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Re: Morpho v molecular (was Re: Tinamous: living dinosaurs)

2011/7/5 Tim Williams <tijawi@gmail.com>:
> Mickey Mortimer <mickey_mortimer111@msn.com> wrote:
> any noise.  This may not always be the case, and third codon positions
> may be especially problematic.  As you know, in protein-coding genes,
> each codon is composed of three bases.  The third bases of codons tend
> to vary more than first bases, which in turn tend to vary more than
> second bases.  This is due to relative levels of degeneracy of the
> genetic code at these three positions.  For this reason, the third
> codon position (the most rapidly changing position) is often
> invaluable for discerning recent divergences.  However, for deep
> divergences, the third positions become saturated.  At this point, the
> third codon positions cease to be useful for phylogenetic analysis.
> This means that a whole third of the dataset is not merely useless for
> retaining the phylogenetic signal (more, if the first position also
> becomes saturated), but acts as a potential source of homoplasy if the
> base substitutions are not evenly distributed.  Thus, this non-random
> 'noise' at the third position can therefore create structure that
> conflicts with the phylogenetic signal, especially in deep
> divergences, but can be mistaken for the phylogenetic signal.

Agreed that it is logical to expect more change, and thus more
homoplasy, in third positions than in the others positions... But this
does not mean that the change in these third positions biased and
non-random. Change at these positions may still be random, so the
characters based on these positions will still be "noise" and not
"bias". And, as you stated, homoplasy (which implies more change than
non-homoplasious characters) cannot be dismissed because it can add
structure to a tree at least close to the terminals, and because it
may demonstrate not to be homoplasy with further data. Unless you can
also say that the change in the third position is biased, with some
bases appearing more often than others.