[Taxacom] Why character-tracking doesn't happen?

[John Grehan]

-----Original Message-----
From: Bob Mesibov [mailto:mesibov at southcom.com.au] 
> The alternative hypothesis is that the shared similarity does not
reflect common ancestry. Instead, it 
> arises because there are selection pressures driving lineages towards
a common phenotype by mechanisms 
> other than simple inheritance of character states.

I'm ok with mechanisms other than inheritance from a common ancestor,
but 'selection pressures' is just one possibility among several.

> In this view of things you are correct in saying, as I did earlier,
that homoplasy is something supposed 
> after the fact of tree-building. It is an explanation for those pesky
non-common-ancestry cases. (IMHO 
> even after a Platnick pruning of mistaken homologies there will still
be such cases.)

I still say that of itself that homoplasy is not an explanation.

> What I would like character-tracking to do is consider those cases
more carefully, rather than dismiss 
> them as evolutionary noise or sampling or analytical error. If there
really wasn't a Type I error, then we
> can learn something about evolution. If there was a Type I error, then
the tree needs re-examining. Either
> way we benefit. The current custom of ignoring the details of
homoplasy seems to me to be throwing away 
> information.

Perhaps so. Some characters that do not define monophyletic groups have
been shown to comprise standard tracks.

John