When I'm designing population genetic studies, I take into account the amount of variation I'm expecting to see, the number of markers I'm using, and the question I'm asking. My gut feeling is that population epigenetics won't play by the same rules per se. Also, I don't have a good way of estimating how much diversity I'll see or even how many variable sites I'll get until I do it.

How do I decide on the number of samples to include for MS-AFLP?

I have a large (~ 200) number of samples (all blood) from what I suspect is a panmictic population of birds. I'm planning to genotype and run MS-AFLP on a subset of the samples. I can stratify my data by sex, location (although I think it won't show anything interesting), and territorial breeding status (hoping for something interesting here). Previous studies of a similar nature in vertebrates have included < 20 individuals per strata. If I carefully select individuals, I can afford to include about 20 per breeding status and make sure that I'm equally representing males and females. That gives me about 40 individuals total from this population. Am I overshooting? Undershooting?

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