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Tree reliability and the bootstrap

scarr at kean.ucs.mun.ca scarr at kean.ucs.mun.ca
Sat Oct 30 12:00:54 EST 1993

>From: gertjan at nl.kun.sci (gertjan)
>Subject:Tree reliability
>Date: Thu, 28 Oct 1993 16:25:53 GMT
>Message-ID:<1993Oct28.173222.27104 at gserv1.dl.ac.uk>

Hi netters,
>I have a set of orthologous sequences of approximately 150 amino acids
>from ten different animal species. The sequences don't differ very
>much, most of them in about ten positions.
>I have made maximum parsimony and neighbor-joining trees with these
>sequences, which are looking quite nicely, but how can I say
>anything about the reliability of these trees?
>Bootstrapping would clearly not be of much use, since in the
resampling process often all significant sites will be removed.
>Or do I just have to accept that trees based on such small data sets
>will never be very reliable?
>Any suggestions will be appreciated.
>					Greetings,
>					Gert-Jan Caspers
>					Dept. Biochemistry
>					University of Nijmegen
>					The Netherlands
>					gertjan at sci.kun.nl


	Bootstrapping is what you want. The bootstrap gives an indication 
of how internally consistent your data are: if all of the informative
(variable) sites give a consistent (or nearly so) phylogeny, any one resampling of
the data is similar to any other, the same clades appear, and the bootstrap
values are high. If on the other hand different portions of the data go
in different directions, the reproducibility of any clade is low and the
bootstrap values low as well. Bootstrap values are NOT statistical
confidences, they are more like consistency checks - the higher the value,
the greater the internal consistency of the data. The fact that most of 
your sites don't vary is unimportant wrt bootstrapping - see Carr and Hughes
(1993) J. Mammalogy 74:331 for a bootstrapped nucleotide data set in which
the majority of positions are invariant.

A bootstrapping algorithm is available in Dave Swofford's PAUP package.

Hope this helps.


Steven M. Carr
Dept. of Biology
Memorial University of Newfoundland
St. John's NF A1B 3X9

(709) 737-4776 office / -4713 lab / -4000 FAX
scarr at kean.ucs.mun.ca

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