“…We used genotype by sequencing (GBS; Peterson et al., 2012) of two Illumina Hiseq libraries, de novo assembly into 90‐bp GBS tags with STACKS (Catchen, Amores, Hohenlohe, Cresko, & Postlethwait, 2011), latent factor mixed modeling [a genotype–environment association (GEA) method; Frichot, Schoville, Bouchard, & François, 2013], and two F
ST outlier methods (Excoffier, Hofer, & Foll, 2009; Foll & Gaggiotti, 2008) to classify putatively neutral SNPS and SNPs exhibiting varying support for being under selection (Pais et al., 2016). Putatively neutral reference SNPs were used to calculate marker‐based inbreeding coefficients ( F ; Keller, Visscher, & Goddard, 2011) and identity‐by‐state matrices using PLINK (Purcell et al., 2007).…”