PHYLIP Consense tree not most parsimonious?

Mark Siddall mes at zoo.toronto.edu
Sat Feb 4 10:05:34 EST 1995

>In article <D3F8CA.Izz at sci.kun.nl> gertjan at sci.kun.nl (Gert-Jan Caspers) writes:
>>Hi phylogeny constructors,
>>In constructing molecular phylogenies using the PHYLIP package,
>>I encountered something which puzzles me.
>>I wanted a maximum parsimony tree with bootstrap values from my 
>>protein data set, so I ran the programs Seqboot, Protpars and
>>Consense, using the output from the earlier as input for the
>>However, when I ran the resulting tree and some other trees I
>>made up myself through Protpars again, using the User Tree option,
>>I found that one of my own trees was one step shorter than the
>>consense, bootstrapped, tree.

This is not at all surprising.  
A bootstrap tree is a consensus of trees based on boostrap replicates.
You must read Felsenstein's 1985 paper regarding bootstrapping and 
understand it before doing bootstrapping!
Also you should read up on what consensus trees are!
If you simply want bootstrap values on your most parsimonious tree(s)
I would be surprised if Joe did not include an option in Phylip to
do this.
My software RandomCladistics does this by default.  That is is enumerates
all clades found in your most parsimonious tree(s) and only those clades
and then looks for their frequency of support in the various trees
in the bootstrap replicates.
If you want to find the bootstrap support value for some other clade
not suggested in the most parsimonious reconstruction(s) you have to
specify it explicitly.
The bootstrap-tree (Maj-rule) is not intended to be a most parsimonious tree.
It is intended to be a 50% cut-off point tree.
I have thought about this a bit recently and have trouble with the
use of parsimony to construct the pseudoreplictes only to 
abandon parsimony for the final best hypothesis.
Neuman characterizes the issues as follows:
Hypothesis Type I: Most parsimonious tree A is the best current estimate
of phylogeny.
Hypothesis Type II: Most parsimonious tree A is a good current estimate
of phylogeny.
Hypothesis Type III: Non-parsimonious tree B is a better current
estimate of phylogeny than is most parsimonious tree A.

Randomization has nothing to offer Type I.  Parsimony quarantees that it is.
Randomization has much to offer Type II.
Type III is false.

Arguably bootstrap trees are hypotheses of Type III.

Mark E. Siddall                "I don't mind a parasite...
mes at vims.edu                    I object to a cut-rate one" 
Virginia Inst. Marine Sci.                     - Rick
Gloucester Point, VA, 23062

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