[Taxacom] New systematics book

[Ken Kinman]

Hi Richard,

 

      I like it---short and to the point.  I particularly like the part about relativity and Newtonian physics.  However, many phylogeneticists will not like the part about an ancestral taxon (I prefer "mother taxon") giving rise to a daughter taxon.  Not so much because it takes an extra step, but more likely because it makes the ancestral taxon paraphyletic.  Of course, I view this as short-sighted, but that is just how strong an antipathy they have been taught to have toward paraphyly.  Maybe you can convinced them to stop sweeping paraphyly under the rug, and to stop throwing the babies out with the bathwater. 

 

                       -----------------Ken

 



Subject: RE: [Taxacom] New systematics book
Date: Mon, 9 Sep 2013 12:44:19 -0500
From: Richard.Zander at mobot.org
To: kinman at hotmail.com; lists at curtisclark.org; taxacom at mailman.nhm.ku.edu





I appreciate the response, pro, con, and incensed. Okay, here is the shortest way I can describe what passes for optimality in phylogenetics.
 
Take two taxa or clades (at the end of a larger cladogram with other taxa or clades), one characterized by advanced traits xy and the other by advanced traits xz. Phylogenetics assumes that parsimoniously the shared ancestor, now extinct through pseudoextinction (anagenetic change into another taxon), had the plesiomorphic trait x, then one daughter taxon differentiated with y and the other with z. That is three (3) steps.
 
Okay. BUT suppose the ancestral taxon did not go extinct but survived and generated a daughter taxon by peripatric evolution. With the same data set, the ancestral taxon had traits xy, and the daughter taxon had trait z and -y (reversal). That is four (4) steps.
 
In phylogenetics, optimality is always BOTH shortest tree and simplest model (i.e., universal pseudoextinction). The argument is that you do get the shortest tree with both assumptions. Of course the parsimony or other optimality part is okay but the simplest model is nonsense, since this sort of argument would throw out that complicated theory of relativity in favor of the simpler Newtonian mechanics. Occam’s Razor does not work that way since the Razor deals multiple explanations for one model.
 
My suggestion is that the best model for any optimality (morphology or molecular) analysis is generating a mixture of pseudoextinction and peripatric evolution for a group, THEN find maximum parsimony, likelihood or credible interval for that evolutionarily composite model. 
 
The old complaint is that detailing such a composite model requires experience, judgment and reasoned evaluation based on theories of taxon transformation in nature. (Read: subjective just-so story.) It is in fact easy to examine a group of classically grouped species and discern generalized species and highly specialized potential daughter species. THEN constrain the cladogram. 
 
Although using universal pseudoextinction makes for ease of generation of cladograms, the results are in often large part imaginary, that is, all divergence branches involving a single surviving ancestral taxon are not real. 
 
 
____________________________
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA  
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