is 
>philosophy.>>
>
>Wishing does not make it so.
        Actually, it isn't a wish. Clades *do* exist, they are out there.
For a group consisting of an ancestral population and all of its descendants
not to exist requires that life evolved independantly at least twice (not
the best bet, especially if you are just looking at vertebrate life). If
they do exist, than we *can* look for the group consisting of "the most
recent common ancestor of _Ephemerella_ and _Pongo_ and all of its
descendants." That group will be monophyletic *by definition*, it simply may
not contain the taxa we think it does.

>Aren't taxonomic analyses interpretations?  
        Ooooh yes!

>Isn't any finding of fact subject to change no matter how well-informed it 
>may currently be?  I believe in logic, but not in its ability to find the 
>only correct answers with limited data and alternate reasonable possibilities.
        True. However, as related above, monophyly by definition is a
philosophical and logical question, not a testable hypothesis. You can
question the logical process used to derive the result, but you cannot test
the result directly (I think... anyone better at this stuff think
otherwise?). What you can do is test the *content* of this defined group.
Think about it liek Heisenberg's Uncertainty Principle: we can (a) know a
group is monophyletic and test which taxa the group includes, or we can (b)
take a group of taxa and test if it is monophyletic. You can't do both, and
different methods approach the problem differently. Herein lies the crux of
the point I was making: Dr. Brochu appears to be doing both in his paper. My
point was that this is an artifact of trying to relate to a "Stage 3" way of
doing things using "(b)" logic, and the "Stage 5" way of doing things using
"(a)" logic.
        There, now why didn't I just think of that two days ago?

>Firing away, I guess...
        Keep on shooting! :)

        Hope this helps.

        Wagner

--------------------------------------------------------------------------------
     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