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Maximum Likelihood Analysis Question

Wnn System Account wnn at evolution.genetics.washington.edu
Tue Aug 20 02:33:38 EST 1996

In article <32195115.7240 at vims.edu>, Mark Siddall  <mes at vims.edu> wrote:
>Ron Kagan wrote:
>> ... to reject the null hypothesis of the molecular
>> clock?  Is p<0.05 still the standard, or should I use a stricter criteria
>> (p<0.01)?
>Since when is the molecular clock a reasonable null hypothesis?!!!
>Molecular phylogenetics in the late 20th century... limited by the 
>arbitrariness of Joe Felsenstein's imagination and Linus Pauling's 
>[no offense Joe... ].

(1) Sure I take offense!   But come to think of it you have put me in
    awesomely good company there!   So, thanks.

(2) The molecular clock is a good, useful, fruitful approximation.
    It is more true the more closely related are the species.  If you're
    comparing archaebacteria to eubacteria to eukaryotes, it is wierd to
    assume it.  If you're doing phylogenies within a genus of dicky-birds,
    it is a natural thing to test.   Does anyone imagine that they would
    have grossly-different rates of molecular evolution?  It would be
    strange if they did.  Morphology is, of course, a different matter.

(3) The molecular clock has been denounced so loudly as nonexistent by
    phylogenetic systematists (and non-parsimony methods frequently, and
    wildly inaccurately, asserted to inherently assume it) that it would be
    helpful to science to have it defended.  It is not true.  But it is
    often pretty nearly true for closely related beasts.  It is therefore
    often worth testing.

Molecular phylogenetics in the early 21st century ... limited by
myths of the total invalidity of the clock?

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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