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
        of homology?

        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?

        James Lyons-Weiler

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