[Taxacom] Molecular phylogenetic hypotheses

[J. Kirk Fitzhugh]

  Bob,

I'm familiar with the paper. When I read this sentence in the abstract, 
however, I knew I'd be seeing a lot of the same old misrepresentations 
of phylogenetic inference and testing. Please keep in mind that the 
tactic I characterized among some moleculoids can just as easily be 
leveled at any class of characters. The more pertinent issue that 
concerns me is that of critical assessment of causal understanding, or 
lack thereof in systematics.

Kirk

On 8/17/2010 4:37 PM, Bob Mesibov wrote:
> 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

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
J. Kirk Fitzhugh, Ph.D.
Curator of Polychaetes
Invertebrate Zoology Section
Research&  Collections Branch
Natural History Museum of Los Angeles County
900 Exposition Blvd
Los Angeles CA 90007
Phone: 213-763-3233
FAX: 213-746-2999
e-mail: kfitzhug at nhm.org
http://www.nhm.org/site/research-collections/polychaetous-annelids
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~