DNA substitutions saturated?

Joe Felsenstein joe at evolution.genetics.washington.edu
Sun Dec 10 07:16:41 EST 1995

In article <4acsqs$bhu at news.nstn.ca>, Andrew Roger  <aroger at ac.dal.ca> wrote:
>It also turns out, annoyingly, that many distance corrections
>do not adequately correct for saturation (you still
>see the saturation pattern)-both simple and complex
>corrections. I can see how saturated
>distances confound distance tree estimation. But its
>not clear that parsimony and likelihood are going to
>be affected in the same way. Can anyone help me
>with this?

If the distances are saturated, this means that there is no sign that any
two of them are related at all -- they look completely random compared to
each other.  That will lead any method -- distance, likelihood, or parsimony
-- to have long and wildly variable branch lengths, and random tree
topology.  The noise has overwhelmed the signal.  So methods will give
purely spurious results.

(That is why many of us are highly suspicious of the method -- which
fortunately seems to have died out -- of using a totally random sequence as
an outgroup when no real outgroup is available.  It would give a result based
only on noise, and connect in at an unpredictable place in the tree.)

Joe Felsenstein         joe at genetics.washington.edu     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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