Journal Article

Harnessing the power of RADseq for ecological and evolutionary genomics

Miller, Michael R., Good, Jeffrey M., Luikart, Gordon, Hohenlohe, Paul A., Andrews, Kimberly R.

2016

Overview

Key Points RADseq 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. Technical differences between the many variant methods that are based on restriction site-associated DNA sequencing (RADseq) lead to trade-offs in experimental design and analysis. Here, the authors comprehensively review the various RADseq approaches and provide general considerations for designing a RADseq study. High-throughput techniques based on restriction site-associated DNA sequencing (RADseq) are enabling the low-cost discovery and genotyping of thousands of genetic markers for any species, including non-model organisms, which is revolutionizing ecological, evolutionary and conservation genetics. Technical differences among these methods lead to important considerations for all steps of genomics studies, from the specific scientific questions that can be addressed, and the costs of library preparation and sequencing, to the types of bias and error inherent in the resulting data. In this Review, we provide a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/158 / 631/1647/1513 / 631/181/2474 / 631/208/514/1948 / 631/45/607/1160 / Agriculture / Animal Genetics and Genomics / Biological Evolution / Biomedicine / Cancer Research / DNA sequencing / Evolutionary genetics / Gene Function / Genetic markers / Genetic research / Genomics - methods / High-Throughput Nucleotide Sequencing - methods / Human Genetics / Humans / Identification and classification / Metagenomics - methods / Methods / Nucleotide sequencing / Restriction Mapping - methods / review-article