rooting as a test of rooting
James Francis Lyons-Weiler
weiler at ERS.UNR.EDU
Mon Sep 15 21:24:57 CDT 1997
On Mon, 15 Sep 1997, Curtis Clark wrote:
> At 04:31 PM 9/15/97 -0500, Byron Adams wrote:
> >>At 02:15 PM 9/15/97 -0700, Richard Zander wrote:
> >>> A series of cladograms,
> >>>each depending on the one previous to establish a correct outgroup, is a
> >>>house of cards.
> >Curtis Clark wrote:
> >>An outgroup is not necessary to form a cladogram, only to root it.
> > I think what you meant to say was that an outgroup is not necessary
> >to form, but only to root a _phenogram_ or _dendrogram_. Assuming one uses
> >cladistic treebuilding methodology, by definition an outgroup is required
> >(in order to establish character polarity) and the resulting tree is a
> See Clark, Curtis and Daniel J. Curran. 1986. Outgroup analysis, homoplasy,
> and global parsimony: A response to Maddison, Donoghue, and Maddison. Syst.
> Zool. 35:150-154.
> >I don't think many would argue with me that these (unrooted
> >phenograms/dendrograms) are not the same thing as cladograms. Nor would
> >they argue that somebody who can arbitrarily polarize characters _sans_
> >outgroup comparison is actually doing cladistics.
> Of course not, but the point of our 1986 paper was that rooting the tree is
> algorithmically independent of finding the shortest tree, and that there
> are good reasons to keep them separate. The "series of cladograms"
> postulated by Richard is unnecessary and counterproductive.
This issue has not yet been completely explored. There are
equally good reasons for exploring the effects of
character assumptions that MIGHT be used at the same
time as rooting the matrix, if not the tree; so keeping
them algorithmically separate may be needed if one is
performing rooting of trees, but is not at all desirable
if one wants to test the consequences of making those
assumptions, such as whether or not the outgroup taxon
one has might mislead the tree-based analyses.
We are using rooted rasa to choose among competing outgroup
candidates, and have learned to distinguish between very poor
outgroup taxa and those that are better suited to the task.
As a result, we've learned a great deal about the utility
of making assumptions for the purpose of testing them, and
can choose among what appear otherwise to be equally good
Hopefully the issue of constraining tree building algorithms
will be more fully explored in this context in the future.
For instance, maximum likelihood is conducted in the same
way whether the tree has an outgroup or not. This feature is
advertised a "time-reversibility". However, models that
are time-reversible may not be realistic. We know that
trends in codon or base usage exist over time, for example.
Whenwe root with rasa, we constrain the putative outgroup states
of the purpose of testing the assumption of plesiomorphy.
When the assumption of plesiomorphy is least violated,
signal increases. It's really quite nice; it's statistical,
but doesn't make as many unrealistic statements about
evolutionary processes as a model approach requires.
There are many subtle points here; I hope no one responds
by saying "but that's not how it's done!". If they do,
my response would simply be "quelle dommage". I have even
gone so far as to say that a cladistic maximum likelihood
approach would be really useful in this respect. I hear
all sorts cringing out there, but certainly one can
determine the log likelihood of an observed distribution
of plesiomorphy? the idea is to make the assumptions
explicit, and therefore testable. Why can't we all just
get along :)?
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