I have data from bat colonies from 5 geographic locations. STRUCTURE has identified 4 clusters/populations and a reviewer for the manuscript I have written is requesting that I show Fst values for the populations suggested by STRUCTURE. As you will know STRUCTURE uses many runs and produces many Fst outputs. Does anyone know of an R package or other software, to collate the Fst values from multiple runs and calculate pairwise p-values please?
Most software will generate p values with statistical comparisons. Take care not to catch bat virus :)
Thank you Andrew, I was look for a stand alone program to read in Stucture output, aggregate it and then calculate Fst. I’ve done it the long way now...using Clumpp, editing excel file and using an AMOVA in GenAlex. Very little (if any) bat virus in the U.K. 😁
I'm sorry, I'm quite late answering this, hope you already found a solution.
In my case I never used Structure Fsts, I prepare the dataset with an extra column with the Structure clusters (new populations suggested by Structure) to which each individual belongs. Then you can calculate plenty of statistics per clusters and check significant differences among them.
There is many software that will calculate the pair-wise Fsts with p-values, probably the easier to use (because it has GUI) is Arlequin.
You will need to transform the input file format, I recommend PGDSpider.
If you are going through R, the best package for that that I have found is StAMPP.
You will probably use Adegenet to import your input file to R, so take the chance and plot a PCR (color it by cluster) and calculate some other diversity indexes with DiveRsity, they can be very informative.
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