Comparison of genome-wide patterns
On a genome-wide level, average intraspecific FST and\({\overset{\overline{}}{H}}_{E}\) were found to be relatively similar between the threespine and tubesnout (Table 1), but ninespine\({\overset{\overline{}}{H}}_{E}\) was tenfold lower and FST was almost four times higher (Table 1). Patterns of variation in these summary statistics involved longer “genomic islands” with elevated FST and lower\({\overset{\overline{}}{H}}_{E}\) in the threespine compared to the tubesnout (Fig. 2; 99th FST quantile threespine = 0.67, tubesnout = 0.55; 99th\({\overset{\overline{}}{H}}_{E}\) quantile threespine = 0.0070, tubesnout = 0.0056). Patterns of FST in ninespines were extremely heterogenous to the point that no peaks could be identified, and \({\overset{\overline{}}{H}}_{E}\) was noticeably lower than the other two species (Fig. 2) with the exception of the sex chromosome (i.e. chr12; Shapiro et al., 2009; Shikano, Laine, Herczeg, Vilkki, & Merilä, 2013).