DNA substitutions saturated?

Jonah Thomas JEThomas at ix.netcom.com
Mon Dec 11 17:13:08 EST 1995

In <4aej39$553 at nntp3.u.washington.edu> joe at evolution.genetics.washington.edu 
(Joe Felsenstein) writes: 

>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.)

Do people very often start with a given sequence and randomize it in plausible 
ways, to observe how well the various methods represent the actual 

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