heteroplasmic mitochondrial STR data

[kristen]

Dear group users,

I would appreciate suggestions for how to analyze heteroplasmic
mitochondrial STR data in IMa, with two to six copies per individual
attached to mitochondrial sequence data. For this species it is known
that heteroplasmy patterns are maternally inherited and do not vary by
tissue type or during development. Intra-individual frequencies of
variants could also be measured based on relative PCR product
concentrations and the most common variant could be used as the repeat
number without incorporating other repeat numbers. Can this type of
data be analyzed in IMa? The data has not yet been collected, I am
designing the methodology around being able to analyze with IMa.

[jhey]

what would you be studying? I don't see any way to have the model
somehow incorporate the heteroplasmy. If you want to focus on the IM
model, then you could just pick one mtDNA sequence per individual in
such a way that you can ignore the heteroplasmy issue.

jhey

[kristen]

Dr. Hey,

Thank you for your reply. I am developing a study of neutral genetic
differentiation in sympatric cod ecotypes driven by empirical evidence
of behavioral and morphological differences at most life history
stages. I think quantifying demographic parameters of the two
ecotypes with IMa is the most important baseline from which to compare
the ecological framework of adaptive divergence (further studies on
speciation-with-gene-flow using candidate genes).

Markers like microsatellites do not show appreciable differentiation
due to recent divergence, suspected large effective population size
and migration. I was hoping that incorporating STR variation of the
mitochondrial control region with microsatellite data may enhance the
estimates of neutral differentiation and demographic parameters. I
may just increase the number of microsatellite loci instead of
incorporating different marker types. Thanks again.