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

Richard Jensen rjensen at saintmarys.edu
Fri Sep 12 10:05:15 CDT 2008


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.

Dick J

Richard Jensen, Professor
Department of Biology
Saint Mary’s College
Notre Dame, IN 46556
Tel: 574-284-4674



Bob Mesibov wrote:
> 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'??
>   




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