Geographic regions as subpopulations/demes I am developing a computational simulation for DNA barcoding. One of the parameters in my simulation is the number of subpopulation/demes, which I label as $K$. Most studies that use DNA barcodes tend to focus on a single geographic region. **My question is** : is it valid to presume that a single geographic region is equivalent to a single subpopulation/deme? For example, if the focus was on cichlids of Lake Malawi, would it be a safe assumption that Lake Malawi comprises a single subpopulation/deme? Eventually, I would also like to incorporate migration rates into my simulation, but these are very difficult to estimate without accurate data on $F_{ST}$. Any insight would be most helpful and is warmly welcomed.

For simulating DNA barcoding, it is valid to presume that a single geographic region is equivalent to a single subpopulation. Although there do occur cases where one or two nucleotides differ at the same location, that is rare, and these few differences would still cluster together in any analysis of barcode data.