I'm a masters student undertaking my research project with RAD-seq data from three species of bumblebee each taken at four different sites. I have used Stacks and populations already and am interested in identifying outlier loci that demonstrate signals of selection.
One of the species has population sub-structure identified by Structure analysis and so I can use outlier detection methods like Bayescan and PCAdapt etc that are based on population-differentiation here.
However the other two species seem to be admixed since samples from the different sites do not seem to represent genetically distinct sub-populations. Therefore, I wonder whether anyone has any advice on methods for detecting selection in species without population structure using RAD-seq data (which is reference aligned)? I'm struggling to find information on this...can it be done?
At the moment I wonder whether applying statistics like Tajima's D to the all of the samples within a species would help here? -To at least identify a list of candidate loci? If anyone had any advice on this/implementation I would be very grateful.