Demographic History
We used the unfolded three-dimensional joint Site Frequency Spectrum (3D-JSFS) to infer the ABFT demographic history. The 3D-JSFS was constructed for Mediterranean Sea, Slope Sea and Gulf of Mexico populations using the allele counts of biallelic variants included in the VCF file obtained from the ‘nuclear mapped + ALB’ catalog, which included 4 albacore samples for variant orientation. Derived allele counts were averaged over all possible resampling of 20 genotypes within each of the three ABFT locations and singletons were excluded. We performed historical demographic model comparison by fitting separately 10 candidate models (Table S6) to the observed JSFS using a diffusion approximation approach implemented in δaδi v1.7.0 (Gutenkunst et al. 2009) and an optimization routine based on consecutive rounds of optimizations (Portik et al. 2017). We adapted existing divergence models to include the three different possible dichotomous branching of the three populations involving two splits, a simultaneous split of the three populations from an ancestral populations and a scenario of split between the Mediterranean Sea and Gulf of Mexico populations followed by an admixed origin of the Slope Sea. We fitted each of these divergence scenarios with or without allowing constant migration rates between populations from split to present. Ancestral effective population size (NA), migration rates and time estimates scaled to theta (4NAμ ) and the percentage of variable sites correctly oriented with respect to the ancestral state were estimated for all models. Model selection was performed using the Akaike information criterion and goodness-of-fit was assessed by generating 100 Poisson-simulated SFS from the model SFS, fitting the model to each simulated SFS, and using the log-likelihood and log-transformed chi-squared test statistic to generate a distribution of simulated data values against which the empirical values can be compared (Portik et al. 2017).