Assumptions when sampling individuals from the same location

[Jane Dostart]

Hi folks,

I am confused. How should we handle data when we have some samples within the same geographic location? I think in our first lecture we talked about having individual versus population-level approaches and how we have to be careful about assuming non-independence with samples collected more closely together. I guess what I'm lacking in knowledge is what analyses can you use for individual-based approaches without breaking the assumptions of your analyses in this context? Side question are there landscape genetic analyses that can handle individual, pairwise, geographic-distance matrices in which parts of the matrix are populated with zeros? 

For my research I have sympatric and allopatric populations of polyploid plants that I am interested in seeing if moths that are closely associated with the plants, and have a preference for ploidy, might be genetically diverging within their species. Ideally I want to use a individual-based approach, but I do not understand when this okay and when it is not. Obviously have more reading and studying to do, but would love some nudges in the right direction!

Thanks,

Jane