“…The union of genome sampling protocols with massively parallel, short-read sequencing has produced an immensely successful research programme in population (Bassham, Catchen, Lescak, von Hippel, & Cresko, 2018), conservation (Dierickx, Shultz, Sato, Hiraoka, & Edwards, 2015) and landscape genomics (Bay et al, 2018), phylogenetics (Spriggs et al, 2019), and epigenetics (Trucchi et al, 2016), creating new experimental space for non-model organisms, and allowing, for example, ambitious sampling regimes in large geographical surveys (Dudaniec, Yong, Lancaster, Svensson, & Hansson, 2018), as well as wide-ranging taxon breadth in phylogenetic studies (Near et al, 2018). Regardless of the analytical approach, and in addition to any challenges of the experimental design, all RADseq strategies present two fundamental issues.…”