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Re: Clade II (long)



At 06:58 PM 1/21/97 -0700, LN Jeff wrote:
>
>     I've mulled things over this past month or so, and I've
>come up with a few arguments against the "real" nature of clades, and the
>value of paraphyltic groups.  I'll be discussing archosaurs in at least
>ONE example, so this shouldn't be too innaproriate.  If the debate gets too
>off the dinosaurian track (which I am sure it will), we can always go to
>private correspondance.  Be warned, this is pretty long.  

Have you gone back to the (non-dinosaurian) systematics literature of the
1960s, 1970s, and early 1980s.  Most of these arguments have been made ad
nauseum, but there may be points on both sides that you have missed.
            
>I. THE DUAL NATURE OF CLADISTICS
>     As I see it cladistics serves two main functions, one very well, the
>other less so.  I feel these functions were confused in the debate on
>cladistics in November, so I want to spell them out now:
>A. PHYLOGENETIC INFERRENCE
>     Determining in what order genera and species branched off from each
>other is what cladistics does well.  Make no mistake, I do believe
>synapomorphies are the best way to infer phylogenetic relationships.

AKA, Systematics.

>B. GROUPING
>     Drawing the little dotted lines after the phylogenetic tree has been
>reconstructed.  It is this taxonomic function taht I feel cladistics needs
>to augment with paraphyletic groups.  More on this later.

AKA, Taxonomy.

The distinction between systematics and taxonomy has long been recognized.

>II. THE ARBITRARY NATURE OF CLADISTICS
>
>THERE ARE NO "REAL" OR "NATURAL" GROUPS
>     Species do not naturally aggregate themselves into "groups".  The
>fact that a species is decended from another does not mean that they must
>form a "group".

Yes, it does: it forms a group composed of common ancestors and all its
descendants (or a common DNA heritage, or however you wish to describe the
lineage concept).  These are real, historical entities.  History happens.

As to whether or not you wish our biological taxa to reflect evolutionary
history rather than ecology or agricultural utility is a matter of taste.
Ever since Darwin advocated (and Haeckel attempted) the use of "propinquity
of descent" as the key feature of biological taxonomy, many biologists
agreed that history should be a major aspect of our nomenclature.  Cladists
argued that it should be THE major aspect of nomenclature.

>Saying clades are "natural" is a bit like saying because
>the border of Australia is defined by a natural coastline, it must mean
>Australia is a "natural" country (I know I've probably grossly
>oversimplified Australia's territorial boundries, but you get the idea).

Actually, you have made a case against your own.  Whereas the general
borders of some geopolitical entities (i.e., Wyoming) are clearly
superimposed by humans over an arbitrary body of land, the border of the
country "Australia" reflects the the natural, physical, non-human boundaries
of the surface of the continent "Australia".

>As people intrerested in paleontology, biology, and zoology, we may PREFER
>to group organisms together based on phylogenetic considerations, but this
>does not make our groupings, regardless of if they are monophyletic,
>paraphyletic, or polyphyletic, more "real" than if we classified them
>based on average size or numbers of individuals.  How could any grouping
>of species, regardless of the criteria, ever be "real"?

History happened.

However, we (as biologists) DO recognize some groupings of animals which are
non-phyletic: ecological groupings such as carnivore, omnivore, herb, shrub,
etc.; "geographic" groupings: littoral, abyssal, fossorial, intestinal
parasite; biogeographic groupings: Nearctic, Carolinian (marine
biogeographic province); use: farm animal, pest, food plant, etc.

For (human) historical reasons, however, it is phyletic history which has
come to be regarded as the central theme in our classifications.

>CLADISTS set the
>rules that groups must begin with a node and end with extinction (or the 
>present day- more on that later), not Nature.

And, of course, these events really did happen in the history of life, so it
makes it nice and convenient.

>How is common descent any
>more real than the possession of scales or the absense of hair, or the
>endothermic or ectothermic metabolism?

It isn't.  And, of course, it is using character states such as those you
mention that allow us to reconstruct phylogenies.  However, by classify by
phyletic history as a total, you incorporate the particular characters as well.

>ANCESTRAL SPECIES ARE PARAPHYLETIC
>    Yes, I know identifying bona-fide ancestral species in the fossil
>record with 100% certainty is impossible.  That is irrelevant: they
>existed, and unless the offspring of every single individual born within
>that species survived to reproduce, these species MUST be paraphyletic.

Yep.  As discussed elsewhere, species are NOT regarded as clades under most
species concepts.  As such, they are not bound by monophyly.

>PARAPHYLY IS AN ILLUSION OF WHERE THE CLADIST STANDS IN TIME
>     Every single paraphyleic group that exists, as diagnosed in the
>Linnaean sense, WAS ONCE MONOPHYLETIC.  Before the evolution of tetrapods,
>ray and lobe finned fish could have been united in a perfectly good
>monophyletic clade.

And they still are: Osteichthyes.  That clade just happens to have some
walking forms these days.

>Before the evolution of therapsids, the same was true
>for "reptiles" (in the Linnaean, not Gauthier sense).

Not really, although there were amniotes.  (Linnaeus' concept of Reptilia is
so useless as to be pathetic: it includes sharks, rays, sturgeons, as well
as amphbibians and nonavian reptiles).

And before the evolution of bats, placentals and marsupials could have been
united in a perfectly good monophyletic clade.  And they still are.

>If clades are
>"real" and paraphyletic groups are not, what does that mean for fish and
>reptiles?
(Recapitulation on the Internet).

As discussed MANY times on the dinosaur net over the past few years, no one
objects to informal terms like "fish" or "lizard", as long as we recognize
that these are not formal groupings (i.e., that we are excluding forms from
them).  It is "Pisces" and "Lacertilia" (formal taxonomic groupings) which
are not considered valid under phylogenetic systems of taxonomy.

Of note, though: Reptilia/Sauropsida is a VERY GOOD, VERY WELL DEFINED
monophyletic group once birds are included and synapsids are excluded, as
recognized by Huxley, Osborn, and others long ago.  Recent decades of
research have shown many soft- and hard-part, as well as molecular,
structures uniting turtles, lepidosaurs, and archosaurs outside of other
living vertebrates.

> They used to be real, but now they're not?

They are still real: they just have some other, specialized members.

>Is the only reason
>monophyletic groups are "real" and paraphyletic groups are not is because
>WE happen to be living at this particular point in time?  How "real"
>a system of classification is that?     

Very real.  Once a clade, always a clade.

>III. THE LEGITAMACY AND VALUE AND OF PARAPHYLETIC GROUPS
>
>EVERY APOMORPHY DEVELOPS AT THE EXPENSE OF A PLESIOMORPHY
>     Paraphyletic clades are therefore NOT just definable by the absense
>of an apomorphy, but by the PRESENCE of a trait no longer possessed by the
>descendant group.  Yes, I know birds and some mammals have scales, but
>everywhere they HAVE feathers or hair they are LACKING scales.  Reptilia
>could be redefined in part as a group POSSESSING scales over these
>particular areas).

Mammal scales are molecularly and biochemically (and anatomically) NOT
homologous with reptile scales.  Reptilia has been redefined BY
herpetologists to include the taxa mentioned above.

>Unless it matrilized out of thin air EVERY apomorphy
>develops at the expense of an ancestral trait through modification of an
>existing feature.  Once the new form of that feature develops, the old
>form of that feature ceases to exist.  The fact that a descent group
>possesses the apomorphy is no more real then the fact that the ancestor
>has the ancestral trait.      

This is why they are called "character state changes".

How about this: every plesiomorphy is an apomorphy at a more inclusive level?

>"BASAL" GROUPS- EVEN CLADISTS USE PARAPHYLY WHEN IT IS CONVENIENT

Yep.  As mentioned above, we can talk about groupings of organims without
regarding them as formal taxa.  We can talk about tetrapods being
four-legged vertebrates, even when they are really zero-to-four limbed
vertebrates.  We just don't formally name biological taxa comprised of "all
tetrapods except snakes", "all tetrapods except whales", and similar groupings.

>     One example is Paul Sereno's paper on "Basal Archosaurs".  He
>mentions ankle bone development in the earliest dinosaurs, pterosaurs,
>and crocodilians, but doesn't pursue its further development in these
>groups. However, he does go into some detail about every other
>monophyletic archosaurian clade that didn't make it out of the Triassic.
>All Archosaurs except dinosaurs, pterosaurs and crocodilians: what group
>is paper really about? (I'll give you a hint- it starts with a "t").

How about: clarifying some confusion with regards to early archosaurian
divergence, especially with regards to functional anatomy?

>ALL MEMBERS OF A MONOPHYLETIC CLADE DO NOT NECCESSARILY HAVE MORE SHARED
>DERIVED CHARACTERS IN COMMON WITH EACH OTHER THEN THEY DO WITH SEPERATE
>CLADE

Yep.  Your point being...?

>    Monophyletic clades are defined by common descent, not greater
>similarity.  For an example, look at this cladogram:
> 
> species A             species B   species D  species C
>     *                    *           *          *
>       *                *               *      * 
>         *            *                   *  X  
>           *        *                      3   
>             *    *                      *
>               2                       *
>                 *                   *
>                   *               *
>                     *          *
>                       *      *    
>                         * *
>                          1 
>
>      A series of apomorhies defines clade 1 that are not present in the
>outgroup (not shown).  Additionally, clades 2 and 3 are monophyletic. 
>Species D may very well share more than it does apomorphies (for clade 3)
>with species C.  This is arguably the case with the reptiles (Linnaean-A,
>B) "basal" synapsids (C) and mammals (D), and also with fish (ray fins A
>and B), Lobe fin C, and tetrapod D.  In all cases, A, B, and D share
>important aspects of behavior, metablism, anatomy, and/or physiology than
>D does with C.

Yes, they may well indeed.  We and amphbians and lungfish have many
biological similarities that are not found in Reptilia.  The recognition of
plesiomorphies is still important, even if it isn't cntral to phylogenetic
reconstruction.
 
>     If the only aspect of evolution we were interested in was "who is
>descended from whom", this would be perfectly good,

Yes.

>but in the words of
>Ernst Mayer, cladisitics "denies other aspects of evolutionary change such
>as the rate of evolution, adaptive radiation, the occupation of new
>adaptive zones, mosaic evolution, and other macroevolutionary phenomena".   

Just because Mayr said that cladistics denies these aspects does not mean it
is so.  Check out the copious literature on phylogenetic systematics to find
a sampling of this.

For example, you cited Sereno's 'blue book' on basal archosaurs above: a
good example of a discussion of an adaptive radiation and the occupation of
new adaptive zones (via bipedality).  How about Vrba's work on
macroevolution and adaptive radiations within bovids?  Hopson's work on the
mosaic evolution of mammalian traits in nonmammalian therapsids?

>     These things may be (somewhat) separate from phylogeny, but
>why do it have to be seperate from taxonomy?  As evolutionists, we are
>interested in these subjects.  Who said, and WHY, that phylogenetic
>relationships were the be all and end all of taxonomy?

Read de Querioz and Gauthier's various papers (cited before, or I could post
the refs again, for the phylogenetic taxonomists' arguments).
    
>    And lets not hear any more crap about paraphyletic groups only having
>value to creationists or people wanting to cast moral aspirations on
>certain animal groups.

Fair enough.

Thomas R. Holtz, Jr.
Vertebrate Paleontologist     Webpage: http://www.geol.umd.edu
Dept. of Geology              Email:th81@umail.umd.edu
University of Maryland        Phone:301-405-4084
College Park, MD  20742       Fax:  301-314-9661

"To trace that life in its manifold changes through past ages to the present
is a ... difficult task, but one from which modern science does not shrink.
In this wide field, every earnest effort will meet with some degree of
success; every year will add new and important facts; and every generation
will bring to light some law, in accordance with which ancient life has been
changed into life as we see it around us to-day."
        --O.C. Marsh, Vice Presidential Address, AAAS, August 30, 1877