[Taxacom] sloppy cladistic analyses

Richard Zander Richard.Zander at mobot.org
Wed Feb 3 09:10:47 CST 2010

And . . .  how many cladistic analyses are checked to see that atomized traits, no matter how homologous, may not be probabilistically analyzed in many cases. Cladistics assumes that:  when you have 3 traits supporting (AB)C and only 2 supporting (AC)B, then chances are the shared ancestor had the three traits. But suppose the three traits are selected for as a package, i.e. all three are necessary to survive in a particular environment, and the other two are unlinked. Then, chances are (AC)B is correct. Morphological analyses are never checked as to the degree of linkage of traits in each species in the data set in any adaptive environment. 
I think this is because systematics is 2-stepped: 1. an evolutionary analysis, then 2. classification reflecting the results. And few systematists also do professional research in evolution. Instead, we rely on software imposing one and only one simple model of evolution on all exemplars in the data set. Yet evolution may be quite complex depending on the expressed traits and environmental history of each different organism.
We are depending on the fact that parsimony and intuitive cluster analyses group organisms so they approximate the results of molecular analyses (genetic continuity and isolation events). Good stuff, but . . . We should not extend that approximation as though we have done a satisfactory evolutionary analysis.
Richard H. Zander
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166 U.S.A.
richard.zander at mobot.org


From: taxacom-bounces at mailman.nhm.ku.edu on behalf of Stephen Thorpe
Sent: Tue 2/2/2010 9:51 PM
To: Kenneth Kinman; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] sloppy cladistic analyses

I'm not sure that the internet is to blame here. It seems to me to be more an intrinsic problem to cladistic analysis itself. Anything that involves numbers is prone to transcription errors, and the nature of some people increases the chances of this happening. How many cladistic analyses get checked for coding errors? This problem on top of the other major problem that most of the relevant data is missing (because only a minute fraction of taxa have been informatively preserved as fossils), not to mention subjectivity in character weighting, polarity estimations, and outgroup choice, and what is the worth of such analyses???

From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Kenneth Kinman [kennethkinman at webtv.net]
Sent: Wednesday, 3 February 2010 4:18 p.m.
To: taxacom at mailman.nhm.ku.edu
Subject: [Taxacom] sloppy cladistic analyses

Dear All:
      Although I don't ALWAYS agree with Michael Mortimer, his cladistic
analyses are far better than most.  Therefore, I find his following
critique of many recent cladistic practices and shortcomings very
seriously.  It reflects a broader problem among computer generated
so-called "information" and an alarming trend of  internet
DISINFORMATION now competing with or even outpacing good information.

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