Re: Further Thoughts on the Origin of Chelonia

["Tim Williams" <twilliams_alpha@hotmail.com>]

David Marjanovic wrote:


> Of course a shift in codon usage can itself be a (rather morphological)
> synapomorphy;

Exactly right.  To give an analogy: it is possible that certain 
morphological features that unite carnosaurs are size-related.  This does 
not necessarily invalidate these characters as potential synapomorphies.  
However, it is also possible that these characters were convergently 
acquired.   So to for codon bias.  Correcting for codon bias in an analysis 
will resolve the problem of unrelated taxa being pulled together by a 
homoplastic codon bias; but it may produce the additional problem of 
splitting up related taxa that inherited a shift in codon usage from a 
common ancestor (= a synapomorphy for this clade).

> but this, too, stays undetected as long as codon usage is
> unknown in the species in question, as it, I assume, usually is. Takes
> experiments in gene expression to find out, right?

No, nothing this drastic is needed.  Determining (and quantifying) codon 
bias can be done by simply dividing the total number of synomyous codons per 
amino acid by the number of times each individual codon is represented in a 
given gene, to get a ratio.  Some amino acids have only one codon, so bias 
isn't a problem; but others have synonymy at the first, second, or third 
positions, which further complicates matters when it comes to phylogenetic 
analysis.




Tim

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