parsimony/biology

[Zden�k Sk�la]

Tom,
you wrote:
> ... all of the biological
> and evolutionary assumptions that are part of a phylogenetic
reconstruction
> effort enter at an earlier stage than the point at which we choose and
> implement the parsimony criterion.
> They enter at the point when we define a character and hypothesize that it
> is a homology.
Then, which source of information you use to distinguish homology from
non-homology? Is a glandular hair of a plant leaf homologous with a similar
one on another plant? If a cladogram is used to distinguish homologies from
homoplasies, the method seems to be clear. And vice versa: if the "true
homologies" are defined at the level of data matrix, how can part of them
turn to homoplasies (non-homologies) during cladogram construction? Which is
then the value of "having homologies" at the character matrix stage?

> whatever one chooses. But the justification for using parsimony is nothing
> but the same justification that one uses in every other (non-phylogenetic)
> instance in which we use parsimony - a logical criterion that constrains
us
> to select the result that most efficiently summarizes the evidence - not
to
> postulate complexity unnecessarily. The phylogenetic use of parsimony
> requires us only to select the tree that has the most support in the
> evidence. That is logic, not biology.
several points:
(1) the parsimony itself (as already stated by others) does not necessarily
invoke the use of character congruence criterion in the cladistic sense. The
nearest-neighbor cluster analysis is parsimonious as well, yet in another
sense and, of course, applied to phylogenetic data gives quite different
solutions.
(2) to "efficiently summarize the evidence" means to summarize under a
particular evolutionary model (also stated by others already). Cladogram can
summarize the evidence (in the sense of phylogen. tree topology
approximation) if and only if its construction principles apply also to the
phylogeny - no matter if the decision about topology is made at the level of
character matrix or the cladogram synthesis. Imagine, e.g., the evolutionary
model in which each character would change each 10th generation. Do yo mean
that cladogram "efficiently summarize the evidence" even under such
conditions?
(3) hence, not only that the "parsimony" (cladistic) is biology as well as
logic; moreover the underlying hypotheses about the character change pattern
(splitting, reticulate...) and speed (low, high) are basically untestable
hypotheses (the "picture of evolution" depends on the methodology which in
turn depends on our assumed "picture of evolution").
Best!
Zdenek Skala



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