Totally RAD

Puritz et al. (2014) weigh the pros and cons of, the aptly titled, “RAD fad” in a comment recently published online in Molecular Ecology. They challenge:

(1) the assertion that the original RAD protocol minimizes the impact of PCR artifacts relative to that of other RAD protocols, (2) present additional biases in RADseq that are at least as important as PCR artifacts in selecting a RAD protocol, and (3) highlight the strengths and weaknesses of four different approaches to RADseq which are a representative sample of all RAD variants.
Artwork courtesy of chrispiascik.com © Chris Piascik

Artwork courtesy of chrispiascik.com
© Chris Piascik

In Box 1, the authors break down four representative protocols: mbRAD (Miller et al. 2007, Baird et al. 2008), ddRAD (Peterson et al. 2012), ezRAD (Toonen et al. 2013) and 2bRAD (Wang et al. 2012).

Then, the mitigation of PCR artifacts is discussed followed by a summary of the pros and cons of each of the four representative RAD protocols.

The most important consideration when selecting a particular RAD protocol are the facilities and molecular experience of the research applying the approach, as well as the biology of the organisms and the hypotheses being tested … at present, there is no reason to broad-brush paint any method as the superior or default protocol.

 

Miller MR, Dunham JP, Amores A, et al. (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers.  Genome Research 17: 240-248. doi: 10.1101/gr.5681207

Baird NA, Etter PD, Atwood TS et al. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PloS ONE, 3, e3376. DOI: 10.1371/journal.pone.0003376

Peterson BK, Weber JN, Kay EH, et al. (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS One, 7, e37135. DOI: 10.1371/journal.pone.0037135

Wang S, Meyer E, McKay JK, et al. (2012) 2b-RAD: a simple and flexible method for genomewide genotyping. Nature methods, 9, 808–10. doi:10.1038/nmeth.2023

Toonen RJ, Puritz JB, Forsman ZH et al. (2013) ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ, 1, e203. DOI 10.7717/peerj.203

Andrews, KR, G Luikart (2014) Recent novel approaches for population genomic data analysis. Molecular Ecology 23: 1661-1667. DOI: 10.1111/mec.12686

Puritz, JB, MV Matz, RJ Toonen, JN Weber, DI Bolnck, CE Bird (2014, accepted article) Comment: Demystifying the RAD fad. Molecular Ecology. DOI: 10.1111/mec.12965

Share

About Stacy Krueger-Hadfield

I am a marine evolutionary ecologist interested in the impacts of seascapes and complex life cycles on marine population dynamics. I use natural history, manipulative field experiments and population genetic and genomic approaches with algal and invertebrate models in temperate rocky shores,estuaries and the open ocean.

This entry was posted in bioinformatics, genomics, methods, next generation sequencing, Uncategorized. Bookmark the permalink.