Hello r-sig-phylo,
I am using the haploNet command of the excellent pegas package to
construct an mtDNA haplotype network with 79 nodes. When I generate
the network I am able to identify the limits of parsimony from the
accompanying table. However, I don't quite understand why this network
contains no loops (79 nodes 78 edges). When I make the network in TCS
the parsimony limits are the same (7 steps), but there are many loops
in the network. The documentation refers to the Templeton et al. 1992
paper and, short of identifying recombination to break loops, I
couldn't find hard and fast rules for breaking loops (I may have
missed them). I know that some post hoc rule exist, such as favoring
links to high frequency and geographically close haplotypes, but I was
wondering how haploNet deals with these loops. Does it present 1 of
the maximum parsimony trees?
Thanks in advance,
Patrick
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