Population differentiation

The levels of nucleotide diversity were comparable across regions, although slightly lower for populations in the West (Table S2). In general, we observed lower values of genetic differentiation as measured by FST for comparisons within regions (distances ranging from 982 to 1,943 Km show FST values between 0.004 and 0.03; Figure 2 and Table S3). The highest values of FST included comparisons with Madeira (West) and sampling locations in the Center region and the Aegean Sea (0.044< FST<0.05). We do not find evidence of isolation by distance across the sampled range (Mantel test; P-value = 0.32). Areas of the genome that correspond to the top PBS outliers per region (the window where one population is the most dissimilar to the other two) show lower recombination rates, and areas of very low differentiation are associated with the highest recombination rates (Figure 3). The gene content of these three outlier windows includes protein involved in otholith formation (East), vasculature and organ formation (Center) and blood coagulation (West) (Table S4).