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Re: Classification: A Definition



----- Original Message ----- From: "Botterweg, Ronald (R.B.)" <Ronald.Botterweg@uwv.nl>
Sent: Wednesday, May 16, 2007 12:52 PM


David Marjanovic wrote:

>Compared to Linnaean classifications, all that phylogenetic
>nomenclature will take away is the illusion that some taxa are somehow
>at some kind of same level and therefore somehow comparable (for
>example, that it's possible to count families). (...)

OK, confessed, I belong(ed) to those many people that thought that a
phylogenetic tree could indeed be translated into a classification, the
extremities of the tree then being the lowest taxonomic levels (usually
species).

It can be done (and has of course often been done), but firstly, there is no unambiguous way to do it (especially in the absence of phylogenetic definitions), and secondly, you lose information in the process.


If, as you state, phylogenetics does away with any absolute ranking and
comparison of taxonomic level, and everything indeed becomes only
relative,

No, I didn't state that. Phylogenetic _nomenclature_ does away with _mandatory_ ranking. Comparison of taxonomic levels has _never_ been meaningful; Hominidae and Protoceratopsidae are not comparable, no matter if I call them families or not; it has always been relative, only now we're admitting it to ourselves (thanks to Mike Taylor); ranks are disinformation.


then in the everyday practice this may become very impractical
and even almost impossible to tackle large numbers of taxa; for
instance, how to deal with: species lists, biodiversity analysis and
mappings, standard works of reference (encyclopedias), without a
practical classification and listing?

The same way as always -- except that now we're allowed to use more names than previously because we can't exhaust the number of levels anymore.


Sure, the number of names, as you
state, only grows bigger (potentially even without limit, for a
potentially limitless number of clades?), but they loose their
significance with regard to any taxonomic ranking/classification.

The potential number is unlimited. Of course, most clades are not interesting enough to talk about them, so they don't need names, and (unsurprisingly) the PhyloCode recommends against naming them.


If I understand you well, then, when applied consistently, there should
no longer be any reference to families (not even to mention higher
ranks), maybe not even genera, and in its most extreme form even the
species itself becomes questionable (though I can hardly imagine that
anybody would drop that concept).

Yes.

Species are a special problem. Unlike for the other ranks, at least 25 species concepts exist, and many of them are useful for many applications, even though each of them fails somewhere. It is therefore not surprising that some indeed want to abolish species, too. The PhyloCode is wonderfully agnostic on this matter: firstly, it will not govern species names -- this will be left to the currently existing codes; secondly, it will allow the use of specimens that do not belong to any named species as specifiers in phylogenetic definitions.

For example, besides the two mentioned amphibia websites, large standard
works (just a few that I happen to know and use) such as Wilson & Reeder
Mammal Species of the World and Walker's Mammals of the World, would
become very impractical, loosing overview without classification in
orders, families, etc.

I don't see why. Instead of "Order Perissodactyla", just say "Perissodactyla".


And if I may say, even the website 'The Speculative Dinosaur Project'
(fascinating site I might add) should not make reference to families,
but just limit itself to trees.

Most pages don't make reference to families, only to clade names. The few remaining mentions of the word "family" can be edited out without any loss of information (and will be as soon as possible... which is not soon).


Is there not a kind of 'reconciliation' possible, for practical reasons,
e.g. 'cut-off' ponits/lines in trees, indicating what we call a
(particular) family, genus, etc. Yes, this would be classification, but
an improved one. Or is this heresy again?

That seems to be what Frost et al. tried: they used ranks up to the superfamily (though they only put a few families into superfamilies) and kept all larger taxa rankless. (Unfortunately they didn't give phylogenetic definitions to most of the names of these larger taxa.) Well, they eliminated part of the problem, but what to call a family or a genus remains as subjective as ever. As I'm sure you have noticed, Frost et al. split the traditionally huge genera *Bufo* and *Rana* into lots of smaller ones -- this is neither right nor wrong, it's subjective.


Bottom-line is: how to present (overview of) large numbers of taxa in
trees, without (tabular) classification?

Either just plot the labeled tree.

Or make an indented list -- that's basically a tree with invisible lines and visible names. That's how Wikipedia does it. However, this requires to repeat "unnamed taxon" again and again.

By the way: do not confuse AmphibiaWeb and Frost, they are not exactly
the same source, Frost is the source of the on-line version of
'Amphibian Species of the World' of the AMNH. AmphibiaWeb is of Berkeley
and partly follows, but does in many parts also deviate from Frost.

Oh, sorry. :-]