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Question Regarding Bootstrap

James McInerney james.o.mcinerney at may.ie
Mon Oct 18 10:31:36 EST 1999


It is an interesting point about branch length and bootstrap support.  I
think it would be incorrect to say that there is a linear relationship
between the two, but in general, an internal branch that is short will
probably receive a fairly low bootstrap value.  The problem is..how
short is short?

If you want to see a manuscript about all of this, then perhaps you
could look at Hirt et al in PNAS this year.

Robert P. Hirt, John M. Logsdon, Jr., Bryan Healy, Michael W. Dorey, W.
Ford Doolittle, and T. Martin Embley. Microsporidia are related to
Fungi: Evidence from the largest subunit of RNA polymerase II and other
proteins PNAS 1999 96: 580-585. 

In this manuscript, they examine the effect of constant sites removal
(CSR) from a protein alignment and look at the effect on bootstrap values.

The question of bootstrapping with or without constant sites is one that
has not yet been adequately answered.  There is the philosophical point
that all sites should be included in bootstrapping, since the raw datum
is a random (?) sample from the universe of sample points (sequences). 
Therefore, in order to adequately characterise this universe from such a
small sample, we must use all the information available to us.

There is then the counterpoint that constant sites convey little or no
information and indeed contribute to a violation of an assumption that
is made by many tree-making methods (the assumption that all sites are
free to change).

It worries me, but I refuse to loose sleep over it.  Anyway, enjoy the
Hirt et al paper.


Luis wrote:
> I was wandering if there is a relation between short branches and low
> bootstrap values for the adjacent nodes, it seems to me that the shorter
> the branch the lower will be the bootstrap value for the node from where
> it comes. Does this always happen, and does the contrary happen for long
> branches? If this is true wouldn't bootstrap go against it's first
> intention of providing a mean for estimating sampling error, since if we
> add invariable positions to  sequences the bootstrap values would
> decrease even though we increase the sampling?
> Thank you
> Luis

             Dr. James O. McInerney,
Dept. Biology,                       Dept. Zoology,
Natl. Univ. Ireland,                 The Natural History Museum,
Maynooth,                  and       Cromwell road,
Co. Kildare, Ireland                 London SW7 5BD, UK.
Phone +353 1 708 3860                +44 171 938 9163
Fax   +353 1 708 3845                +44 171 938 9158
email james.o.mcinerney at may.ie       j.mcinerney at nhm.ac.uk

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