Can I estimate LD among species using SNP data?

Question

[tianying]

I'm working on a project using SNP data from 9 closely related plant species. For each species, I only have one individual. All species were mapped to the same reference genome. I'm planning to do some phylogenetic and admixture analyses next, and I'm not sure if I should estimate the linkage disequilibrium among species? Any thoughts is appreciated!

Answer 1

[Bioaln]

Conducting LD tests having only one individual might provide valuable insights into data, but be very careful, from my experience one individual on species level cannot clearly reveal all the differences present which might interest the researcher.

[tianying]

I just want to use LD analysis to estimate the spacing filtering parameter. I actually ran a plink LD analysis. The result showed a dramatic decay after 20bp, and became stable after 50bp. So is it reasonable to use 50 bp spacing to filter my vcf file? Or is there any other method I can estimate the spacing parameter? Thanks!