[Taxacom] Molecular phylogenetic hypotheses

[Stephen Thorpe]

this raises something I have been wondering: in general, if different subsets of 
data point to different results, why would the "total evidence approach" (i.e. 
the complete set of data, or at least a more complete subset of data) be 
expected to necessarily point to the "truth"???




________________________________
From: Bob Mesibov <mesibov at southcom.com.au>
To: kfitzhug at nhm.org
Cc: TAXACOM <taxacom at mailman.nhm.ku.edu>
Sent: Wed, 18 August, 2010 11:37:26 AM
Subject: [Taxacom] Molecular phylogenetic hypotheses

Hi, Kirk.

Many thanks for the draft. I'm copying this portion of my reply for Taxacom 
because there's what might be seen as a counter-example in the recent 
literature, which Taxacomers might like to read.

You make the point that a typical molecular systematics research stream consists 
of building a phylogeny from sequence data, publishing it and moving on (to 
either another group or the same group with more data) to do the same thing 
again and again, with no attempt to understand the result. This freely available 
paper

http://rspb.royalsocietypublishing.org/content/early/2010/08/05/rspb.2010.0590.full.pdf+html


does something more. The authors examine the possibility that the disagreements 
between certain published phylogenies are due in part to *analytical biases*. 
They apply very simple tests which support this idea.

What is surprising and disappointing to me is that one or more of those tests 
might have been done earlier by any of the research groups working on arthropod 
phylogeny. They weren't. For some molecular systematists, the way to get better 
phylogenies is to use more or longer sequences and more terminals. The hope here 
is that if you throw more data at the problem, any systematic biases will be 
swamped by 'signal'. If there are disagreements between research labs, you 
*suspect* bias but you don't test for it, maybe because your previously 
published work would be revealed to be... less than useful.

Perhaps for some molecular systematists, the analytical method of choice is an 
oracle whose pronouncements cannot be questioned, only published. No wonder you 
see that sterile sequence-analyse-publish repeat. The same oracle-worship is 
seen in *choice* of inference method. In a post earlier this week, Thomas 
Simonsen compared neighbour-joining 'phylophenetics' unfavourably with 
other-inferential 'phylogenetics'. Thomas might be right in the particular case 
he's considering, but distance-based trees are often very close to maximum 
likelihood trees for closely related taxa (you might say 'close within the 
uncertainty of the method'). Should you not do distance-based analyses because 
of a philosophical distaste for them, even though they give the same result as 
another method?

[Hoping this doesn't spawn a long thread, off to the field for several days 
shortly]

Best wishes,
Bob
-- 
Dr Robert Mesibov
Honorary Research Associate
Queen Victoria Museum and Art Gallery, and
School of Zoology, University of Tasmania
Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
03 64371195; 61 3 64371195
Webpage: http://www.qvmag.tas.gov.au/?articleID=570

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