[Taxacom] Clade age (was: Taxacom Digest)

Lynn Raw lynn at afriherp.org
Thu Nov 10 17:10:00 CST 2011


Thanks, Richard. I think you may have also answered another question relating to the possibility that primers and PCR might selectively collect DNA base pairs from other parts of the DNA. From what you say it seems unlikely.

The second question was not theoretical. It resulted from the geosynclinal uplift of a once single habitat followed by the incision of deep river valleys that has resulted in 7 morphologically distinct, dare I call them, taxa. DNA studies were unable to separate them, my guess is that this looked at a stable sequence in this group that did not change. Perhaps choosing another region could show some differences but I can see just how a tree / cladistic approach would not be able to deal with it.

Lynn Raw


On 10 Nov 2011, at 22:03, Richard Zander wrote:

My understanding is that reversals in DNA sequences are rare if one chooses well the sequence to study. The mutations change only a small portion of the sequence among the taxa studied. Only when there is rapid mutation for those taxa for a poorly chosen sequence will there be lots of overwriting of informative base changes and thus loss of data on shared ancestry.

Your second question is interesting in that it posits a theoretic scenario not tolerated in cladistics, therefore there is no problem and no answer. You imply that one or more descendants arise from a single progenitor. Although cladists might allow such might happen at times, cladistics does not model this. Cladistics models clades, and classification is by clades. Progenitor-descendant pairs or series are eliminated by the classification principle of holophyly. 

There is my take on your questions, the Good and the Ugly answers. Astrology takes astronomy, a good thing, and maps every other pattern onto it, a bad thing. So also goes phylogenetics, with molecular trees revealing quite interesting patterns of evolution (genetic continuity and isolation events), and cladistics mapping morphological traits, biogeography, and kitchen sinks onto the pattern.


* * * * * * * * * * * *
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

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Lynn Raw
Sent: Thursday, November 10, 2011 3:15 PM
To: TAXACOM
Subject: Re: [Taxacom] Clade age (was: Taxacom Digest)

Dick, while you are at the séance, could you also find out whether reversals are taken into account in Bayesian methodology. With only 4 basic components of DNA, surely the probabilties of reversals are extremely high. I would also be interested to learn how these methods deal with a group of closely related but morphologically distinguishable groups that have resulted from vicariance from a single more widespread species. I am not trying to be facetious, these are genuine questions.

Lynn Raw


On 10 Nov 2011, at 20:24, Richard Petit wrote:

There will be a séance at Sister Fatima's on Saturday night. I will try to 
get a definitive answer for you (unless the dna folks have already booked 
all the available times).

dick p. 


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