This strategy seems to be most commonly used for plants. When crossing animals isn't possible, how can I do a similar study to identify a particular locus responsible for a polymorphic trait (specifically, the pigmentation of a beetle)?
I'll have a go at answering this. I don't understand beetles within Insecta: I am well aware they very distinct, obviously in phenotype and ecology, but also genetically. I think they have unique compositional bias even amongst holometabolous insects.
Personally I think if you've a recent genetic trait, e.g. insecticide resistance, that evolved within the last 30 years or less, you're dealing with pretty homogeneous backgrounds between traits. In this example trait, bulk segregant analysis might work.
Beetles are really ancient. I suspect their families are particularly ancient, because they are just so successful and I'd guess Scarabaeidae are ancient too, i.e. the family scarab beetles. This family could easily be 50 million years old, or older. Each species therein could a few million years old. For insects thats normal and these are beetles.
The concern here is over million+ years of evolution (I don't know the study size), they will comprise loads of neutral signal that would act as noise, i.e. there will be excessive third codon wobble which will mask SNPs/genes causing colour (color) variation.
My approach, given I know nothing about colour (color) variation in insects other than "white-eyed" phenotype in Drosophila melanogaster,
- assess genetic complexity of colour variation in other insect Orders;
- get hold of as many proteins involved in colour in insects as possible;
- particularly get hold of colour variation proteins in beetles;
- sequence the genome of a representative scarab beetle (which I think your doing)
psi-blastusing the hypotheses from 1., 2. and particularly 3. to assess which proteins in the scarab beetle might be responsible.
- perform deep sequencing on those targets, because they could be multigene families *.
The next step is phylogenetics to assess convergent and/or parallel evolution **. That in my view is a separate question because its quite complicated and you'd need to write your own pipeline to automate it (you could do it by hand however).
What I would be cautious about is that beetles are not any other insect so inter-Order homology needs to be treated with caution.
*, Just to point out, there are lots sequencing strategies its not my thing, e.g. low coverage draft genomes. PCR deep sequencing for a given gene target, without any draft genomes and isn't conserved e.g. rRNA types genes, will need small PCR fragments because of the neutral mutations which will disrupt primer specificity. If you're good at sequencing a draft genome could be cool (just guessing).
**, A phylogenetics approach would dovetail with the COI and rRNA gene sequencing (28S?) already underway, because these genes should approximate to the species phylogeny. What is sought are residues within the colour genes (or perhaps presence/absence genes) that will cluster not according to their evolutionary descent but according to their colours (colors).