[Taxacom] Molecular phylogenetic hypotheses

[Kim van der Linde]

Truth is overrated. Philosophically impossible (you can never know 
everything to know for sure you know the truth(tm). All we do is talk 
about likelihoods.

My experience, most of the time, morphology and DNA correspond. Often, 
when not, there was already doubt about the position of a species. So, I 
actually do not see the problem so much.

Kim

On 8/17/2010 7:45 PM, Stephen Thorpe wrote:
> 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

-- 
http://www.kimvdlinde.com