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

Bob Mesibov mesibov at southcom.com.au
Fri Sep 12 18:01:49 CDT 2008


Many thanks for the interesting nibbles. An analysis of the discussion
so far would show incipient speciation with incomplete lineage sorting,
but that's OK!

Pierre Deleporte wrote:

"if I understand well your proposition, the secondary inference of 
homoplasy for some characters would make the phylogeny inacceptable"

That's nearly what I'm thinking. I started by asking 'How can we test a
phylogenetic hypothesis?' The many existing 'tests' (think of
bootstrapping, jackknifing, etc) only examine how the tree was derived
from the input data. They don't test the *result*, i.e. the tree. I
began to wonder whether further study of the character states involved
and how they are related on the tree (character-tracking) could generate
evidence to assess the plausibility of the tree.

I'm still wondering that. It's always amazed me that after the
publication of so many trees there is no big compendium 'The
Evolutionist's Book of Homoplasies' which reviews and considers not only
character-tracking for genuine homologies, but also the non-homologies
that Platnick referred to.

Steve Manning wrote:

"Second, it seems to me that probability needs to be put front and 
center both with character tracking and with phylogenetic 
hypotheses."

I couldn't agree more, although it would be hard to develop a
statistical-inferential methodology for evaluating homologies, which is
what character-tracking would involve. The method might eventually arise
from developmental genetics, which follows the links between sequences
and phenotypes.

I also agree with you that many phylogeneticists don't appreciate that
the uncertainties in their trees need to be made explicit. Bootstrapping
and leaving models up to MODELTEST aren't enough. I personally like the
networks approach, e.g. with SplitsTree4 software, where the output is a
network which graphically displays areas of uncertainty in the
relationships.

Neil Bell wrote:

"Incomplete lineage sorting and 
reticulation occur and should be identified, but they are not the 
dominant patterns in the relationships between phylogenetically distant 
eukaryotic organisms."

You've identified an interesting methodological issue, namely the
enthusiasm with which some methods are applied at every level of the
lineage hierarchy. The same software is used to generate trees showing
relationships between orders and between populations. Same reasoning,
same assumptions, but the underlying set of objects being studied have
different behaviours and change at vastly different time-scales. I think
there could be a problem here.
-- 
Dr Robert Mesibov
Honorary Research Associate
Queen Victoria Museum and Art Gallery and
School of Zoology, University of Tasmania
Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
(03) 64371195; 61 3 64371195
http://www.qvmag.tas.gov.au/mesibov.html





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