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Re: The Papers That Ate Cincinnati

On 5/7/07, Anthony Docimo <keenir@hotmail.com> wrote:
>I think that's absolutely fine. In mammals, _Cetacea_ is part of
>_Artiodactyla_. In insects, _Isoptera_ is part of _Dictyoptera_ and
>_Siphonaptera_ is part of _Mecoptera_. If opisthocomiforms are
>cuculiforms, great. We've learned something new and the nomenclature
>can help communicate that.

So...the nomenclature would change?

No, the nomenclature (names coupled with definitions) would stay the same, but our understanding of the content associated with those definitions (and hence with those names) would change. That is (to continue with the example), under all circumstances _Opisthocomiformes_ would still refer to the total hoatzin clade and _Cuculiformes_ would continue to refer to whatever clade it's defined as (e.g., the least inclusive clade containing _Cuculus_ and _Musophagus_, or whatever). Under some phylogenies, they may be distinct clades. Under others, _Cuculiformes_ may include _Opisthocomiformes_. In the latter case, we could say, "Opisthocomiforms are a type of cuculiform," and that would actually mean something, since the names would be tied to rigorous definitions.

There are still people who don't call Brontosaurus by its proper name of
Apatasaurus........what're we going to do when a species has a *dozen*
scientific names?

Again, the PhyloCode isn't going to cover species, at least at first. But in the case of a clade having more than one name (which is possible), there are rules about priority (see Ch. V, starting at http://www.ohiou.edu/phylocode/art12.html).

Then what's the role/purpose of nomenclature?

Names. Specifically, the role of phylogenetic nomenclature is to associate names with phylogenetic definitions (e.g., node-, branch-, and apomorphy-based clade definitions).

>The PhyloCode's job is not to tell us the phylogenetic position of 

and what's going to tell us that? *is curious*

As Andreas Johansson said, cladistic analysis is one tool (probably the best tool we have so far). But it's possible to use phylogenetic nomenclature while using some other method of obtaining phylogenetic hypotheses--look at Greg Paul's _Dinosaurs of the Air_ for one example.

I've heard talk of scrapping Linnaean classifications.

Actuall, as Kevin de Queiroz has pointed out (I can try to find the reference), many of the things phylogenetic nomenclature is seeking to abandon, such as coordinated ranks, are post-Linnaean. Linnaeus did use ranks but they were not reflected in the names he gave taxa (e.g., no standard suffixes that had to change when the rank was changed).

Phylogenetic nomenclature does eschew (or at least sidestep) absolute
ranks, since they are phylogenetically meaningless. But it still uses
names from Linnaean/traditional taxonomy.

>(Incidentally, "mammal-like reptiles" are often not considered
>reptiles any more. A better, more succinct term would be

I thought there was a difference between "stem mammals" and "mammal-like
reptiles"...one can be the other, but not vice versa.  (like cacti and

"Mammal-like reptile" is a misnomer because: 1) It makes it sound as if they are coincidentally mammal-like (like "wolf-like marsupial"), when in fact they are mammal-like because they are actually related to mammals. 2) They are actually closer to mammals than to any extant reptile (and some are closer to mammals than others).

"Stem-" can be used with the name of a crown group to indicate its
stem lineage, that is, the total group minus the crown group. Other,
more long-winded ways of saying "stem-mammal" are: "non-mammalian
synapsid", "non-mammalian theropsid", or "non-mammalian pan-mammal".

Similarly (to bring this back to the forum's topic), all non-avian
dinosaurs, as well as _Lagosuchus_, pterosaurs, etc. can be referred
to as "stem-avians".

It's true, though, that sometimes "stem" is used in a different way,
to indicate a member of a crown group that is not part of any crown
subgroup. For example, on TaxonSearch, Sereno uses "Stem Archosauria"
to indicate non-avian (=non-neornithian), non-crocodylian archosaurs.
In that sense, "stem-mammal" would indicate any mammal that was not a
monotreme or a therian (e.g., multituberculates). Personally, I prefer
the other usage (where "stem-archosaur" would indicate a
non-archosaurian archosauromorph). I think it's more consistent with
the original definition of "stem group".
Mike Keesey