[Taxacom] Why character-tracking doesn't happen?
mesibov at southcom.com.au
Thu Sep 11 22:53:57 CDT 2008
There were no serious nibbles at the bait I dangled here recently on
character-tracking, i.e. investigating apparent homoplasy as a way to
evaluate the plausibility of a phylogenetic hypothesis.
I'm now aware that there are two philosophical objections to what I
suggested. First, some cladists don't think of trees as history.
Homoplasy is just a nuisance in their attempts to build a robust
classification. This classification *reflects* history but isn't the
same as history, so character-tracking would be meaningless.
Second, some people accept homoplasy as an explanation for character or
gene-history incongruence when *building* trees, but not as an
explanation for *understanding* what happens in the tree they built.
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 incongruence
is explained *after the fact* as due to homoplasy.
The 'after-the-fact'er' stands by the phylogenetic hypothesis as simply
the best available under the optimality criterion used in the analysis.
It may or may not reflect historical reality. There is therefore no
reason to track characters through the tree. My earlier, imagined, inner
conversation - 'Hmmm. If this tree is correct, then this character must
have had this interesting history...' - never happens. Optimality slays
homoplasy, but there's no corpse.
I think the same loss of information occurs when people build supertrees
from separate phylogenetic hypotheses, or combine data before analysis
using 'total evidence'. [Which is no such thing. It's short for 'data I
can code and treat as equivalent and independent', and excludes relevant
data that can't be coded in that manner.] Both methods give consensus
trees in which the entities being 'treed' are nearly indefinable
(Richard Zander says combining apples and oranges and lemons gives you
fruit salad), and in which homoplasy is an explanation at a level deeper
than the one at which the analysis operates.
Do people working at this higher level think something like: 'The genes
and/or morphological characters disagree. I don't know why and it's not
feasible to investigate. All I know is that this is a pretty good tree
based on sound methodology'??
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
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