Not sure what species you are working on but FST is probably the most widely used measure. That being said, there is a bit of discussion on what should be used. I would recommend you to look into the differences between the metrics and decide what is best in your case (based on what your ultimate goal is). To get you started I am including a link that talks about the different measures and also points you to a good set of papers to help you. Also the recent paper from Current Zoology can help you see the differences between the measures.

http://www.molecularecologist.com/2011/03/should-i-use-fst-gst-or-d-2/

Article Statistical measures of genetic differentiation of populatio...

Swetha Peteru,

I have ever read this page from molecularecologist some time ago, but I didn't know this paper yet. I was exactly searching for a recent review, and this one looks a good one.

Thank You!

João Vieira and Ayman Ahmed, I am glad to have been of help.

This topic helped me too:

https://www.researchgate.net/post/Population_genetics_differentiation_analysis

 Hi João Vieira!

I recently worked with population genetics on butteflies throug ISSRs markers (dominant). I used GST, although i know the FST can be calculated too. I don´t know what are the species that you work with, but, for insects (Lepidoptera) i know some works with that you can compare the levels of genetic differentiation, as: (works specifically with ISSRs)

1) Chen, F., Ahmed, T., Liu, Y., He., K., Wang, Z. (2014). Analysis of genetic diversity among different geographic populations of Athetis lepigone using ISSR molecular markers. Journal of AsiaPacific Entomology. 17: 793-798. 

2) Luque C, Legal L, Machkour-M’Rabet S, Winterton P, Gers C, Wink M (2009) Apparent influences of host plant distribution on the structure and the genetic variability of local populations of the Purple Clay (Diarsia brunnea). Biochem Syst Ecol 37:6–15

3) Machkour, S. Leberger, R. (2014). Population structure and genetic diversity of the only extant Baroninae swallowtail butterfly, Baronia brevicornis, revealed by ISSR markers. Journal of Insect Conservation. 18:385–396. 

4) Yang, J., Tian, L., Xu, B., Xie, W., Wang, S., Zhang, Y., ... & Wu, Q. (2015). Insight into the Migration Routes of Plutella xylostella in China Using mt COI and ISSR Markers. PloS one, 10(6), e0130905.

I hope this information be useful for you.

Hi Jovana,

Thanks for your answer. I'm working with tropical grasses and I'm using ISSR too. Thank you very much for the literature recomendations, I'll give a look all of them.

By the way, I have recently read Holsinger (2009) and he says ɸst has a advantage of allow mutation rate to be different among loci, givin a unbiased measure. Since I'm using ISSR technique, which marks unknown regions through genome, I think the loci can be different mutation rate.

Please, correct me if I'm wrong.

Article Genetics in geographically structured populations: Defining,...

Hi, 

The HICKORY test is believed to be proper method of analyzing genetic differentiation for dominant molecular markers. 

A new program call HICKORY and developed by Kent Holsinger and Paul Lewis at the University of Connecticut will calculate F-statistics, including FST, and the inbreeding coefficient, f. Some of the analyses included in this software using Bayesian statistics to estimate population genetic parameters. See Holsinger et al. (2002) for more details about analyses performed by HICKORY.  

HICKORY (K. Holsinger, P. Lewis) – Free at http://darwin.eeb.uconn.edu/hickory/hickory.html

Good Luck 

Masoud 

Hi Masoud,

Thanks for your answer. I can't open the link you shared, but I have ever tried Hickory. Its F-statiscs are good, but according Foll et all (2008), there are some problems using the inbreeding coefficient f from Hickory. Thus, I'm using Foll's ABCF4 program instead.

João

Article An Approximate Bayesian Computation Approach to Overcome Bia...

Hi João 

Thank you for the paper. I sen you two papers with regard to genetic differentiation which may be helpful.

Good Luck

Hi Masoud,

I have ever read these papers, but i appreciate your help. Thanks!