Lositan, He and Microsats (expected heterozygosity measures plot higher than expected)

Question

[goatsrunfaster]

When I load my data into Lositan, the loci plot at higher He than expected given the measures produced by Arlequin and Genepop. Does Lositan not plot the mean He for each loci, or is this another measure of He (an upper quartile or something)?

I checked another paper that provides a lositan output, as well as summary stats, and found the same result: (http://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-014-0276-y)

It is not the Genepop input file, I double checked it, and used it to get mean He using Genepop for my loci.

Is this some sort of flaw in the program? Any help would be greatly appreciated!

Answer 1

[goatsrunfaster]

found the answer in another post:

"In Lositan the Heterozygosity is h_b rather than h_t - i.e. it is the probability of choosing two alleles at random that are different, one from each deme, rather than the prob of picking two alleles at random that are different irrespective of deme. With two demes it can reach 1 when FST is 1. So the reason why it is so high is that you are probably looking at very inbred populations."