Hello,

Really negative values so high are not common, however, some things need to be taken into account for the AMOVA analysis:

1. You are working with populations who are supposed panmictic?

2- What kind of reproduction you expect (clonal, sexual, mixed?)

If you are wanting to check subdivision structuring in its population, my suggestion is to be based on a more specific analysis (eg. DAPC)

A problem associated with this result may be that a fraction clonal within each year can be quite high, and the distribution of the alleles between samples within a year may be very homogeneous.

Suggestion to know what is happening to the population:

1- find what their clonal fraction of these populations;

2- Check the clonal fraction  within each year;

3- Perform AMOVA with clone correction;

4- Perform AMOVA for each year separately (it is easier to see the differentiation within each hierarchical unit);

4- Do the DAPC analysis (in Poppr);

I hope I've helped,

 Hi Saulo,

Thank you for your kind reply! That definitely helps.

A little bit more information about the populations (they are Phytophthora isolates, a soil-borne plant pathogen),  based on the results generated in Poppr, the population is clonal. I'm still trying to determine if there are both mating types in the populations phenotypically. 

I have a quick question about the clonal fraction, is Poppr able to find out the clonal fraction in the populations? 

The results I attached above were generated after clone-correction.

I did the DAPC analysis, I am not quite sure how to interpret the result. I attached some results here, really hope that you could take a look. I would really appreciate it if you could explain a little bit about what DAPC analysis does.

Thanks,

Jing

You are dealing with a flawed estimation procedure. Please consult chapter 1 of my recent book: Quantitative Genetics and Its Connections with Big Data and Sequenced Genomes. Also have a look at chapters 3,4,and 5, on direct estimated of covariance matrices. The paper back version of the book can be preordered at Amazon.