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relative rate test

Joe Felsenstein joe at evolution.genetics.washington.edu
Mon Jul 22 23:45:57 EST 1996

In article <31F3BE3C.79EA8BB8 at kurtz.bio.psu.edu>,
Spencer Muse  <muse at kurtz.bio.psu.edu> wrote:
>Joe Felsenstein wrote:
>> In article <4sjta2$poo at nntp3.u.washington.edu>,
>> Spencer Muse <muse at kurtz.bio.psu.edu> wrote:
>> >On a cynical final note, I do find it a bit intriguing that so much
>> >concern is given to multiple correlated tests in one paper, but the
>> >problem is almost completely ignored when a result from one paper is
>> >followed up (in a correlated way) in other papers. (This is meant to be a
>> >general comment, not poined at the rr test problem in particular.)
>> Here I am less clear where the correlations come from.  If you look at a
>> different locus in the second paper, how is that result correlated with
>> the previous one?
>I don't see any problem in moving to additional loci at all. But there are a
>number of "stories" that continue to be perpetuated in the literature by the
>addition of more taxa. Unfortunately, there is little that we can do to avoid it
>in studies of evolution. It certainly would be foolish to say "Smith published a
>very interesting paper on this topic with data from the same gene. While your
>analysis is interesting as well, we can't accept it until you deal properly with
>the correlations between the two studies." I just think it is interesting that
>multiple tests arising from different papers are not considered at all, while they
>are one of the first things that reviewers pounce upon if they show up in a single
>paper. Fortunately, they don't seem to be rejecting otherwise good papers because
>of multiple test problems.

I can see that if you include a wider set of sequences, and do a RRT, 
while including the sequences from a previous study, these two tests are
not independent.  I suppose that if you pointed this out, people might not
be too confused.  But if you ignore the previous study you could be accused
of re-publishing their test.

Even if you test only the new sequences, this test is not independent, to
the extent that the paths between all your pairs of sequences include any
branches of the tree that were in the previous study.  The sequences
((pigeon,duck),(American_crocodile, alligator)) lead to a test that is NOT
independent of the test using, say:  ((crow,goose),(Nile_crocodile,moongoose)).

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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