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Question Regarding Bootstrap

Joe Felsenstein joe at evolution.genetics.washington.edu
Mon Oct 18 10:13:34 EST 1999

In article <7ucsoq$cnf at net.bio.net>, Luis  <luismms at mail.telepac.pt> 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

Not always.   It depends on the structure of the rest of the tree.
But for very long branches the bootstrap support will decline, also, as
the homoplasy will start getting large.  So the general pattern is
not as you expect.

>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?

If we add invariable positions the bootstrap values change very little,
as was explained by John Harshman in a paper in Systematic Biology in
1995.   Your intuitive expectation that bootstrap values will decrease
significantly is simply incorrect.  As you add invariable positions the
number of sites sampled in the bootstrapping also increases.

(Note I said "decreases significantly".  There is a slight decrease but
it is not important.  Some critics of Harshman's paper have made it sound
as if the issue is whether there is any change at all.)

Joe Felsenstein         joe at genetics.washington.edu
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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