Using RAD-seq to recognize sex-specific markers and sex chromosome systems

Next-generation sequencing methods have initiated a revolution in molecular ecology and evolution (Tautz et al. 2010). Among the most impressive of these sequencing innovations is restriction site-associated DNA sequencing or RAD-seq (Baird et al. 2008; Andrews et al. 2016). RAD-seq uses the Illumina sequencing platform to sequence fragments of DNA cut by a specific restriction enzyme and can generate tens of thousands of molecular genetic markers for analysis. One of the many uses of RAD-seq data has been to identify sex-specific genetic markers, markers found in one sex but not the other (Baxter et al. 2011; Gamble & Zarkower 2014). Sex-specific markers are a powerful tool for biologists. At their most basic, they can be used to identify the sex of an individual via PCR. This is useful in cases where a species lacks obvious sexual dimorphism at some or all life history stages. For example, such tests have been important for studying sex differences in life history (Sheldon 1998; Mossman & Waser 1999), the management and breeding of endangered species (Taberlet et al. 1993; Griffiths & Tiwari 1995; Robertson et al. 2006) and sexing embryonic material (Hacker et al. 1995; Smith et al. 1999). Furthermore, sex-specific markers allow recognition of the sex chromosome system in cases where standard cytogenetic methods fail (Charlesworth & Mank 2010; Gamble & Zarkower 2014). Thus, species with male-specific markers have male heterogamety (XY) while species with female-specific markers have female heterogamety (ZW). In this issue, Fowler & Buonaccorsi (2016) illustrate the ease by which RAD-seq data can generate sex-specific genetic markers in rockfish (Sebastes). Moreover, by examining RAD-seq data from two closely related rockfish species, Sebastes chrysomelas and Sebastes carnatus (Fig. 1), Fowler & Buonaccorsi (2016) uncover shared sex-specific markers and a conserved sex chromosome system.