title: Trade-offs and utility of alternative RADseq methods: reply to Puritz et al.
abstract: Puritz et al. provide a review of several RADseq methodological approaches in response to our 'Population Genomic Data Analysis' workshop (Sept 2013) review (Andrews & Luikart 2014). We agree with Puritz et al. on the importance for researchers to thoroughly understand RADseq library preparation and data analysis when choosing an approach for answering their research questions. Some of us are currently using multiple RADseq protocols, and we agree that the different methods may offer advantages in different cases. Our workshop review did not intend to provide a thorough review of RADseq because the workshop covered a broad range of topics within the field of population genomics. Similarly, neither the response of Puritz et al. nor our comments here provide sufficient space to thoroughly review RADseq. Nonetheless, here we address some key points that we find unclear or potentially misleading in their evaluation of techniques.
authors.affiliation: School of Biological & Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK.
authors.forename: Kimberly R
authors.initials: KR
authors.lastname: Andrews
authors.forename: Paul A
authors.initials: PA
authors.lastname: Hohenlohe
authors.forename: Michael R
authors.initials: MR
authors.lastname: Miller
authors.forename: Brian K
authors.initials: BK
authors.lastname: Hand
authors.forename: James E
authors.initials: JE
authors.lastname: Seeb
authors.forename: Gordon
authors.initials: G
authors.lastname: Luikart
mesh_terms: D056186:Metagenomics / Q000379:methods*; D015183:Restriction Mapping / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: PCR duplicates; allele dropout; genotyping error; next generation sequencing; pooling; population genomics