Some of the first methods used for studying genetic variability at multiple loci included gel electrophoresis and restriction enzyme mapping.
In the study of Schizosaccharomyces pombe (more commonly known as fission yeast), a popular model organism, population genomics has been used to understand the reason for the phenotypic variation within a species.
[5] A 2007 study done by Begun et al. compared the whole genome sequence of multiple lines of Drosophila simulans to the assembly of D. melanogaster and D. yakuba.
[6] In 2014 Jacquot et al. studied the diversification and epidemiology of endemic bacterial pathogens by using the Borrelia burgdorferi species complex (the bacteria responsible for Lyme disease) as a model.
In tunas, traditional markers such as short-range PCR products, microsatellites and SNP-arrays have struggled to distinguish fish stocks from separate ocean basins.
These studies identify putatively adaptive loci that reveal strong population structure, even though these sites represent a relatively small proportion of the overall DNA sequence data.
In contrast, the majority of sequenced loci that are presumed to be selectively neutral do not reveal patterns of population differentiation, matching results for traditional DNA markers.
[9][10][11][12] The same pattern of putatively adaptive loci and RAD sequencing revealing population structure, compared to limited insight provided by traditional DNA markers is also observed for other marine fishes, including striped marlin[13] and lingcod.
[20] Another relatively new approach is reduced-representation library (RRL) sequencing which discovers and genotypes SNPs and also doesn't require reference genomes.