UC Davis

Key PointsRADseq has fuelled studies in ecological, evolutionary and conservation genomics by using next-generation sequencing to uncover hundreds or thousands of polymorphic loci across the genome in a single, simple and cost-effective experiment. RADseq does not require any prior genomic information for the taxa being studied, and is therefore particularly advantageous for studies of non-model organisms.Numerous technical variations on RADseq have been developed, which promise to increase the flexibility and decrease the cost and effort of genomics studies. Differences among the methods lead to important considerations for all steps of genomics studies, from the types of scientific questions that can be addressed and the costs of library preparation and sequencing to the types of bias and error that are inherent in the resulting data.Allele dropout, PCR duplicates and variance in depth of coverage among loci are important sources of error and bias in RADseq studies, and the prevalence of these phenomena will vary across RADseq methods.Other important considerations when designing a RADseq study include the number, length and coverage of loci needed to address the research question; the availability of prior genomic resources; the budget; and the consistency of data across sequencing runs and laboratories.There is no single best or most flexible RADseq method. Researchers must consider the trade-offs of the different methods, and choose the approach that is best suited to their study goals.