I am trying to determine if a highway is too much of a barrier for shrews to cross and breed freely. What I have to work with is ~1080 bp of the mitochondrial cytochrome b gene (we did not do microsatellites which most researchers do use and I think it is the source of a lot of my troubles using common programs and R packages). I have 3 sites north and 3 sites south of a highway and I want to see if the Fst values I have calculated through DNAsp are significantly different from zero or each other. Does anyone suggest a way I can organize my data so that I can put it in R to determine the significance or another route I should take? Thank you for your time!
I hope this tutorial may help you (with FST estimation and other analyses):
https://popgen.nescent.org/PopDiffSequenceData.html
*I may also suggest you to look for the snp-sites tool (or any other that may help you transform your sequences into other formats, such as .vcf, or .gen):
https://github.com/sanger-pathogens/snp-sites
That will give you the freedom to analyze deeply with other tools (Arlequin, Genepop, Genodive...)
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