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).