Our collaboration with a number of NC State folks empirically compares ddRADseq results from a variety of species using shared protocols - should be a great resource for people planning RADseq experiments in non-model organisms!
Burford Reiskind MO, Coyle K, Daniels HV, Labadie P, Reiskind MH, Roberts NB, Roberts RB, Vargo EL, and Schaff J. 2016. Development of a universal double-digest RAD sequencing approach for a group of non-model, ecologically and economically important insect and fish taxa. Molecular Ecology Resources.