Re: Defending grades (Was: Re: Archaeopteryx (rant))

["Tim Williams" <twilliams_alpha@hotmail.com>]

Torfinn Ørmen <torf-o@online.no> wrote:

> The reason we still use the Linnean system is that it is a very good tool 
> for information storage.

Agreed.  However, ranks such as Phylum (or Division, for the botanically 
minded) and Class are misleading in evolutionary discussion.  Sure, they can 
be used as markers or signposts.  But too much evolutionary debate has been 
bogged down in sterile arguments about whether this-or-that group should be 
a phylum or a class or an order.

Even worse are the useless debates over the placement of those taxa close to 
the base of these "Classes".  This is a perennial issue with "Class Aves".  
Who's in and who's out?  Do _Rahonavis_ and  _Caudipteryx_ and _Microraptor_ 
get promoted to the Aves (*sound of trumpets*) - after all, they have 
feathers!  Or are one or more of these feathered taxa forced to languish in 
the Reptilia.

> Dealing with extant taxa (especially higher levels) analyses are now often 
> almost exlusively based on DNA because it is more reliable regarding 
> ancestry.

??????!!!!!!!!!!   #@*&%@

(Excuse me while I dust the dust of my clothes after falling off my chair.)

As a microbiologist who works with DNA almost very day I can tell you that 
in response to the assertion that "Analyses based on DNA are more reliable 
regarding ancestry" I would say "I WISH!".

Unfortunately, DNA analyses are not the universal panacea to resolving 
phylogenies.   Even mitochondrial analyses generate very different 
phylogenies based on whether you use (a) whole mitochondrial genome 
sequences; (b) all mitochondrial genes; (c) all nucleotides of 
protein-coding genes; (d) all nucleotides of protein-coding genes with the 
third base of each codon removed; (e) amino acids of protein-coding genes; 
(f) transfer tRNA sequences.  I only mention this because mitochondrial 
sequences are often regarded as the gold standard in eukaryote phylogenies.

This is not a personal criticism of Torfinn Ørmen - I'm just trying to draw 
attention to the fact that phylogenies based on DNA (or other molecular 
data) have their own diffuculties.  Again, I wish DNA analyses were the 
answer to every evolutionary question regarding extant taxa.  (Dear God, I 
wish!)

> Working with extant anatomy you would e.g. never get the whales dumped in 
> the middle of Artiodactyla.

In this case, the fossil evidence indicates that Cetacea probably arose from 
basal Artiodactyla.  (Check out taxa such as _Artiocetus_, _Rodhocetus_ and 
_Ambulocetus_).  DNA will never replace paleontology.

> BTW, this is another example where the anatomy of a group of animals have 
> changed so much that it is defensible to classify it outside the parent 
> taxon instead of squeezing it inside, e.g. as a sistertaxon to 
> Hippopotamidae.

First of all, as I said above, I think the molecular phylogenies that regard 
cetaceans as the sister taxon to hippos are probably not quite correct.  In 
other words, I am not a fan of Whippomorpha (I like the name, but not the 
clade).

Second of all,  I don't see the problem of including the Cetacea as a clade 
*withinin* the Artiodactyla.  Similarly, I don't see the fuss in putting 
Aves inside the Theropoda.  After all, that's where evolution put them.  Who 
am I to argue?


> Daniel Grossberg wrote:
> >Classification is intended to ease our understanding of a species' 
> origins.
> >One can note that aves evolved from reptiles, while still maintaining 
> them as
> >a separate class.
> :-)
> (Loud applause)

Boo hiss!!!!

(Reaching for my crate of tomatoes...)

:-)

Why bother putting birds in a separate class?  To do so actually *impedes* 
an objective understanding of a species' origins.  IMHO.




Tim

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