if samples are limited, e.g., less than 10 samples per population, which molecular markers are suitable(Microsatellites or SNPs generated by RAD-seq)? If you can provide some references for your opinion, it would be better. Thank you for your attention!
I personally think that SNPs will be preferable due to the data resolution that you will get. SNPs also can be on both neutral or under selection regions on the genome as well as on the be on single or biparental inheritance so you can assess broader research questions from evolutionary history relation, population admixture, to simply assessing genetic diversity. But Depending on your study objectives, microsatellites marker might be used as well.
I guess the paper by Landguth et al 2012 will be a good starting point.
You'll have a hard time getting any population-scale resolution with < 10 samples per population. With that said, more is always better when it comes to number of genetic markers. RADseq would be your best bet in that case.
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