I am working with genomic data from multiple species, where I will be prospectively having the demographic histories for each of the species.

I will also be having the genomic features which are associated with a particular trait of those species.

I would like to test whether lineage-specific demographic histories (e.g., bottlenecks or low Ne periods) are associated with the temporal changes in the genomic features, and whether bottlenecks facilitated the fixation of certain genomic loci. My question is, are there any approaches that give information about the historical conditions of genomic loci, given that I only have a genome for that species.