[Taxacom] Zander's point on linked-traits

[John Grehan]

I appreciate that Ken may not be opposed to cladistics (although how one
does that an accept paraphyletic tress is not quite clear to me), but
the point I was raising is that criticisms are often leveled at
cladistics as if they may not apply to non-cladistic approaches, or any
approach at all.

As for getting the wrong answer when one thinks one has found the right
answer, I suppose that is always possible, but in the absence of any
demonstrated evidence to the contrary I won't lose sleep worrying about
that with respect to the current phylogeny produced by a particular
analysis.

As for regulatory links - maybe they are there, maybe not. Either way it
does not matter much since the range of uniquely shared human-orangutan
characters currently far outnumber those of humans and chimpanzees
(currently only one or two that are verifiable).

John Grehan

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Kenneth Kinman
> Sent: Wednesday, February 03, 2010 1:19 PM
> To: taxacom at mailman.nhm.ku.edu
> Subject: [Taxacom] Zander's point on linked-traits
> 
> Dear All,
>      First let me remind John Grehan that I do NOT oppose cladistics,
> and never have (it is mainly strict cladism's attack on paraphyletic
> taxa that I oppose).  My goal is to make cladistics better and more
> reliable, and Richard Zander brought up an important point.  Parsimony
> can fail to find the right answer if a bunch of linked traits
> (conceivably even the result of a single mutation in a regulatory
gene)
> are each weighted equally with more informative unlinked traits (the
> latter thus being numerically overwhelmed, resulting in a severe
> dilution of valuable information).
>      In a couple of Taxacom posts back in April 2003, I warned John
> Grehan that many of his orangutan-human "synapomorphies" seemed
> clustered in body regions with regulatory links.   I still believe
that
> this will eventually explain why he is finding such
> "pseudo-synapomorphies", which would thus actually be homoplastic
> (plesiomorphic or convergent).  And ANY morphological cladistic
analysis
> which contradicts the findings of many different molecular cladistic
> analyses should be evaluated for this problem.  You can read my
concerns
> in the following Taxacom posting:
> 
> http://mailman.nhm.ku.edu/pipermail/taxacom/2003-April/006934.html
> 
> ----------------------------------------------------------
> Richard Zander wrote:
> 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.
> 
> 
> 
> 
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