James Francis Lyons-Weiler
weiler at ERS.UNR.EDU
Fri Mar 7 15:43:46 CST 1997
On Fri, 7 Mar 1997, Tom DiBenedetto wrote:
> , James Francis Lyons-Weiler wrote:
> >The answer to the first question (does the parsimony algorithm reveal a
> >truly spurious pattern) is, precisely, yes.
> >How would it do that? There exists for EVERY matrix (with variable
> >states among taxa) a set of shortest trees.
> First off, a set of shortest trees can mean a lot of trees. We have a
> convention of calculating strict consensuses of sets of MP trees
> which end up returning an unresolved topology for many such sets. The
> more pointed question is whether random data ever returns single MP
> trees, or sets that preserve resolution through strict consensus
> calculations even for large data sets.
I think a more pertanent question is how often does screened
data result in a lot of trees, and how can you tell the
difference a lot of tress generated by random data, and
a lot of trees generated by screened data. Moreover,
how can on tell the difference between the degree of
resolution is a consensus tree (Nelson? Strict? Semi-strict?
combinable component? Adam's? n-trees?).
One approach that has been proposed is whether or not
we expect the degree of consensus observed among
the set of mpts _by chance alone_, another role for
probability in cladistics (Simberloff).
By the way, consensus trees were originally designed to deal
with summarizing congruence among trees from different data
sets, not among the thousands of equally mpt trees that exist
for a single data set.
By the way I'm curious; if you find 1,000 equally parsimonious
trees, which one provides the critical test of hypotheses
Consensus tree also don't really tell you that your data are
uninformative ,or ambiguous; they may also tell you the
criterion you're using finds conflicting evidence.
It does not, however, provide further info, e.g.,
what are the sources of conflict?
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