relative rate test

Spencer Muse muse at kurtz.bio.psu.edu
Mon Jul 22 12:45:32 EST 1996


Joe Felsenstein wrote:
> 
> In article <4sjta2$poo at nntp3.u.washington.edu>,
> Spencer Muse <muse at kurtz.bio.psu.edu> wrote:
> 
> >In article <4sgfu9$mcv at nntp3.u.washington.edu>,
> >joe at evolution.genetics.washington.edu (Joe Felsenstein) writes:
> >|> Actually likelihood ratio tests can also be done with three species,
> >|> it is just that one of the key programs (DNAML) happens not to be
> >|> able to cope with three species, for purely silly reasons.  We're
> >|> working on fixing that
> >|> in the next major version.
> >
> >[useful citations to many statistical relative rate tests done by a many
> >people.]
> >
> >|> No one has ever
> >|> specified what one does with the RRT with more than three species,
> >|> nor even how to do the three species case statistically.
> >
> >I'm not sure what you mean here, Joe. Clearly valid statistical versions
> >of the relative rate test exist. Could you clarify?
> 
> I stand corrected by your useful citations.  Clearly there *are* lots of
> statistically formulated relative rate tests for three taxa.  I note that
> often people who tell me they're doing "the relative rate test" are not
> doing anything statistical, nor were the original formulations of the RRT.
> 
> >|> If you want to know which branch or clade in the tree is responsible
> >|> for the rate heterogeneity, one could fit trees that were clocklike
> >|> except for having that branch (or all of that clade, alternatively)
> >|> evolving at R times the rate of the rest of the tree.  This is not
> >|> easy to do with present-day programs, alas.  Aside from making that
> >|> possible, there are very interesting questions about how to test
> >|> which branch (clade) it was that was going R times as fast.
> >|>
> >|> But however that is to be done in a likelihood framework, the RRT has
> >|> more problems as it cannot tell you how to combine all the
> >|> three-taxon tests.
> >
> >Agreed. BUT, that does not imply that doing many or all pairwise
> >comparisons is a useless thing to do. And, in fact, many of the tests
> >_are_ independent (this can be argued along the lines from Felsenstein's
> >1985 (?) article on independent contrasts). Patterns arising from
> >exhaustive pairwise tests are often amazingly strong; so strong that it
> >would take incredibly high levels of correlation to explain them.
> 
> But when they *aren't* that strong you are at a loss what to do.
> 
>
> >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.

Spencer

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Spencer V. Muse                               | (814)863-7045
Institute of Molecular Evolutionary Genetics, | muse at kurtz.bio.psu.edu
Department of Biology                         |
Penn State University                         | FAX: (814)865-9131
University Park PA 16802-5301                 |
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