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Re: The Papers That Ate Cincinnati

The point is rather than non-monophyletic descent
*also* exists, and not actually little of it.

(T) (A)
|   |
 \ /

This is a crude representation of the internal pattern
of the _Triticum_-_Aegilops_ clade. What would
PhyloCode do with it?

Apply Articles 2 and/or 16; in this case, 2. http://www.ohiou.edu/phylocode/art1-3.html http://www.ohiou.edu/phylocode/art16.html

(In general <broad grin>, you should read the PhyloCode. Everyone interested in biology should. It's short and easy! Takes maybe one good evening.)

Then, lichen. May or may not have a single basal node.
This node or nodes unites 2 lineages of descent from
entirely different clades into a new organism.

If lichens are monophyletic, they are monophyletic. If they are diphyletic and produced by convergence, then they are diphyletic. Where is the problem?

Then, anything that is unicellular and reproduces
clonally. In these cases, ontogenetic genetic changes
(eg by HGT) *are* possible phylogenetic changes. How
to define clades in these?

I don't see where the problem is. Please explain.

Or try Woese
(http://www.pnas.org/cgi/reprint/97/15/8392 and

Article 2.

The point seems not that phylogenies are unfeasible as
a classification framework; they better should be
useful and they are.

But, you see, we don't even try to use them as a classification framework. We don't "translate the tree into a classification". We have stopped classifying in the first place. Instead, we tie labels to defined places on the tree.

(If you like to lose respect in Mayr,
http://www.pnas.org/cgi/reprint/95/17/9720.pdf for his
critique of Woese's "Henningian" decision to recognize
the distinctness of the Archaea. Bleh.

The situation has been explained to me as follows: Mayr wrote in a readable style but was not a deep thinker; Hennig is a pain to read, but he was right.

He should have stuck to the BoPs.

(Birds of paradise, right?)