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

John Grehan jgrehan at sciencebuff.org
Fri Sep 12 10:57:03 CDT 2008

> bounces at mailman.nhm.ku.edu] On Behalf Of Richard Jensen
> Sent: Friday, September 12, 2008 11:05 AM
> To: Bob Mesibov
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Why character-tracking doesn't happen?
> There's another way to view homoplasy. I believe it was Norm Platnick
> who wrote that homoplasy is an indication that we have made incorrect
> assumptions about homology. If character state 1 in taxon A and
> character state 1 in unrelated Taxon B represent a homoplasy on the
> tree, then they are not the same thing.

But why could they not represent the "same" thing as a plesiomorphic
character which is represented in just some members of the ingroup
(being list in others) and the outgroup - or do I misunderstand?

> Bob Mesibov wrote:
> > It works like this. A tree is built on an optimality criterion, say
> > parsimony. Within this tree there's incongruence: not all the
> > morphological characters, or all the sequences in a multi-locus gene
> > set, will give the same tree when analysed separately. This
> > is explained *after the fact* as due to homoplasy.

I thought homoplasy was just a term to describe character similarities
that do not match the preferred tree, and as such they are not an
explanation of anything. The homoplasies themselves are then 'explained'
as convergence, parallelism etc.

> > Do people working at this higher level think something like: 'The
> > and/or morphological characters disagree. I don't know why and it's
> > feasible to investigate. All I know is that this is a pretty good
> > based on sound methodology'??

In morphology at least, the problem might sometimes lie more with
character state identification and underlying assumptions. For example,
there is supposed to be rampant homoplasy in the evolution of large
bodied hominoids, but this extensive homoplasy only occurs when the best
supported tree (human-orangutan) is rejected using other criteria (such
as a prejudged preference for molecular trees), or characters are
erroneously included because the outgroup is highlight restricted (e.g.
just gibbons for the large bodied hominoids, or just one or two monkey
species), or characters are just not correctly delineated (such as
saying something is present when it is not).

John Grehan

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