Re: Classification: A Definition

[Colin McHenry <cmchenry@westserv.net.au>]

Tim Williams wrote:

> I would have said the same thing (though perhaps not as articulately 
> as Jerry).  At the end of the day, phylogenetic nomenclature does 
> "classify" organisms, insofar as taxa are grouped by common descent to 
> produce a hierarchy.  _Tyrannosaurus_ is inside Tyrannosauridae, which 
> is inside Coelurosauria, which is inside Theropoda, and so on...  
> Similarly, _Passer_ is inside Passeridae, which is inside 
> Passeriformes, which is inside Aves, which is inside Coelurosauria, 
> and so on...
Hear, hear.  The question is, if you're not putting together the 
phylocode as an alternative classification system, then why are you 
doing it?

> As for the example of protists (which also surfaced on this list), the 
> old "Protista" is the poster child for just how BAD the Linnaean 
> system was (and still is).  Not only did the "Protista" concept vastly 
> understate the huge phylogenetic diversity of single-celled 
> eukaryotes, but we even had a situation where certain protists were 
> classified as BOTH animals and plants (e.g., _Euglena_).  The latter 
> was a product of grouping organisms based on "key features" or "gross 
> physical similarities" (as Jerry puts it).  Euglenids moved and fed 
> like animals, but they also possessed chlorophyll like plants, 
> therefore they got put into both Animalia and Plantae.
Hang on, I think this is a little unfair on Linnaeanists.  Whilst the 
old system was absolutely and horribly biased towards multicellular 
eukaryotes, I don't think it's fair to say that this was due to the ills 
of the Linnaean system.  I think that the available technologies were 
more of a factor in this - without a damned good light microscope, the 
incredible differences in cellular organisation between Homo, Amoeba, 
Paramecium, and a bacterium aren't as obvious as we know them to be 
today.  The two kingdom classification that many of us were taught (I 
still shudder at the thought of it - I remember my high school biology 
teacher talking about Euglena: "it's a plant!  No, it's an animal.  No, 
wait...") was a result of ignorance stemming from the lack of the right 
tools, not the fault of the classification system.

It was only when we were able to appreciate the vast range of cellular 
anatomy in eukaryotes, thanks to the uptake of electron microscopy, and 
the profound differences in biochemistry between the prokaryotes and 
eukaryotes, that people realised that the old system wasn't an accurate 
representation of life's diversity.  And the attempts to address this - 
the three kingdom, the five kingdom, and then Woese's three domain 
system - were all made within a traditional Linnaean framework.  Even 
though Woese used results from molecular biology to highlight the 
existance of an important new clade, his proposed classification 
explicitly used ranks to accomodate the deepest divisions in the tree of 
life.  So to claim that our improved understanding of basic diversity is 
thanks to people abandoning Linnaeus is something I would dispute.  
Insistance of the importance recognising major monophyletic groups?  
Sure.  Committment to abandoning ranks?  No.

Of course, if Margulis is right about the eukaryote cytoskeleton being a 
result of endosymbiosis with a spirochaete-type bacteria, then the 
Eucarya are merely a symbiosis between one branch of the Bacteria and 
one branch of the Archea.  I'm still confused about how the Phylocode 
will deal with these sorts of tree topologies; if the e.g. Archea 
includes all of its descendants, including the Eukarya, and the Eukarya 
include the descendants of one branch of the Spirochaetes, then surely 
the clade that contains all spirochaetes contains the Eukarya (which are 
a subclade of the Archaea) as well.  So how does the Archaea not contain 
the Spirochaeta and the Spirochaeta not contain the Archaea?  Maybe 
there's a simple way for a logical system based around divergent 
branching patterns to deal with convergent branching episodes: I just 
haven't figured out how it works.  Maybe I should just read the 
Phylocode - does it cover this issue?

Cheers
Col


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Colin McHenry
School of Engineering (Mechanical Engineering)
University of Newcastle
Callaghan NSW 2308
Australia
Tel: +61 2 4921 8879
Fax: + 61 2 4921 6946

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