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

Mickey Mortimer <mickey_mortimer111@msn.com> wrote:

> I don't see anything different here than what happens in morphological 
> analyses.

Nor do I.  I guess that's my point.  Molecular-based analyses are
dogged by the same problems as morphology-based problems.

The major difference with morphology-based analyses is that we can
literally see what the homoplastic characters are.  For example, if
hupehsuchians and ichthyosaurs are being linked by characters that
relate to an aquatic mode of life, and these characters evolved
independently, then we can readily identify what those characters are.
 By contrast, all molecular characters are 'hidden'.  Out of sight,
out of mind.

> Adding genes is better even if it causes more homoplasy, because all that 
> means is that the topology isn't as well supported as we thought,

Not necessarily.  Random noise will be reduced by adding genes, but
non-random noise (bias) will increase.  If the latter is causing
homoplasy, then adding more genes is not going to solve the problem,
but make it worse.  You'll get a stronger signal based on homoplastic
characters - so the wrong topology will get *higher* support.

To use the third codon position as an example, if this position is
saturated (or effectively so) then it has ceased to provide any
phylogenetic signal.  If this position is actually serving as a source
of bias in the dataset, because of (say) differential substitution,
then this will be interpreted as structure, and mistaken for the
phylogenetic signal.

> and the "non-random noise" may be a signal of the true phylogeny.

Yes, exactly.  But how do we know the difference?  The algorithm is
searching for structure.  Both non-random-noise and the phylogenetic
signal generate structure.  Further, both can be manifested as bias.