analysis of cytoplasmic diversity

[Jan Aagaard]

Hello All.  I'm a grad student working on population genetics of forest trees, 
specifically comparing nuclear and cytoplasmic (mitochondrial) diversity.  
Recently I've been weighing the pros and cons of analyzing my cytoplasmic 
markers (diversity, population differentiation) using allele frequencies 
(i.e., multiple mitochondrial loci) -vs- haplotype frequencies (i.e., all 
markers a single locus).    

Does anyone have any comments/suggestions on using either method, and 
specifically in comparisons with nuclear diversity and population 
differentiation?

Thanks much!

Jan Erik Aagaard
Dept. of Forest Science
Oregon State University