[Taxacom] New systematics book

[Richard Zander]

Curtis:

I appreciate your interest. Taxacom is kind of a twitter in which to get
anything across it has to be to the point. A book? Well, one can
digress.

My two points from a previous email were:

" ... parsimony and other optimality analyses only work with accuracy
with pseudoextinction (dying ancestor, two new species). The correct
optimality for branching analysis is that which makes the shortest (most
likely, most credible) tree given identified surviving ancestors and
their daughter taxa based on other information. This is merely, MERELY
less precise, correctly less precise and therefore with more uncertainty
about evolutionary relationships. 

"...  molecular "lineages" are molecular strains, and ancestral taxa in
stasis generate lots of molecular strains before and after generation of
one or more daughter species. The DNA continues to mutate in isolation
while expressed traits remain in stasis for millions of years. Molecular
phylogenetics gives precise sister group analyses of extant strains, not
taxa. Evidence? Molecular paraphyly. What about extinct or unsampled
strains? They could have diverged molecularly long before or after any
extant strain."

Sometimes "short" is too short, so this justifies the long-windedness. 

A practical solution would be software that uses optimality criteria to
make best fit for a model that included both pseudoextinction with
extinction of ancestral taxon AND budding evolution with survival of
ancestral taxon. No autapomorphies is not the only result of such
survival. Such a model is not as simple as universal pseudoextinction,
but is more realistic.

For the molecular strain problem, only dense sampling worldwide of
individual taxa can even start to fix the molecular paraphyly problem
since so much informative paraphyly is doubtless extinct.

Richard

____________________________
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA  
Web sites: http://www.mobot.org/plantscience/resbot/ and
http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site:
http://www.mobot.org/plantscience/resbot/21EvSy.htm
UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA


-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Curtis Clark
Sent: Sunday, September 08, 2013 2:27 PM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] New systematics book


Could you elaborate on "Can anyone on Taxacom address my two 
attributions of error in phylogenetics? Directly? Without regressing 
into nostalgia?" by enumerating the two attributions?

-- 
Curtis Clark        http://www.csupomona.edu/~jcclark
Biological Sciences                   +1 909 869 4140
Cal Poly Pomona, Pomona CA 91768


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