Dave Carmean asks how to tell if mtDNA sequences are saturated. ONe way
is to graph the number of transversions versus the number of transitions.
If the graph levels off - i.e. number of transitions reaches some sort of
ceiling - then the sequences in this range are probably saturated for
transition substitutions. Note that this can occur at what seems a fairly
low divergence: sequences of COI that are 12% different may in fact be
saturated for transitions at silent sites. Note also that saturation can
be reached at lower divergence values if there is strong nucleotide bias
as in insect or crustacean mtDNAs.