Dear Dr. Seyed,

I think, you can do some statistical analysis like F-test.

Kindly enclosed some papers reveal some ideas may be help.

Good Luck! 

http://www.biomedcentral.com/1471-2148/14/165

Dear Dr. Seyed

I have worked with genetic diversity and structure in animals with intense dispersion, this way some considerations maybe has some bias for organisms that you have studied.

However, I think that the mixture of three clusters at two first localities perhaps be due an isolation process or secondary contact, considering that you use a DNA with uniparental segregation. Individual assignments shows the existence of a potential migrant in site 3 and the last individuals in group 4 with low mixed ancestry. Thus I think that on this last group, apparently, there was a vicariant event between sites 2 and 3 that leaded a isolation of populations from localities 3 and 4 (I'm assuming that the disposition of sample sites are sequential), that increased the red cluster frequency in this places. Although, I agree with Dr. Dadamouny , and recommend you perform F-stats tests to determine how great is the structuring level. 

This follow papers may help you too.

Strasburg et al. Phil. Trans. R. Soc. B (2012) 367, 364–373

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233712/pdf/rstb20110199.pdf

Eckert et al. Genetics (2010) 185, 969–982 

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2907212/pdf/GEN1853969.pdf

I hope helped you!

Best regards.

Dear Dr Seyed,

By chloroplasmis do you mean you sequenced cp regions? In this case, hybridization is not possible since you use non recombining genomes, this also normally prevent to use Structure. What you can do, if you have cp data, is to use SAMOVA, which is intended for this kind of studies.

Best regards

Thanks all for your valuable notes/

Philippe, again sound OK. Let me ask from my colleague. Actually, my major is animal biodiversity and this one is his question who has nor RG account yet. I'll say you something in this thread. 

Kind Regards

Just wanted to point out that STRUCTURE needs unlinked markers so can't be used for chloroplast data!