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This script performs an AMOVA based on the genetic distance matrix from stamppNeisD() [package StAMPP] using the amova() function from the package PEGAS for exploring within and between population variation. For detailed information use their help pages: ?pegas::amova, ?StAMPP::stamppAmova. Be aware due to a conflict of the amova functions from various packages I had to 'hack' StAMPP::stamppAmova to avoid a namespace conflict.


gl.amova(x, distance = NULL, permutations = 100, verbose = NULL)



Name of the genlight containing the SNP genotypes, with population information [required].


Distance matrix between individuals (if not provided NeisD from StAMPP::stamppNeisD is calculated) [default NULL].


Number of permutations to perform for hypothesis testing [default 100]. Please note should be set to 1000 for analysis.


Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].


An object of class 'amova' which is a list with a table of sums of square deviations (SSD), mean square deviations (MSD), and the number of degrees of freedom, and a vector of variance components.


Bernd Gruber (bugs? Post to


#permutations should be higher, here set to 1 because of speed
out <- gl.amova(, permutations=1)
#> Starting gl.amova 
#>   Processing genlight object with SNP data
#> Completed: gl.amova