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relative rate test

Joe Felsenstein joe at evolution.genetics.washington.edu
Tue Jul 16 11:27:53 EST 1996

In article <v01510100ae0fe8aa18c8@[]>,
Michael Nedbal <dna_seq at FMPPR.FMNH.ORG> wrote:
>With regards to the LRT, how does one determine
>which taxon (or taxa) are responsible for the rate heterogeneity?  The RRT
>is a three taxon statement (not a pairwise comparison as you correctly
>pointed out) comprised of an outgroup and two "ingroup" taxa.  Comparing
>the results from several tests reveals exactly which taxa demonstrates the
>rate deviation.  Maximum likelihood requires a four taxon statement thus
>making it difficult to pinpoint the rate heterogeneity.  With a minimum of
>five taxa (with only one of the five demonstrating rate heterogeneity), a
>series of taxonomic sampling would demonstrate which taxa is reposible for
>the significance of the LRT.  This may get more complicated with an
>increase in the number of taxa and the number of taxa demonstrating rate

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.  One would test whether a nonclocklike tree with
three species fit as well as one with a clock.  The advantage of this framework
is that one can do a single test when there are many species.  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.

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.

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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