David B. Lowry, Sean Hoban, Joanna L. Kelley, Katie E. Lotterhos, Laura K. Reed, Michael F. Antolin, Andrew Storfer

We thank McKinney et al. (2017) and Catchen et al. (2017) for their recent commentaries on Lowry et al (2017), "Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing scans of adaptation." Both articles argued that we overstated the limitations of RADseq for studies of local adaptation and McKinney et al. (2017) argued that "RADseq provides unprecedented insights" into mechanisms of evolutionary adaptations. While we agree with some of the comments made by the authors of the two papers, we still believe caution should be employed in RADseq studies that aim to detect loci that contribute to adaptation. In this rebuttal, we evaluate the key points made in these papers, attempt to identify a middle ground, and make suggestions for responsibly conducting future studies to understand the genomic mechanisms of adaptation. This article is protected by copyright. All rights reserved.