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relative rate test

dna_seq at FMPPR.FMNH.ORG dna_seq at FMPPR.FMNH.ORG
Mon Jul 15 07:18:47 EST 1996

Thanks for responding Joe.  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
heterogeneity.  I suppose one could duplicate a taxon, thereby simplifying
taxonomic sampling.  This would also alleviate the problem of testing fewer
than four taxa (demonstrating rate heterogeneity with respect to the
majority of taxa) to determine of they have nonsignificant rate deviations
from one another.  Thanks again for your earlier suggestion and I welcome
any further comments.
Michael Nedbal
Geology Department
Field Museum of Natural History
Roosevelt Road at Lake Shore Drive
Chicago, IL 60605-2496

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