[Taxacom] Fish phylogenetics paper

[Bob Mesibov]

Hi, Karl.

So you didn't find the discussion on characters and homology interesting? I did, because Mooi and Gill seem to be asking molecular systematists to be aware of, and think about, character homologies in the same way that morphological systematists do. And it's pretty obvious that many molecular systematists couldn't care less about molecular characters, the exceptions being those working on the higher levels of sequence data, i.e. whole genes, gene families, etc.

I think there's a reason for this and that Mooi and Gill are being unfair to molecular systematists. I'll try to explain what I mean, but first understand that I'm not talking about homology at the molecular level. When you compare sequences, homologies are alignment columns. The column is the character, and the nucleotide in that column is the character state. These homologies cannot be inferred in the same way that morphological homologies can be. Instead, they are either created in toto by MSA optimisation, or (in the case of dynamic optimisation) inferred and tweaked by an algorithm that is simultaneously looking for a tree meeting certain criteria.

OK, so the characters (columns) are now defined. Now what? Well, in morphology structures don't evolve from nothing, and changes (even when drastic) have observable roots in pre-existing structures. In sequences, character state changes aren't like that. It's possible for any nucleotide to change into any other nucleotide. There are constraints, but we don't know what they are at any given position. Instead we have a zoo of models which give transition probabilities (that's mathematical transition, not transition/transversion transition), and fudge factors for autocorrelation along the sequence.

Do you agree?
-- 
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/mesibov.html