Hello Mehvish,

it seems you have panmixia, no differences among population or any other group you may consider (have you try to cluster pops in any way?). Please always check if the differences are significant (p-values), that is the final answer for your test. I would suggest you to use Arlequin instead for calculations: http://cmpg.unibe.ch/software/arlequin35/.

Best,

Roberto

Dear Mehvish,

Interpretation of AMOVA is easy. Please read our article to understand the interpretation of AMOVA. Link for the article is as follows-

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5708757/

Negative values of FST are due to the method of calculation and are equivalent to 0. Instead to use Genallex I Suggested to use more sophisticated software like Arlequin, or an r package like Adegenet. According the amok results you only have a single pop. As you are using Genallex I suggested to perform a principal coordinate analysis to visualize the genetic variation and to confirm that you only have one pop. Also, please check the genallex documentation , for some kind of molecular markers the author suggests to calculate Rst instead Fst, the two both index are analogous.

Your interpretation may be wrong. If the gene flow between the populations is zero, the variation among the populations must be very high. Gene flow is inversely proportional to genetic differentiation between populations. Rerun the program again and read the manual carefully. Genelyx gives only the information of genetic variation between and within populations.