Confusion regarding number of haplotype on DNaSP6

Question

[enrico104]

Good afternoon, I have a problem regarding the generation of the index "number of haplotypes" on DnaSP6. I'm currently working on a sample made up of historical and modern specimens. When calculating haplotype diversity for all samples together, looking at the display windows the number of haplotypes for historical samples is 10. However working only on the historical samples, the number of haplotypes is 11. That because two specimens that were previously grouped together in a haplotype in the first case are then divided with each one having a different haplotype. Did someone had the same problem before? Is there a solution to this?

Kind Regards

[Fabio Marroni]

How many markers are you using? Is it doable to check which of the two approaches is "right"?

In addition, you can try to identify the marker that is creating the 11th haplotype and see if the marker is still present when the analysis is performed on the whole sample. I suspect that when analyzing the whole dataset a marker that is polymorphic in the historical samples is discarded (maybe because the allele frequency is below a given threshold).