C.S. Wilding BGYCSW at leeds.ac.uk
Wed Nov 20 04:54:03 EST 1996

I have a dataset concerning mtDNA haplotypes with restriction 
site data, and the frequency of these haplotypes across 12 
populations. I want to obtain a dendrogram with support 
levels at the nodes that displays some genetic distance 
between populations. I can bootstrap the haplotype data to 
show relatedness of haplotypes but want to do a similar thing 
with populations. I have the restriction enzyme analysis 
package (REAP, McElroy et al.) and can get a single measure 
of nucleotide divergence between populations but some 
populations have -ve values due to high diversity. After 
correcting to zero the UPGMA dendrogram of this clustered 
data yields an equally likely number of trees and the 
concensus invloves an 11 population unresolved node. I really 
want a more informative tree. Do I have to feed the 
bootstrapped haplotype datasets back into REAP to produce 100 
(possibly) different population trees and put these into 
consense in say PHYLIP, or is there an easier way?
Craig Wilding
Leeds University

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