[Taxacom] Molecules wins over morphology again

John Grehan jgrehan at sciencebuff.org
Thu Sep 1 12:57:20 CDT 2011

I'm not surprised by the situation as I have seen it for decades in

I am regarded by some on this list as an ignorant clod who should know
better abut cladistics, phylogenetics, molecules etc, but I was
pleasantly surprised that some in the fish world share similar, if not
sometimes identical, points of view.  For example, Mooi and Gill
(Zootaxa 2450: 26-40 2010)state the folling:

It should come as no surprise that we urge a careful review of methods
in modern molecular systematics when pumpkin pie can be shown to be the
sister taxon to a crayfish with 100% bootstrap support (Buhay 2009:
106,fig. 7). 
For phylogenetics to remain relevant, its practitioners need to get back
to understanding the basics of cladistics: that we do not "test"
phylogenies-we test assumptions of homology. The only evidence for
phylogenetic relationship is homology represented as
synapomorphy-presenting phylogenies without synapomorphies is not
cladistics. The addition of taxa to a study should not generally alter
the relative topology of the original taxa if homologies are understood;
if topologies do change, characters need reexamination and not mere
optimization on the new topology. Optimizations are not so much
phylogenies as they are odes to algorithms, ways to explore statistics
rather than ways to explore biology. Optimization does not differentiate
between homology and nonhomology; resulting topologies are "solutions"
to datasets that have not taken the foundations of phylogenetics into
account. In our view, all of this amounts to a crisis in
phylogenetic systematics

John Grehan

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of J. Kirk
Sent: Thursday, September 01, 2011 1:36 PM
Subject: Re: [Taxacom] Molecules wins over morphology again

Welcome to the slanted review process. I've encountered this attitude 
with nearly every manuscript I've submitted that addresses philosophy of

systematics (and calls into question many of the methods used). Quality 
of science seems to have a much lower priority in the review process, 
where it's more important to be a good little trooper who totes the 
party line of methodological mediocrity.


On 9/1/2011 7:31 AM, John Grehan wrote:
> Here is a recent example of how prejudice against morphological
> systematics and the resulting orangutan theory of human origin can
> adversely affect publication opportunities.
> "Thank you for submitting this manuscript. It has been assessed by one
> of our senior editors, who sees no basis for your argument that orangs
> and humans are sister taxa (based on your analysis of phenotypic
> or for your assertion that (authors) are wrong to believe that
> data are sufficient to prove that chimps and humans are monophyletic.
> Unfortunately we cannot consider your submission further."
> Note how the editor is able to just dismiss the published evidence as
> non existent (no basis). What is truly bizarre is that this rejection
> morphological evidence having any independent scientific validity
> from the editor of a journal that has anatomy as its core subject!!!!
> Anyway, it has just been brought to my attention that Zootaxa not only
> allowed molecular evidence to be contested, but also promoted a debate
> with respect to fish systematics. So perhaps we will have more luck
> this journal by drawing attention to the same kind of problem in
> primate systematics.
> John Grehan


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