The traditional methods to detect population structure like Fst sometimes are not able to detect differences among locations or populations even when they exist. In a case where there seems to be slight differences but there are a high number of private haplotypes, I wonder if there are some method where I can explore this?
DnaSP will probably help to define your haplotypes but further you will have to analyse them as haplogroups, as it's done with mithocondrial DNA. An alternative is to label your haplotypes and analyse them as they were single markers, and then apply Fst measures.
Thank you for your help. I already used DNAsp to calculate mitochondrial DNA diversity indices like the number of haplotypes and haplotype diversity. Nevertheless the genetic structure was tested with AMOVA in Arlequin considering the haplotype frequencies. Is there a way to define a structure uniquely based on private haplotypes without considering the haplotype frequencies but taking into account haplotype identity? For microsatellites there are new methods that consider the identity of the alleles like compositional differentiation (Gillet, 2013).
I will explore this idea specially because I have also a high number of private alleles. Thank you very much for your help!
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