On 22 Sep 1999, James McInerney wrote:
> In reality, if an aromatic amino acid is needed at a particular
> location, then the replacement of phenylalanine by tryptophan or
> tyrosine is much more likely and also the existence of homoplastic
> changes for this site is probably more likely than at the nucleotide
> level when there are four alternatives, rather than (_effectively_) two!
>> So, stepping off my soapbox for a second, does anybody agree with this
> comment, or is it completely wrong? I have inferred amino a
I'm not sure I would agree with the last comment about homoplasy
being more common at the amino acid level, but there would seem
to be no reason to doubt that 1) there is homoplasy and 2) in
some cases the pattern of homoplasy will be increased to a level
greater than expected by whatever causes GC-related bias in
amino acid composition (presumably a mutation bias). With respect
to #1, I seem to recall a site in hemoglobins, I think it
is canonical position 104, that has either Lysine or Arginine
in most vertebrates, and which seems to have toggled back and
forth between them a number of times in evolution. It is a
"phylogenetically informative" site, but not a reliable one.
Obviously #1 influences the reliability of your inferences, but #2 is
probably more problematic, because a bias of the same type can
systematically make two sequences look more related than they
are. I think Peter Foster has actually been working on how to
cope with this in phylogenetic inference.