Using Fst

I wondered if any of the fine minds here would care to shed light on a little conundrum I've encountered regarding the use of Fst and clustering populations by admixture. I've clustered my populations in question using UPGMA with pairwise Fst values, but I'm not entirely sure if this is the right approach to take. I understand that UPGMA relies on the assumption of similar evolutionary rates and that if that assumption is violated any ultrametric trees derived will have incorrect topology and essentially be a useless waste of time. However, the SNPs I'm using are all synonymous or non-coding (though that doesn't discount linkage with functional untyped variants of course), so am I right in assuming equal evolutionary rates between populations? Or would I be better off using a different statistic to cluster my populations?

I essentially just want to show that the population substructure I am seeing for a particular locus is in general agreement with historical models of human evolutionary distance and admixture.

Could someone help a poor struggling student?