Question on Fst values gl.fst.pop

[Gabriella Scatà]

Hi everyone,

I am just wondering whether the Fst associated p-values obtained with gl.fst.pop() are corrected for multiple testing?

And if so, which multiple testing correction method is used?

I can't find this information even in the StAMPP package.

Thanks!

Gabriella

[Jose Luis Mijangos]

Hi Gabriella,

The function gl.fst.pop() uses Bootstrapping to test the null hypothesis of FST > 0. The bootstrapping method used in this function resamples the individuals "nboots" times and calculates FST every time for each locus. Then all the calculated FST > 0 are summed and divided by "nboots" to get the p-value. In other words, the proportion of bootstrapped FST values equal to zero or less (no differentiation between populations) is used as the p-value.

So, the Bootstrapping method generates its own data to produce a distribution to test the null hypothesis. Other hypothesis testing methods, for example the exact test used to test the significance of departures from Hardy-Weinberg Equilibrium, the null hypothesis is tested using the distribution of the observed data.

In few words you don't' need correction for multiple testing when bootstrapping is used to test a null hypothesis. 

You can increase the number of bootstraps ("nboots") to be more confident in the statistical significance of your results.

Cheers,

Luis